August 2014

SCHOOL OF PLANT BIOLOGY

Research Project ideas for Prospective 4th Year, Honours, Postgraduate Diploma, MSc and Higher Degree Preliminary

Students in 2015

Marine Systems

Plant Production

Systems

Natural Terrestrial Systems

TABLE OF CONTENTS

SCHOOL OF PLANT BIOLOGY

INTRODUCTION ................................................................................................................................ 4

SELECTION OF TOPICS FOR LEVEL 4 AND LEVEL 5 PROJECT STUDENTS ........................ 6

FURTHER POSTGRADUATE STUDY - PhD OPPORTUNITIES .................................................. 6

THE THREE RESEARCH AREAS OF THE SCHOOL .................................................................... 7

1. PLANT PRODUCTION SYSTEMS ....................................................................................... 7

2. MARINE SYSTEMS ............................................................................................................... 7

3. NATURAL TERRESTRIAL SYSTEMS ................................................................................ 7

PROJECTS FOR 2015 ......................................................................................................................... 9

OTHER ORGANISATIONS AFFILIATED WITH THE SCHOOL OF PLANT BIOLOGY .......... 34

BOTANIC GARDENS & PARKS AUTHORITY ........................................................................ 35

THE CENTRE FOR PLANT GENETICS AND BREEDING (PGB) .......................................... 42

THE COMMONWEALTH SCIENTIFIC AND INDUSTRIAL RESEARCH ORGANISATION (CSIRO) ......................................................................................................................................... 46

DEPARTMENT OF AGRICULTURE AND FOOD WESTERN AUSTRALIA ......................... 48

DEPARTMENT OF PARKS AND WILDLIFE ............................................................................ 49

THE UWA INSTITUTE OF AGRICULTURE ............................................................................. 56

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THE SCHOOL OF PLANT BIOLOGY

LEVEL 4 AND LEVEL 5 PROJECTS AVAILABLE IN 2015

INTRODUCTION A variety of Level 4 and 5 projects are available in The School of Plant Biology and research partner organisations to students who have completed three years of study in an appropriate field towards a Bachelor of Science degree either at this University or elsewhere and who have satisfied any other degree-specific requirements. The Honours programme is normally for students proceeding immediately from the third year of their BSc degree course (e.g. with a major in Agricultural Science, Botany, Conservation Biology, Environmental Science, Marine Science or Natural Resource Management). It typically consists of a research thesis plus four coursework units completed in approximately 9 months of full-time study or over 17 or 21 months of part-time study. Entrance into the Honours programme also requires that a student has obtained at least 65% in four units making up a science major. The Graduate Diploma and Masters by Coursework programmes are designed for students who already hold a Pass Degree at the BSc level and subsequently wish to extend their qualifications/expertise. The Graduate Diploma course is substantially the same as the Honours course, while the Masters by Coursework provides students with greater discipline-specific knowledge and more extensive skills than the Honours. The Level 4 Fourth-Year project, the Level 4 Honours project and the Level 5 Masters by Coursework

project comprise the relevant four-part research project units. All units have the same requirements and timeline as the unit set Research Dissertation Parts 1-4 (SCIE4501 – SCIE4504). This group of units contributes 24 of the 48 points you need to pass your final year. During the research project units, students will receive basic training in a variety of generic skill areas, all necessary for you to work effectively as a professional scientist, as well as undertaking, under supervision, a major independent research project. Completing the Research Dissertation units gives you a taste of what is involved in undertaking independent, supervised research that is real and relevant. For fourth-year and Honours students, the Research Dissertation mark will be taken into account when determining whether you will graduate with honours. Assessment for the Research Dissertation is based on the ungraded Research Outline and Proposal Seminar, and on the graded Research Proposal (20%), Final Research Seminar (10%) and the Research Article (70%). A separate information booklet confirming these details and outlining the organisational details of the SCIE4501 – SCIE4504 units will be issued at the start of the SCIE4501 unit. In the Research Dissertation units, you will be working with a particular team of supervisors, and with other members of the School, in an area of research that you find personally exciting. We know, in completing a pass degree, that you can absorb scientific information and reproduce it under examination conditions. In the Level 4 / 5 project units, you will demonstrate that you can gather, generate, distil and communicate scientific information to your peers. At the end of the year, our staff will assess your performance in comparison with others who have passed through the School, and in relation to what we can expect from someone working in the particular programme you have selected. Of course, the research problems addressed and the methods of approach will differ amongst students, as they will depend upon the area of expertise in which each student is being trained; for example, some programmes may be essentially descriptive, others experimental. Nevertheless, there are some general features and qualities to be sought in all research, and these will be outlined in the unit information booklet to be provided at the commencement of the course. This booklet will also provide details of the assessment procedures for the units.

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FACILITIES AND RESEARCH SUPERVISION

The School of Plant Biology is particularly well equipped for a wide range of projects in plant research. Facilities and equipment include: HPLC units, gas chromatographs, an atomic absorption spectrophotometer (housed in the School of Earth and Environment), portable infra-red gas analysers, portable chlorophyll fluorescence equipment, thermocyclers, gel documentation equipment, a real-time PCR instrument and UV/VIS spectrophotometers. The West Australian Biogeochemistry Centre housed within the School also provides facilities for measurement of stable isotopes through high precision mass spectrometry. The School is well equipped for molecular biology, radio isotope work and plant pathology. Computing facilities include IBM compatible PCs, Apple Macintosh computers and connections to the Campus network and the Internet. The School has a close association with the Centre for Microscopy, Characterisation and Analysis through joint research programmes. The School maintains a reference herbarium of the flora of the southwest of the State. Field work is facilitated by a well-maintained fleet of vehicles, including 4WD’s and boats.

The School utilises numerous serviced glasshouses providing extensive bench space, and access to controlled growth cabinets and constant temperature rooms, including PC2 facilities. About one hectare of garden space is available on site and space is available at a field station at Shenton Park, about 6 km away. The School controls two relatively undisturbed areas of native vegetation within the metropolitan area (at Shenton Park and the Alison Baird Reserve, Kenwick), and is in close proximity to Kings Park and Bold Park, which each contain about 300 hectares of relatively undisturbed native vegetation and 17 hectares of developed botanical gardens.

Based within the School, The Centre for Plant Genetics and Breeding provides advanced education and research in plant breeding to enhance the world’s future supply of plant-based food, fodder, fibre and industrial raw materials in an era of changing climates. The School has an integral role in the UWA Institute of Agriculture. The Institute is the University’s gateway to education, training and research in agriculture and resource management. The Institute is based in the Faculty and integrates the Faculty’s activities with those of other groups in the University with interests in agriculture, land and water management, rural economy, policy and development, food and health.

While much of the south-western part of Western Australia has been cleared for agriculture, large habitat areas comprising native flora, often approaching pristine conditions, have been preserved through a system of National Parks and Reserves. The proximity of this unique natural resource to the modern facilities available in the School makes botanical research at this University particularly attractive. Joint research interests are encouraged between the School and institutions having practical needs for the information generated. These institutions include the Department of Agriculture and Food Western Australia, Australian Institute of Marine Science, Botanic Gardens and Parks Authority, CSIRO, Department of Parks and Wildlife, Department of Planning and Infrastructure, Environmental Protection Authority, Department of Water, WA Water Corporation, and a number of mining and forestry companies. Projects involving joint participation with other institutions and/or other Schools at this University can involve the participation of outside supervisors.

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SELECTION OF TOPICS FOR LEVEL 4 AND LEVEL 5 PROJECT STUDENTS Projects suitable for Level 4 and 5 students are given in the following pages, broadly grouped into the School’s three Strategic Research Areas and with the names of academic staff and post-doctoral research staff who would supervise the projects. Each student is expected to have at least two supervisors. The School encourages you to bring your own ideas for topics other than those listed. In this case you should approach an appropriate supervisor, including staff in the School who may not have projects listed below. For further guidance in the selection of topics, see: Agricultural Science Horticulture Landscape Management

Assistant Professor Michael Considine Telephone: 08 6488 1783 Email: michael.considine@uwa.edu.au

Genetics or Genetics and Breeding

Associate Professor Susan Barker Telephone: 08 6488 2435 Email: susan.barker@uwa.edu.au

Botany Natural Resource Management

Dr Pauline Grierson Telephone: 08 6488 7926 Email: pauline.grierson@uwa.edu.au

Climate Studies Conservation Biology Conservation Biology & Management

Assistant Professor Pieter Poot Telephone: 08 6488 2491 Email: pieter.poot@uwa.edu.au

Marine Biology Marine and Coastal Management Marine Science

Winthrop Professor Gary Kendrick Telephone: 08 6488 3998 Email: gary.kendrick@uwa.edu.au

For further information on the structures of the 4th year, Honours, Graduate Diploma and MSc programmes contact the 4th and 5th year programme coordinator, Associate Professor Patrick Finnegan; Telephone: 08 6488 8546; email: patrick.finnegan@uwa.edu.au

FURTHER POSTGRADUATE STUDY - PhD OPPORTUNITIES The research areas given in this handbook may be of interest to students enrolling in a PhD degree. Students intending to enrol at this higher level should contact one of the School of Plant Biology Postgraduate Co-ordinators: Professor Erik Veneklaas Telephone: 08 6488 3584 Email: erik.veneklaas@uwa.edu.au

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SCHOOL OF PLANT BIOLOGY

THE THREE RESEARCH AREAS OF THE SCHOOL

1. PLANT PRODUCTION SYSTEMS

The Plant Production Systems focus includes broadscale agricultural and the horticultural areas of research. Agriculture and horticulture apply and integrate the disciplines that form the foundation of modern plant sciences – genetics & plant breeding, ecology and physiology, developmental biology, molecular biology and natural product chemistry. These areas of research are also greatly impacted by the interactions of plants with pathogens, an area covered by the discipline of plant pathology. Opportunities exist for professional career development and for crop scientists to contribute to global social and economic well-being. Research funds are increasingly directed towards these goals and many opportunities for collaboration exist with organisations such as CSIRO, Department of Agriculture and Food (WA), Centre of Excellence for Ecohydrology, ARC Centre of Excellence in Plant Energy Biology, international aid organisations and researchers from other Schools

in this and other Universities, both within and outside of Australia.

2. MARINE SYSTEMS

The University of Western Australia has a multidisciplinary programme of Marine Science research and teaching that transcends Faculty and School boundaries and has been consolidated within the UWA Oceans Institute. Staff from the School of Plant Biology have a broad range of interests in Marine Ecology. Research interests and activities range from habitat mapping, basic taxonomy and physiology of marine plants to population and community ecology of plants, invertebrates and fishes. Research is currently conducted in areas as diverse as Esperance, Albany, Cape Naturaliste, Rottnest, Cockburn Sound, The Abrolhos Islands, Shark Bay, Ningaloo, and overseas such as Malaysia, Oman and Brazil. Challenging questions relate to the functioning of marine plants and animals in their environment and on the significance of their communities for the fisheries industry. Important collaborative research links are with Australian Institute of Marine Sciences, CSIRO Marine Research, Department of Fisheries, RMIT Faculty of Engineering, Western Australian Marine Science Institution, and State Natural Resource Management agencies and community groups.

The Western Australian coast is long, covering latitudes from tropical to temperate, with a variety of coastal habitats and hence, an interesting and diverse marine flora and fauna. Western Australia provides many opportunities to study the adaptations of marine plants and animals to their environment and the interactions between them. In particular, research is carried out into the processes which influence the distributions of marine flora and fauna, from the biogeographical scale to their ecophysiology, and the significance of physico-chemical controls versus biological interactions in the partitioning of marine habitats. This research is extended into the examination of disturbed (polluted) habitats, and more practical applications such as prediction of environmental impacts.

The timing of the start of the research projects listed below will vary depending on weather patterns and equipment availability. If you have any queries please contact the supervisors listed to discuss. Scuba diving is a useful, but not essential skill for potential students unless specifically listed for a project. Again, please contact potential supervisors to check.

3. NATURAL TERRESTRIAL SYSTEMS

This research area focuses on issues arising through the interactions of plants with their physical and climactic environments, with each other and with symbiotic and pathogenic microbes. A major theme is plant conservation and environmental rehabilitation. All scales of biological organization are examined, from the molecular to ecosystem level. Many interactions occur between members of this staff group and the other research areas within the School along with the Botanic Gardens and Parks Authority, the Bushfire CRC, Department of Agriculture and Food (WA), Department of Parks and Wildlife, the ARC Centre for Excellence in Plant Energy Biology, the Forest Products Commission, a variety of mining companies, special interest groups and other stakeholders.

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Western Australia, especially the southwest corner, is regarded as one of the world's hot-spots of terrestrial and marine plant diversity. Many researchers focus on the communities, species and genes found in the region, and employ the best available systematic, evolutionary, ecological and physiological science to underpin their work. Others work on threatening processes and their mitigation, such as loss of biodiversity due to habitat destruction, fragmentation of wild areas, dieback disease, invasion by feral animals and weeds, salinity and nutrification.

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SCHOOL OF PLANT BIOLOGY

PROJECTS FOR 2015 The projects being offered and project ideas for development are listed below under the name of the main supervisor. The supervisors are listed alphabetically by last name.

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EMERITUS PROFESSOR CRAIG ATKINS Room 2.20 Botany Building; Ph 9380 2262; Email: craig.atkins@uwa.edu.au

PLANT BIOCHEMISTRY, PHYSIOLOGY AND MOLECULAR BIOLOGY Research Interests The regulation of gene expression in relation to nodule development, N2 fixation and N metabolism in

legumes is a major area of research. Current projects include the isolation of enzymes and genes involved in ureide and purine biosynthesis, studies of enzyme and gene regulation, organelle isolation from nodules, dual targeting of single gene products to 2 organelles (plastids and mitochondria) and a detailed examination of the ultrastructure of Rhizobium infected cells. A second area involves studies of the molecular mechanisms of short and long distance transport in plants, especially of nitrogenous solutes and of factors regulating seed development. A number of projects are related specifically to the genetic improvement of the major grain legume crop of WA, the narrow-leafed lupin (Lupinus angustifolius). These will use recombinant DNA technology and genetic engineering and could involve the use of HPLC and GC/MS analysis. Signals transported in phloem of lupin Plants are continually responding to signals that allow them to modify their development in response to their changing environment. A good example is the way many plants analyse environmental conditions to determine when to produce flowers. The signalling molecule “florigen” involved in this most basic process (flowering) has still not been identified but it is known to be transported in phloem. We are trying to identify this and other signalling molecules in phloem by isolating peptides and small regulatory RNAs (called microRNAs, miRNA and small interfering RNAs, siRNA). We have identified a number of miRNAs in phloem and aim to determine which genes they target, how they are transported around the plant and how they affect developmental processes. Other work aims to identify peptide signals transported in phloem. 1. Use a GFP gene with a miRNA binding site within it to study sites of miRNA action in transgenic

Arabidopsis. 2. Lupin seeds are currently being studied to see whether they are a good alternative to soybean as a

human food. Lupin milk products have been developed and lupin protein extract can be used in a similar way to soybean meal in food processing industries. However there is evidence that lupin seed causes an extremely severe allergic reaction in some individuals. You could identify the proteins in lupin seeds which cause the allergic reactions.

Other project ideas

• Physiological, biochemical, microbiological or structural studies of the ant:bacteria:extrafloral nectary association in cowpea and other legumes.

• Molecular biological studies of the regulation of gene expression in N2-fixing legume nodules, particularly in relation to nitrogen assimilation and purine/ureide biosynthesis.

• Development of techniques for genetic transformation and regeneration of transgenic lupins (Lupinus

angustifolius).

• Studies of abscission in lupins using novel non-abscising mutants.

• Establishment of the molecular basis for source/sink relations in legumes.

• Molecular studies of flower and pod abortion in lupins.

• Studies on localisation of purine biosynthesis enzymes. This project will study the mechanisms by which enzymes are transported into plastids and mitochondria. This could be studied using immunolocalisation, plant transformation and in vitro import techniques.

• The role of plant hormones in determining the partitioning of assimilates in plants.

• Isolation and characterisation of a cytokinin-specific isomerase from developing legume embryo tissues.

• Isolation and molecular characterization of phloem mobile ‘signals’ of biotic and abiotic stresses in lupins.

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WINTHROP PROFESSOR MARTIN BARBETTI Room 1.104 Agriculture Central Wing; Ph 6488 3924; Email: martin.barbetti@uwa.edu.au

PLANT PATHOLOGY AND MYCOLOGY In January 2004 I commenced with the School of Plant Biology following more than 30 years as a Plant Pathologist with the Department of Agriculture and Food Western Australia identifying, researching and resolving plant pathology issues through ‘on-farm’ research in relation to pathology problems facing the wool, oilseed, pulse, cereal, horticulture, meat and dairy industries of Western Australia. Consequently I have wide interests in relation to plant pathology and mycology applicable across the whole of the agricultural sector. The Plant Pathology program at UWA is a collaborative program with Assistant Professor Ming Pei You, also in the School of Plant Biology, and all projects will have the benefit and security from joint supervision and enjoy a strong network of support within the group. It is the vision of this Plant Pathology group to foster both plant pathology and mycology interest and skills development in each generation of students passing through UWA.

DISEASES OF CROPS We have a very active Brassica pathology program (among several other programs as well) here at the University and the plant pathology group at UWA was the first anywhere to report the occurrence of a new resistance-breaking race of the blackleg fungal pathogen, Leptosphaeria maculans, that overcame the Brassica rapa ssp. sylvestris-derived single dominant gene resistance, and which has since broken out and caused severe damage to canola crops across Australia. The Plant Pathology group at UWA currently is a world leading group in terms of diseases of oilseed Brassica crops, and has strong international linkages to leading research programmes on Brassicas both nationally (Victoria) and internationally (France, the United Kingdom and Poland). Current programs include durability of polygenic and single dominant gene-based host resistance in oilseed Brassicas and how this relates to changes in Brassica-pathogen interactions and in the pathogen populations; understanding infection processes of the blackleg pathogen; ways of disrupting the pathogen life cycle; etc. In addition to blackleg disease, we have active in relation to Australian spring-type canola varieties for a range of other diseases such as downy mildew (Hyaloperonospora parasitica), white rust (Albugo candida), Sclerotinia (Sclerotinia sclerotiorum) and white leaf spot (Pseudocercosporella capsellae) in relation both to host resistance, host-pathogen interactions and also in relation to defining the survival mechanisms and parasitic behaviour of these pathogens under the Mediterranean conditions that prevail in much of southern Australia and particularly in WA. We also have programs investigating the race status of these pathogens in Australia.

DISEASES OF PASTURES The Plant Pathology group at UWA currently has a strong collaborative research program on understanding and managing diseases of pasture legumes, including both those which have been (e.g. subterranean clover, annual medic) or are being developed (many new annual and perennial species) for Western Australia. Particular fungal diseases of current research include Phytophthora root rot, clover scorch disease, rust, and Cercospora on subterranean clover, Rhizoctonia root rot and Botrytis blight of new pasture legume species, and Phoma on medic and its role in stimulating phyto-oestrogens in annual medics. We are currently commencing a new large project with Meat and Livestock Australia to look at the causes, impact, epidemiology and management of soilborne diseases on pastures across southern Australia. DISEASES OF HORTICULTURE, FLORICULTURE AND FORESTRY There are currently programs within the School investigating root and crown diseases of strawberries in Western Australia and Sclerotinia on vegetable Brassicas. Please also contact me if you are interested in any pathogen of any other crop, including all pulse and cereal crops

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ASSOCIATE PROFESSOR SUSAN BARKER Room 202 Botany Building; Ph 6488 2435; Email: susan.barker@uwa.edu.au

Research Background I was appointed at UWA in 1998 to help bring molecular biology and molecular genetics research tools into the Faculty. I have very wide ranging interests, and I have co-supervised projects as varied as: genetics of white coat colour in alpacas; development of seedless citrus; characterization of heritage olive trees in Western Australia; zinc nutrition in barley; towards cloning a self incompatibility gene from Phalaris; mapping a mycorrhizal symbiosis gene in tomato; genetic modification of lupin for improved agronomic traits including disease resistance and herbicide tolerance; characterization of the role of apoptosis in blackleg disease of canola; assessment of genetic diversity in a native pasture species; etc (for a complete list please contact me!). Research Advice I sometimes find myself giving advice to students about half way through their research project when they realize that they need to develop a genetic or molecular biology approach to answer their research question. If you find yourself in this situation of needing advice at any stage in your research, please feel free to contact me and I will be happy to advise you about what might be your next steps. Research supervision Examples of current projects that can be completed in a short time period are listed below. Contact me if you would also like to discuss other options, including projects that you have developed yourself, or if you would like to involve me as a second supervisor in order to accomplish a small genetic analysis as part of your project.

• Genetic characterisation of flower colour and seed marking in lupin Some appearance characters of lupin might be very useful as visual markers for a GM lupin crop, to allow segregation of the crop from other conventional cultivars. Two such characters are petal coloration and seed hilum marking. F1 seed is available from crosses between parent lines that differ in these characteristics. The project involves determining the genetics of inheritance of each trait, to establish its genetic basis. If single genes are involved in each trait, then the utility of these for tagging GM lines will be assessed further by crossing and segregation analysis.

• Genetic characterisation of bacterial speck disease resistance in currant tomato A well studied disease resistance system is that of the gene-for-gene interaction between bacterial speck and the Pto locus of tomato. In the near relative, currant tomato, instead of a single gene, it appears that two different genes segregate independently that both are required for resistance to bacterial speck. This project will follow up that observation, using material that has been selected by single seed descent, to identify and characterise the two genes, including determination of whether one of these genes is the Pto gene and if so, what is the other gene?

• Role of mycorrhizal symbiosis in P nutrition of native plants

Australian native species have evolved to cope with very low available phosphate (P) in soils. Some plants have evolved the capacity to access P without apparently utilizing the root fungal partnership known as mycorrhizal symbiosis. However, studies with mycorrhizal species have challenged the assumption that the symbiosis is not functioning in P uptake. This project will examine the role of mycorrhizas in P nutrition of “non-mycorrhizal” native plant species.

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WINTHROP PROFESSOR TIM COLMER & PROFESSOR ED BARRETT-LENNARD Room 1.127 Agriculture Central Wing; Ph 6488 1993; Email timothy.colmer@uwa.edu.au; edward.barrett-lennard@uwa.edu.au

SALINITY AND WATERLOGGING TOLERANCE IN CROPS AND PASTURES Crops and pastures with greater salt and waterlogging tolerance than current options are required to make saline land more productive. There are many opportunities available for research in this field and we would be happy to have discussions with any student interested in working in this general area. The following are examples of projects of current interest to us:

• Salinity and submergence tolerance in halophytes. Halophytes grow naturally in saline soils – but

many of these soils are also prone to waterlogging and plants can even experience complete

submergence during floods. Mechanisms of salinity tolerance in halophytes have previously been

studied, but physiological responses of halophytes to complete submergence in combination with

salinity need to be further elucidated. The scope for projects is large, as various physiological

aspects need to be studied.

• Variation for salt tolerance within Medicago polymorpha. Recent experiments have found

variation in salt tolerance within a commercial cultivar of burr medic (Medicago polymorpha).

Further experiments are needed to determine the source of this variation and utilise it for developing

a more salt tolerant burr medic cultivar.

• Waterlogging/salinity tolerance in clones of puccinellia. Puccinellia is a halophytic grass used for

pasture on saltland. It is a cross-pollinating plant and seed lines are therefore genetically diverse.

This species can be exceptionally tolerant to waterlogging under saline conditions, with increased

growth under waterlogged/saline compared with drained/saline conditions (most rare amongst

higher plants). However, we suspect that different accessions/seed sources vary in tolerance. This

project will screen a range of vegetatively propagated clones of puccinellia for tolerance to

waterlogging/salinity. The best selections will be further tested for K+/Na+ regulation and traits

associated with better root aeration.

• Screening barley cultivars for tolerance to salinity at germination. Barley is well known as a

relatively salt-tolerant cereal. However, this reputation is based mainly on its tolerance to salt after

establishment. Saltland in Western Australia is generally most salty at the start of the growing

season as seeds germinate. However, little is known about how this salt impacts on the germination

of different barley cultivars. This project will assess the salt tolerance at germination for a range of

barley cultivars. There are two critical research questions: (a) Do cultivars differ in their ability to

withstand salt before germination occurs? (b) Do cultivars differ in their ability to tolerate salt

during germination?

• Interactive effects of waterlogging and salinity on rhizobia for Melilotus siculus. Melilotus

siculus (messina) is a new annual pasture legume that can grow in highly saline and waterlogged

soils. Messina roots form a special layer called ‘phellem’, which is filled with air spaces that act as a

‘snorkel’ to allow oxygen transport to roots. However, the role of phellem in supplying oxygen to

waterlogged nodules is not known. This project will determine if phellem on roots and nodules is

important to waterlogging and salinity tolerance of messina inoculated with rhizobia.

Contacts: Tim Colmer (timothy.colmer@uwa.edu.au) AND/OR Ed Barrett-Lennard (Centre for

Ecohydrology - DAFWA/Plant Biology) (edward.barrett-lennard@uwa.edu.au)

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ASSISTANT PROFESSOR MICHAEL CONSIDINE Room 1.029 Agriculture North Building. Ph 6488 1783. Email michael.considine@uwa.edu.au Oxidative stress Oxygen is highly reactive and toxic – just google “the great oxidation event”, or better yet, search the Nature journal. Plants played an enormous role in this, and have far greater experience in managing oxygen than animals. Yet we still understand relatively little about how plants manage oxygen during germination, development, reproduction and dormancy. These phases involve massive changes in cellular oxygen, which creates enormous chemical and physical stress. We’re using cutting-edge technology – from Next Generation Sequencing to clinical intervention studies – to understand these events in crops as well as what it means for human dietary health. We have a number of excellent opportunities for Honours, MSc and PhD students to contribute to exciting research, from agronomy through to genomics or pharmacology. Oxygen and ROS regulate germination and dormancy Bud dormancy is the most critical and sensitive stage of many economically and ecologically important trees. The bud is a compressed shoot, which houses the leaf and fruit primordia for the coming spring and summer growth. Through several approaches, from respiration to advance microscopy and gene sequencing, we’re investigating how this organ maintains dormancy with very little oxygen, and then manages the massive oxidative stress of bud burst and regrowth. Much of the work is currently done with grapevine buds. Additional research is being conducted with model plants such as Arabidopsis. We currently have two PhD students and a visiting research associate studying this in collaborations with a world-leading UK scientist, Prof Christine Foyer, a national authority on grape and wine, E/Prof John Considine, and DAFWA staff across the state. Project opportunities include field, controlled environment, biochemical or genetic studies. Dietary flavonoids, plant breeding and cardiovascular disease

What is the connection? Apples! Apples are rich in flavonoids, which are known to lower the risk of cardiovascular disease in humans. Our research has shown that flavonoid-rich apples can improve cardiovascular function within 24hrs – even in healthy adults. We’re leading national research with DAFWA’s apple breeding program, and eminent colleagues in the School of Medicine and Pharmacology to develop ways to breed flavonoid-rich apples. Project opportunities include breeding and genetic research, molecular and genomic research and even marketing and economic policy studies. Sulfur dioxide toxicity and defence-activation

Sulfur dioxide is an enormously useful preservative in many foods (E220-E228). Grape berries have a unique, worldwide exemption to a ban on SO2 use in fresh foods. The FAO are likely to change this in future, so we need to find safer alternatives. Our research shows that SO2 activates defence mechanisms in grape berries but also affects dietary antioxidants. Project opportunities include chemistry, biochemistry, winemaking and molecular biology. Genomic basis of clonal identity

What is a clone? That is exactly what Next-Generation-Sequencing is about to find out in Cabernet Sauvignon wine grapes. Our national project, with W/Prof Ryan Lister (www.listerlab.com), is sequencing several unique clones to identify functional differences, and how these affect wine qualities. This exciting project has many opportunities for students to contribute. Project opportunities include ampelography, genome sequencing, metabolomics or tasting studies.

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PERMANENT VISITING PROFESSOR KINGSLEY DIXON Director, Science, Kings Park and Botanic Garden, West Perth - Phone 9480 3614 Email: kingsley.dixon@bgpa.wa.gov.au Web: http://www.bgpa.wa.gov.au/science/staff/kingsley-dixon CONSERVATION BIOLOGY AND RESTORATION ECOLOGY Seed Biology ~ Restoration Ecophysiology ~ Cryogenics in conservation ~ Restoring degraded sites

~ Rehabilitate disturbed/mined lands ~ Rescuing our terrestrial orchids ~ Invasive weed research

~ Saving endangered flora from extinction ~ Climate change effects on native flora ~ and much

more. Based in the Science Laboratories at Kings Park and Botanic Garden, students would work alongside more than 45 research scientists and postgraduate students. Kings Park and Botanic Garden enjoys an international reputation for excellence in biodiversity conservation science, undertaking integrated research focused on practical outcomes in native plant biology, rare plant conservation and bushland restoration. For information about Prof Dixon and the research at Kings Park and Botanic Garden, please visit http://www.bgpa.wa.gov.au/o/content/section/6/29/ Honour students can choose from an exciting selection of projects, or are welcome to suggest their own. Areas of supervision expertise include: Seed Banking and Seed Science – research native plant biology, ecology and dormancy release. Research projects could include - using a recently discovered compound to investigate whether synchronized germination is possible, or seeking the optimum techniques to trigger germination of native plant seeds for effective propagation, or stimulating germination of exotic (weed) species for improved control, or the most effective way of storing seeds into the millennium, or how to improve the efficiency of seedling survival in bushland restoration. Restoration Ecophysiology – research plant responses to abiotic (salinity, drought and heat) stress factors, and use plant signaling compounds to regulate stress responses. Research projects could include - seeking ways to enhance abiotic stress tolerance in native plant seeds/seedlings, or improving the use of native plants in mining and agricultural landscapes. Rare Plant Biology – biotechnological research is critical to the success of off-site conservation and translocation of endangered plant species. Research projects could include - in vitro technology (tissue culture, micropropagation, somatic embryogenesis), cryostorage and mass production of plants for restoration/translocation projects. Bushland and Mine Site Restoration – involves undertaking innovative research and operations to enhance, rehabilitate and restore the conservation of degraded lands including urban bushland remnants, agricultural and post-mined lands. Research projects could include - the effects of changed site conditions such as topsoil in restoration success, or ways to optimize seed broadcast and seedling establishment, or why weeds are so invasive. Orchid Biology – orchids have a complex ecological relationship with fungi which provide essential nutrients. They are a flagship species for investigating changes in natural ecosystems. Research projects could include - pollination ecology and natural vs artificial pollination, or how climate changes impact on mycorrhizal interactions, growth, flowering and reproductive success. More detailed project information can be found in the Kings Park and Botanic Garden section of this booklet, or by telephoning Prof Kingsley Dixon on 9480 3614.

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ASSOC. PROF. PATRICK FINNEGAN & ASSIST. PROF. RICARDA JOST Room 1.027 Agriculture North Wing; Ph 6488 8546; Email: patrick.finnegan@uwa.edu.au

PLANT MOLECULAR PHYSIOLOGY AND BIOCHEMISTRY

Research Interests Every plant cell contains at least 30,000 genes! We are working to understand how each cell determines which subset of these genes will be expressed into proteins at any given time in the life cycle of a plant. We know that the specific sub-set of genes that are expressed is tailored to cell function – for example, leaves make photosynthetic enzymes, roots do not – but the mechanisms of the decision making process are very murky and few of the genes involved have been identified. To better understand these complex mechanisms, we are researching molecular physiological questions within two broad areas of plant biology in collaboration with W/Prof. Hans Lambers, W/Prof. Martin Barbetti, W/Prof Tim Colmer from the School of Plant Biology and W/Professor Harvey Millar, Prof Ian Small and Dr Nic Taylor, ARC CoE Plant Energy Biology. 1) Plant nutrient acquisition. We add chemical fertilizers to our gardens and agricultural land because plant growth and productivity requires the acquisition of inorganic nutrients from the soil. In the absence of phosphate, most plants increase the expression of the proteins that transport phosphate from the soil into the plant cell. In addition, some plants produce specialized root structures to enhance nutrient acquisition. For example, Australian native Proteaceae such as Hakea and Grevillea produce cluster roots to actively mine phosphate from the soil. There is also the fascinating possibility of a link between phosphorus nutrition and the susceptibility of some native plants to dieback disease caused by the phytopathogen Phytophthora cinnamomi. With the assistance of research students, and using native and model plants, we are identifying the genes that control the up-take and transport of phosphate around the plant and are possibly responsible for linking phosphorus nutrition with dieback susceptibility. 2) Plant mitochondrial biogenesis and function. As in animals, mitochondrial respiration in plants is necessary for the production of usable chemical energy (ATP). Plant mitochondria are also responsible for many other vital biochemical functions and so are critical for successful plant growth and reproduction. Generally, plant cells die if they are unable to produce the correct mitochondrial proteins at the correct time. Therefore, the appropriate patterns of gene expression are absolutely crucial to plant cell viability. We are keen to identify and characterize the activity of the proteins that are responsible for controlling mitochondrial protein expression. We are also interested in how these proteins are activated by cell development or in the plant’s response to stress, such as a change in the environment, wounding or exposure to chemicals. Our philosophy. We believe it is absolutely essential for a research student to investigate a research question that they are truly interested in answering. While we have listed some project ideas below, we are pleased to discuss any other ideas that fall within the two general areas presented above. This collaborative approach will allow interested students to formulate a project that best serves their career goals. Ideas for possible projects 1. Identify the proteins that bind to and control the function of mitochondrial DNA in plants.

2. Track the movement of selected fluorescently-labelled proteins through plant cells to determine if the proteins are destined for the mitochondria.

With W/Prof Hans Lambers and Research Assistant Professor Ricarda Jost:

3. Mine hakea transcriptome data to identify candidate genes for cluster root development and other unique features that enable these plants to thrive on extremely nutrient-impoverished soils.

4. Investigate the role of individual phosphate transporter proteins and how their activity is regulated to adapt to differences in soil phosphorus availability and optimize the plant’s phosphorus use efficiency.

5. Investigate the roles of genes involved in photosynthesis, respiration, lipid metabolism or protein synthesis in providing Proteaceae with unique mechanisms for the high P use efficiency we would want to be present in crop plants.

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DR KEN FLOWER Teleconference room; 1st Floor Agriculture Central Wing; Ph 6488 4576; Email: ken.flower@uwa.edu.au

My work involves agronomy and farming systems, with an emphasis on no-tillage. 1. Understanding the impact of gravel in Western Australian soils (Collaborator Dr Bill Bowden, DAFWA)

Gravel is a largely ignored but important component of soils, particularly in the high rainfall zone (HRZ) of WA. Some classes of gravels are not necessarily inert and can absorb water and nutrients. Gravels introduce heterogeneity into soils which can have positive and negative effects on crop production. The results will have relevance for the wide geographic distribution of gravelly and stony soils cropped in Australia.

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DR PAULINE GRIERSON, DR GREG SKRZYPEK & THE ECOSYSTEMS RESEARCH

GROUP Room 2.16 Botany Building; Ph 6488 7926; Email pauline.grierson@uwa.edu.au Website: http://www.plants.uwa.edu.au/home/research/research_centres/ergo

ECOLOGY & BIOGEOCHEMISTRY OF NATURAL ECOSYSTEMS

Do you like getting out in the bush? Getting hot and dirty (and sometimes wet)? Doing analytical work in the lab? Identifying plants and working collaboratively with DEC, CSIRO, forest and mining industries? Interested in applying science to better management of our natural environment? The Ecosystems Research Group (ERGo) has an extensive research programme focussed on key processes that determine the productivity and long-term sustainability of natural ecosystems. As process-based ecologists, we study:

� impacts of bushfires on ecological processes and relationships between productivity and biodiversity

� carbon and nutrient cycling in forests and semi-arid ecosystems, including the Pilbara � litter decomposition and ecosystem functioning, including organic matter inputs in to streams � constraints to water and nutrient acquisition and use by trees under a range of conditions � the ecological water requirements of riparian ecosystems � understanding vegetation response to climate change using tree rings to construct climates

(dendroclimatology) Most research that we undertake is strongly field-based, with study sites across much of WA. We complement our field studies with comprehensive analytical work in the laboratory and in the glasshouse. Project ideas for 2009 - please feel free to discuss any other ideas that you may want to pursue with

Pauline, Matthias or Greg How low can you go?: Vulnerability to cavitation in Australian conifers & shrubs (with Dr Tim Bleby & Dr Jochen Schenk) Vulnerability or resistance to cavitation (the development of ‘air bubbles’ in xylem) is an important trait of drought tolerance. This project would examine vulnerability to cavitation in a range of species across a rainfall gradient and within an evolutionary context and explore whether lower vulnerability helps explain the ability of different genera to survive in arid environments. Litter decomposition and root interactions under Allocasuarina fraseriana

Allocasuarina fraseriana is a fire-sensitive species in the understorey of jarrah (Eucalyptus marginata) forest. Actinorhizal roots often proliferate through the litter and probably contribute to N acquisition and litter decomposition. This project will characterise aspects of litter quality and decomposition by looking at different chemical and biological indices including root-microbe associations and how these associations may affect nitrogen cycling processes. Hydraulic structure and function of deep roots of tall trees

Deep roots are the key to success for many large tree species that grow in seasonally dry environments, yet we know next to nothing about how deep roots are constructed or how they work. This project would examine the structural and functional characteristics of deep roots that allow tall trees to efficiently uptake and transport water from deep in the soil profile. The project would include sampling deep roots of karri trees via cave systems in the southwest of WA. Root segments would be measured in the laboratory for (1) xylem anatomy using microscopy techniques (xylem vessels are the microscopic 'pipes' plants use to transport water), (2) how efficiently they conduct water, and (3) how vulnerable they are to cavitation (the development of 'air bubbles' in xylem). The aim of the project would be to compare deep and shallow roots and assess how the number and width of xylem vessels relates to the amount of water that can be transported (hydraulic efficiency) and the likelihood that water transport may break down due to cavitation under drought conditions (hydraulic safety). This project would be co-supervised by Dr Tim Bleby, Research Associate in the School of Plant Biology (tim.bleby@uwa.edu.au). Other possible research topics:

• Oxygen isotopes of sediments as records of environmental change

• Plant species effects on organic matter cycling in freshwater bodies in WA (with CSIRO Land & Water)

• Predicting canopy leaf area in plantations and native forest

• Nutrient cycling in termite mounds and ant nests

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PROFESSOR RICHARD HOBBS, RESEARCH ASSISTANT PROFESSOR RACHEL STANDISH,

DR JODI PRICE, DR MELINDA MOIR, DR MIKE PERRING, DR LEONIE VALENTINE Room G.33 Botany Building; Ph 6488 4691; Email: richard.hobbs@uwa.edu.au Ecosystem Restoration & Intervention Ecology Research Group (ERIE) http://www.erie-research.org/index.html PLANT ECOLOGY APPLIED TO CONSERVATION & RESTORATION South-western Australian ecosystems are remarkable on a global scale for their floristic diversity and the strong abiotic controls on ecosystem processes—nutrient-impoverished soils, summer drought, fire. For these reasons, they are valuable “end points” for understanding many of the key ecological theories that underpin ecological restoration. Yet our ability to restore these ecosystems is limited by the very qualities that make these ecosystems so unique. This means that south-western Australia is a very interesting and challenging place for a restoration ecologist to work! Research in the Hobbs lab is grounded in theory but driven by an interest in developing practical outcomes for restoration in a rapidly changing world. We use an experimental approach to research that is informed by observations of what occurs in nature and we encourage students to do the same. We have listed some projects and co-supervisors below. These projects include a mix of fieldwork, lab work and/or glasshouse experiments. Also, we are happy to help students develop their own ideas as long as these fit within the broadly defined research interests we have described above. A trait-based approach to jarrah forest restoration

There is increasing interest in using a trait approach to understand the restoration of ecosystem functions. Traits determine how species respond to their environment and also how they affect ecosystem functions. Examples of plant traits are seed size, life form, palatability and fire response. The aim of this project would be to measure the traits of common jarrah forest species to determine if the traits represented in restored jarrah forest were similar to those represented in the reference (unmined) jarrah forest. The project would involve a mix of field and laboratory-based research and would be supervised by Asst. Prof. Rachel Standish and Dr Matthew Daws (Alcoa of Australia). Multi-trophic responses to restoration

This is part of a larger project using a trait-based approach to determine the different responses of various interacting groups to old-field restoration. The old-field restoration site is located at the UWA future farm (Ridgefield). To date, the traits of herbaceous plants and herbivorous insects have been assessed. The student would be required to record and assess changes in the traits (e.g., wing length, body weight, etc) of the next trophic level from samples already collected; the parasitoides and/or predators (e.g., wasps, spiders). The student will then relate any trait patterns to those of lower trophic levels and determine what synergies are present in recolonisation success. No background knowledge of invertebrates is required, however, an enthusiasm to learn is essential. This project would be supervised by Dr Melinda Moir and Dr Jodi Price.

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WINTHROP PROFESSOR STEPHEN D HOPPER Unit 1, Centre of Excellence in Natural Resource Management, UWA ALBANY; Ph 9842 0842; Email steve.hopper@uwa.edu.au

EVOLUTION, ECOLOGY, CONSERVATION AND CROSS-CULTURAL KNOWLEDGE SYSTEMS OF

TEMPERATE GLOBAL BIODIVERSITY HOTSPOTS I’ve developed theory (Plant & Soil 322: 49-86 2009) centred on the importance of OCBILs (old, climatically-buffered, infertile landscapes) as drivers of accentuated evolution and ecological relationships rarely investigated, but prominent in the Southwest Australian and South Africa’s Greater Cape Floristic Regions, in Venezuela’s pantepui, parts of Brazil, eastern Australia, etc. Novel biological and ethnobotanical discovery abounds in this context. If you enjoy field work, amongst collaborative cross-disciplinary and cross-cultural teams, and working in a well-resourced Centre offering modern research training and capability, consider the UWA Albany option for your honours or higher degree project (see http://www.cenrm.uwa.edu.au/research/opportunities). Potential Honours projects include:

• Quantification and definition of OCBILs in the Southwest Australian Floristic Region

• Understanding rarity, endemism and local dispersal in Haemodoraceae (Conostylis or the kangaroo paws)

• Biological specialisation and restoration of herbfields of granite outcrops

• The James Effect tested in eucalypts on OCBILs

• Conservation, ethnobotany and land management on OCBILs

• Accentuated persistence of old herbaceous lineages in the Southwest Australian Floristic Region

• The Semiarid Cradle hypothesis tested with Haemodoraceae and eucalypts

• Pollination ecology and the accentuated persistence of old herbaceous lineages in the Southwest Australian

Floristic Region

• Phylogenetics and pollination ecology of disputed subspecies in two Banksia species of the south coast

• Comparative pollination ecology of generalist-pollinated versus vertebrate-pollinated eucalypts

• Regional pollination ecology of Hakea laurina as a keystone species in the Great Southern

• Urban pollination ecology: interactions of native and exotic players

• Molecular phylogenetics and taxonomy of Eucalyptus tetraptera and related species

• Species relationships and biology of the south coast endemic red and green kangaroo paws

• Floristics and seed biology of gnamma (rock pool) plants

• The impact of spraying phosphite to manage dieback in plant communities

• The role of inter-fire recruitment in maintaining populations of long-unburnt obligate seeding bradysporous

species

• Pollination biology of the critically endangered Banksia montana in the Stirling Range

• Honey possums, dieback disease and local extinction

• Are lizard traps effective on granite rocks?

• Were eucalypts dispersed by Noongars to inland granite rocks?

• Remapping Yingilit’s boodja (country) between Denmark and Albany

• Taxonomy of new species of eucalypts on the South Coast

• Cross-cultural studies of grasstrees (Xanthorrhoea)

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PROFESSOR ROGER JONES Room 1.123, Plant Biology First floor; Ph 6488 1484; Email: roger.jones@uwa.edu.au

PLANT VIROLOGY The Plant Virology program at UWA under Prof. Roger Jones is a collaborative one with the Plant Virology research team at the Department of Agriculture and Food Western Australia (DAFWA) headed by Ms Brenda Coutts. All projects will have the benefit and security of joint supervision and enjoy a strong network of support from UWA and DAFWA. It is this groups’ vision to foster plant virology interest and skills development in each generation of students passing through UWA. We currently have active research activities studying virus diseases and their vectors in grains (currently of wheat, canola, pea, lupin), vegetables (cucurbits, potatoes, tomatoes, capsicums, brassicas), pasture plants (tedera, annual medic) and wildflowers. Examples include projects developing innovative real-time PCR procedures for large-scale detection of mite and fungus vectored viruses of wheat; identifying the cause of black pod syndrome in lupin; studying the resistance phenoptypes and genes controlling them in germpasm of brassica species including canola, mustards and diverse vegetable brassicas; investigating the genes controlling resistance to aphid-vectored and contact transmitted viruses in potato; unraveling the cause of viroid outbreaks in tomato; and studying the etiology and epidemiology of Solanaceous vegetable viruses in

WA. Also, a program is planned that will look at the causes, impact and epidemiology of virus diseases

infecting new alternative pasture legumes and grasses. Research is also underway to identify and understand the biological and molecular properties of viruses threatening native plants at the interface between natural and managed vegetation, at mine sites and in wildflower nurseries.

Examples of 4th

Year Project, BSc Honours or MSc Ideas:

Characterisation of virus resistance pathotypes and genes in faba and common bean. Some faba and common bean cultivars contain resistance genes specific to different virus pathotypes. We need to unravel the relationships between virus pathotypes and cultivars with resistance.

How do perennial pasture species respond to invasion by viruses? We know surprisingly little about the threats posed to perennial pasture legumes by viruses. Given the considerable research activity currently underway on perennial pasture grasses and legumes at UWA, we are ideally placed to study this here.

Understanding breakdown of virus resistance in cucurbit cultivars in tropical and subtropical

environments. Single virus gene resistance in cucurbits is effective overseas but not in Western Australia. We urgently need to understand why this is so since virus disease currently threatens continuation of the states cucurbit industry.

Aphid vector biology and the roles of different aphid species as vectors of cucurbit viruses. We know surprisingly little about the biology of aphid vectors and the roles of different aphids as vectors of cucurbit viruses that currently threaten the wellbeing of continuation of the states cucurbit industry.

How do native plants respond to invasion by introduced viruses spreading from introduced crops and

how do introduced crop plants respond to invasion by indigenous viruses spreading from native

plants. We know very little about the threats posed to native plants from introduced viruses and to crop plants from indigenous viruses. Viruses evolve and adapt to new hosts very rapidly and, because agriculture is so recent here, we are ideally placed in Western Australia to study this process.

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WINTHROP PROFESSOR GARY A KENDRICK Room 1.24 Botany Building Link and UWA Oceans Institute; Ph 6488 3998; Email gary.kendrick@uwa.edu.au

ECOLOGY AND DEMOGRAPHY OF MARINE PLANTS Gary Kendrick’s research interests are in the study of the interrelationship between abiotic and biotic processes in the marine environment and their impact on the patterns of distribution and abundance of communities and populations of organisms. This general research interest has recently led me to concentrate on scaling of marine ecological processes. He is presently studying the links between vegetative growth and recruitment processes within seagrass populations and patterning of seagrass meadows across submarine landscapes. His other major interest is in the ecology of marine seaweeds and biological (fish and invertebrate grazing, space pre-emption by sessile filter feeding invertebrates) and physical (influence of waves and currents) processes influencing them. Project topics for 2014-2015 include 1. Reproductive and recruitment ecology of seagrasses 2. Ecology of benthos across the tropical- temperate transition zone from Rottnest to Houtmans

Abrolhos 3. Restoration ecology of tropical and temperate seagrasses (with John Statton) 4. Population genetics of the kelp Ecklonia radiata (with Thomas Wernberg) 5. Population genetics and mating systems of seagrasses (with Liz Sinclair) See http://www.uwa.edu.au/people/gary.kendrick Project Ideas 1. Matching bed stress and benthic habitats for specific regions (Geographe Bay, Rottnest etc) Supervisors: Chari Pattiaratchi, Gary Kendrick, Kimberly Van Niel, Euan Harvey 2. Seagrass genetics (Posidonia) Supervisors Elizabeth Sinclair, Siegy Krauss, Gary Kendrick; Contact (elizabeth.sinclair@uwa.edu.au) Seagrasses belong to a large group of marine flowering plants, adapted for an entirely submerged life. They produce flowers and seeds, with pollen and seed dispersal occurring within the water column. Seagrass meadows also exhibit extensive vegetative (or clonal) reproduction. The meadows are extremely productive ecosystems and play a vital role in providing fish nurseries and stabilising seabeds and coastal shorelines. Extensive decline in seagrass meadows has been documented around Australia, and globally, with experimental restoration efforts requiring donor plant material. Eight (of the nine) Posidonia species occur within waters of the south-west region of Western Australia. Ecological, morphological, and molecular tools are being used to addresses a range of issues relating to population structure, adaptation, and mating systems to contribute to the long-term success of restoration efforts. Microsatellite DNA markers are specifically being used to answer questions relating to clonal diversity, gene flow among meadows and the role ocean currents play in pollen and seed dispersal, and hybridisation. Several options for projects are available, and can be developed around student skills and interests. 3. Connectivity, reproduction and recruitment of seagrasses in Shark Bay – Supervisors Gary Kendrick and John Statton Connectivity, reproduction and recruitment of seagrasses in Shark Bay – Shark Bay World Heritage Region presents a unique climatic interface between temperate and tropical realms. The high species diversity of seagrass in this region coupled with representative species from each climatic realm delivers a rare opportunity to compare distinct reproductive and recruitment strategies employed by each species and how these strategies contribute to the persistence and resilience of seagrass populations in this region and elsewhere. This research will focus on understanding how underlying abiotic processes influence seagrass reproductive ecology in the face of changing climatic conditions 4. Fish grazing pressure on tropical seagrasses in Shark Bay – Supervisors: Gary Kendrick, Mat Vanderklift, Gavin Coumbes This is an opportunity to build your research skills within a supportive and multi-disciplinary research team in a World Heritage Area. This project can answer questions relevant to the international scientific community. For more information, visit http://www.science.uwa.edu.au/students/fourth-year-research-projects and refer to the Marine Honours project booklet.

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PERMANENT VISITING ASSOCIATE PROFESSOR SIEGY KRAUSS Senior Research Scientist (Conservation Genetics), Kings Park and Botanic Garden; Ph 94803673; Email: siegy.krauss@bgpa.wa.gov.au Web: http://www.bgpa.wa.gov.au/science/staff/siegy-krauss CONSERVATION GENETICS I head up the conservation genetics laboratory team at Kings Park, where we are applying molecular tools such as AFLP, microsatellites, population genomics and DNA sequencing for largely practical genetic contributions to native plant conservation, ecological restoration, systematics and native plant breeding. We also use these tools for a better understanding of key evolutionary processes within natural plant populations such as mating and dispersal. In collaboration with Dr Matt Barrett, Dr Janet Anthony, and Dr Liz Sinclair, we offer honours and 4th year research projects within the following broad topics: Seed sourcing for ecological restoration. A major issue affecting restoration success. How do we determine the extent of the local genetic provenance? Applying molecular tools such as AFLP or microsatellites for the rapid genetic assessment of population genetic structure is one powerful contribution. Various species from the Swan coastal plain and Darling Scarp (as well as marine seagrass meadows) are available for population genetic assessment in a genetic provenance context. In addition, there are opportunities to develop and assess patterns of variation in non-neutral markers being developed for iconic species such as tuart, to more directly assess adaptive variation. What are the consequences of sourcing seed from non-local populations? Opportunities exist for cross-pollination experiments to assess the negative genetic consequences of wide outcrossing (outbreeding depression). Additionally, glasshouse growth trials and/or reciprocal transplant experiments provide powerful tests for the extent of local adaptation and “home-site advantage”. Direct assessment of dispersal within and among native plant populations. Quantifying dispersal of pollen and seed within and among plant populations is critical for understanding these important evolutionary dynamics that affect, and are affected by, genetic structure, especially in a conservation and management context with widespread habitat fragmentation and climate change. Are fragmented populations doomed, or able to move, in response to climate change? Is inbreeding increased in fragmented populations due to genetic isolation, and does this affect the long-term viability of populations? What is the impact of introduced honeybees on pollen dispersal and mating in plants historically pollinated by vertebrates? Powerful molecular tools such as microsatellites and AFLP, coupled with statistical approaches for paternity and/or population assignment, offer the potential to generate exciting new data on direct estimates of dispersal in banksias, peas, seagrass, darwinias, orchids, and sedges. Resolving evolutionary relationships and taxonomies using DNA sequences. DNA sequences provide powerful data to generate accurate taxonomies, and to identify the systematic evolutionary relationships among taxa. The accuracy of this knowledge underpins the effectiveness of all other biodiversity conservation and management activities. In addition, recent interest and progress internationally in DNA barcoding offers exciting opportunities for the rapid identification and cataloguing of species, but still requires development and local application. We offer a wide range of opportunities in molecular systematics, that extend to horticulturally and/or conservation significant groups such as grevilleas, kangaroo paws, sedges, wax plants and seagrasses, as well as research in the development of DNA barcoding tools in key local plant taxa. For more information, see the BGPA page in this booklet, or www.bgpa.wa.gov.au/science.

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WINTHROP PROFESSOR HANS LAMBERS Room 2.127 Agriculture Central Wing; Ph 6488 7381; Email: hans.lambers@uwa.edu.au Web: http://ps-hlambers.agric.uwa.edu.au/

ECOPHYSIOLOGY OF MANAGED AND NATURAL SYSTEMS In collaboration with Greg Cawthray, Professor Kingsley Dixon, Dr Patrick Finnegan, Dr Etienne Laliberté, Dr Martha Ludwig, Dr Stuart Pearse, Dr Pieter Poot, Dr Michael Renton, Dr Megan Ryan, Dr Mike Shane, Dr François Teste, Dr Erik Veneklaas and others For more information, please refer to Prof Lambers’ website: http://ps-hlambers.agric.uwa.edu.au/

• Carbon metabolism, exudate production and phosphorus acquisition in cluster roots of Proteaceae and Fabaceae: physiological and molecular processes involved in nutrient acquisition from severely nutrient-impoverished soils.

• Understanding how phosphite protects native plants from the pathogen Phytophthora cinnamomi (dieback)- this is part of a larger project titled “Phosphate toxicity and susceptibility to Phytophthora cinnamomi (‘dieback’) in Proteaceae: why are they linked?”.

• Trialing chemical alternatives to phosphite for dieback management in low-phosphorus ecosystems.

• Improving P efficiency in agriculture by understanding phosphorus acquisition and utilisation strategies in crop or potential crop species.

• Rarity of species in the Banksia genus: highly specialised nutrient-acquisition mechanisms appear superior on severely nutrient-impoverished sites, but maladaptive in other habitats.

• Phosphate-acquisition strategies in native legumes with potential as pasture species.

• Understanding root interactions and their implications on plant coexistence, interplant nutrient transfer, community-level nutrient retention in poor soils

• In situ development (minirhizotron) of Proteaceae cluster roots in the field and interaction with other roots from surrounding vegetation

• Examining the conceptual model of resource partitioning for acquisition of soil phosphorus (P) in natural systems – how does the Peppermint gum (Agonis flexuosa) vary its relative investment in its various P-acquisition strategies (e.g., via extracellular phosphatase production, mycorrhizal associations, carboxylate release) as dependent on sites with contrasting P-availability?

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ASSOCIATE PROFESSOR MATTHEW NELSON Room 1032 Agriculture North Wing; Ph 6488 3671; Email: matthew.nelson@uwa.edu.au

CROP GENOMICS AND BREEDING

We are entering a pivotal period in crop breeding. The bad news is that crop productivity is struggling to keep up with increasing demand for food and fodder, with projections that the World will demand 70% more than current production levels by 2050. The good news is that there are more tools than ever in the hands of plant breeders to create more productive and adaptable varieties. One of the most powerful tools is genomics, which can transform the efficiency of selection in breeding programmes. New genome sequencing technologies are making the discovery of genes underlying important crop traits much easier than could have imagined even 5 years ago.

I am part of the UWA / CSIRO team sequencing the genome of Australia’s most important grain legume species: narrow-leafed lupin (Lupinus angustifolius). There is plenty of scope for students wanting to make their mark on crop breeding by identifying genes controlling key domestication traits in lupin: the genes that make the difference between crop varieties and their wild relatives. I particularly focus on genetic and environmental influences on flowering time in lupin and canola. There are also ongoing projects in Brassica species (such as canola) and in the drought tolerant legume pasture species Tedera, where your input could result in new discoveries and new genomic tools for crop breeding.

If your research interests lean more to basic genetics and evolution, you can join me in asking questions about genome evolution such as how polyploidy has shaped chromosome evolution in crop species and their wild relatives, and in exploring the mechanisms for polyploid formation.

Here are some specific project ideas:

• Finding genes underlying domestication traits such as early flowering, pod shattering and alkaloid content in narrow-leafed lupin. This project will draw genomics resources we developed in the lupin genome sequencing project (a collaborative project between UWA and CSIRO) and other lupin genomics projects. Activities would involve design of molecular markers, monitoring gene expression using qRT-PCR and finding marker-trait associations in sets of wild and domesticated germplasm.

• Investigating genetic diversity of different gene pools of narrow-leafed lupin such as Australian and European cultivars, landraces and collections from the wild (in collaboration with Dr. Jon Clements (DAFWA) and Dr. Jens Berger (CSIRO)).

• Despite the massive impact that the time to flowering makes on canola yields, we know surprisingly little about how genes and environment interact to control flowering time in canola. With climate change already upon us, we must get a clearer understanding of how the environment (temperature and day-length) interacts with genes to result in flowering time variation in canola varieties. Join with us to redress this knowledge gap to help develop canola adapted to climate change (in collaboration with W/Prof Wallace Cowling).

• Mining genomic resources for marker-assisted breeding of Tedera (Bituminaria bituminosa), a drought tolerant pasture legume. Traits that could be targeted are drought tolerance, flowering time or furanocoumarin biosynthesis (in collaboration with Dr. Daniel Real, DAFWA).

• Every chromosome of every eukaryote species has one functioning centromere that is crucial for cell division. Despite the vital role of centromeres, we don’t know even know where they are located relative to genes in most species, including Brassica species (e.g. canola). We have developed model systems for mapping for mapping Brassica centromeres (in collaboration with Dr. Annaliese Mason, University of Queensland).

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ASSOCIATE PROFESSOR PIETER POOT Room 2.127 Agriculture Central Wing; Ph 6488 2491; Email: pieter.poot@uwa.edu.au

Co-affiliation with the Department of Parks and Wildlife (DPaW).

Plant Conservation Biology/Plant Ecophysiology SW Australia is one of the world’s 34 biodiversity hotspots as a result of its extraordinary plant diversity and the great threats that many species face. Over 50% of the flora is endemic with many of these species restricted to a small geographic range. However, other species are much more widespread. I am interested in better understanding the reasons for these large differences in success amongst species, the key traits that determine success in particular habitats and how these traits are related to the persistence of species under climate change. Projects can include glasshouse or field studies and physiological as well as morphological measurements and can include a range of co-supervisors within our Faculty, Kings Park or DEC. Possible projects could involve: 1. Comparing traits of several closely related species that are restricted to particular habitats. Closely related species that occur in the same region but in different habitats (e.g. granite outcrop, jarrah forest, heathland) are likely to be very similar, except in those traits that are essential for success in their own habitat. 2. Comparing traits of populations of a common species that occur in different habitats. In this case the different populations of a species may have already evolved into different ‘ecotypes’, each adapted to their own particular habitat, or the species is simply very plastic and acclimates to the different environmental conditions in each habitat it occurs in. 3. Comparing closely related rare and common species. Closely related rare and common species within the same genus are likely to differ in traits associated with their relative success. 4. Determining success of rare flora translocation. DPaW is responsible for the conservation of our rare and threatened flora. For many of the critically endangered species either Interim or Full Recovery Plans have been written or are currently being prepared. Due to the large number of declared flora species and the many DPaW officers involved in managing them, there are numerous possibilities for projects, including defining a species’ critical habitat, its physiological/ecological requirements, and comparing the ‘health’ of translocated versus natural populations. 5. Weed biology/ecology

For many of our declared rare flora weeds are listed as one of the major threats. However, a lack of knowledge of the biology of many weed species hampers our efforts to eradicate them. Often an increase in nutrient and/or water availability (e.g. on roadsides) is thought to give weeds an advantage. Possible projects could involve glasshouse studies that compare growth and development of some major weed species, with that of native species they compete with, under different levels of watering and nutrition. Metropolitan Turf Research (in collaboration with Tim Colmer and Louise Barton) Within the Perth metropolitan area I am also involved in turf research aiming at conserving water by decreasing turf’s dependence on irrigation. Possible projects could involve glasshouse trials with a range of turf species to examine their drought tolerance and to test the effectiveness of a range of organic and inorganic soil amendments on increasing our sandy soil’s water holding capacity.

→→Of course I’m more than happy to discuss and consider any of your own project ideas ! ←←

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WINTHROP PROFESSOR STEPHEN POWLES & Dr’s Roberto Busi, Danica Goggin,

Michael Walsh and Qin Yu

AUSTRALIAN HERBICIDE RESISTANCE INITIATIVE (AHRI) Room G.008 Agriculture North Wing; Ph 6488 7833; Email: stephen.powles@uwa.edu.au

HERBICIDE RESISTANCE IN CROPS & WEEDS: RESEARCH PROJECTS FROM

MOLECULAR GENETICS OF RESISTANCE THROUGH TO ON-FARM MANAGEMENT

ISSUES AHRI is a GRDC and ARC funded multi-disciplinary research team investigating herbicide resistance in weed and crop species. Full details of AHRI people and research projects can be seen on the website http://ahri.uwa.edu.au Potential AHRI supervisors for 2015 student research projects are Prof. Powles, Dr’s Busi, Goggin, Walsh, Yu. Each year, students undertake their final year research project within AHRI. Some students who see their future in broadacre cropping undertake applied projects whereas others acquire more fundamental training by undertaking a biochemical/genetics based research project. Because of the diverse projects underway in AHRI (see website http://ahri.uwa.edu.au), fourth year students can conduct research ranging from biochemistry and molecular genetics of resistance, simulation modeling of crop weed management, herbicide evaluations in the lab, glasshouse and field, agro-ecology of resistance, seedbank dynamics, through to on-farm management. We aim for students to undertake a research project of sufficient quality to result in them being an author on a scientific paper published in an international research journal. AHRI has close contacts with grain growers, farmer groups, public and private sector crop agronomists and with CSIRO, Department of Agriculture & Food and other agencies and there is the opportunity to work with individuals from these groups. AHRI research projects for 2015 embrace a number of crops and weeds of direct relevance to broadacre Australian cropping.

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ASSISTANT PROFESSOR CHARLES A. PRICE Email: charles.price@biology.gatech.edu

Website: www.chuckprice.info (best place to get more information)

Key Areas of Interest

• Biological scaling

• Plant functional traits and how they are linked to environmental variability

• Ecological community organization

• Plant biomass partitioning (leaves, stems, roots)

• Structure of plant and animal distribution networks

• Size distributions in ecological communities

• Plant optimization models

• General approaches to modeling in ecology

• Conservation/restoration ecology

• Making the world a better place I find student projects are most successful when we identify projects that are of interest to us both. Biological scaling is a very broad field, and many types of projects fit within its domain. I have a lot of student projects already outlined or I am always happy to kick around ideas. Send me a note if you’d like to learn more.

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ASSOCIATE PROFESSOR MICHAEL RENTON Botany Building; Ph 6488 1959 Email: michael.renton@uwa.edu.au

As a plant modeller, I am interested in using computer, mathematical and statistical models to help understand all aspects of how plants grow and interact with their environments. This can be at the scale of genes, physiology, structural development, environmental interactions, ecological interactions, or the long-term processes of evolution. I am fascinated by the way models can give us insight into the relationships between plant processes occurring at different scales eg. how the ways that different species compete for resources in different ways lead to varying degrees of productivity in a field of crops or a forest; or how the interaction between genetics, management, seed ecology, inter-species competition and environment can increase or decrease the risk of developing herbicide resistance; or how the interaction between environmental effects and physiological processes lead to the intricate structure of a tree. I also think models can play a very important role in experimental design, in identifying which areas of enquiry need to be focused on. Honours scholarships of up to $6000 may be available for these projects, from organisations including CSIRO, GRDC, DAFWA, the Centre of Excellence for Climate Change, Woodland and Forest and Health and several CRCs. I have listed some possible projects below, and encourage you to talk to me about any other projects you might be interested in, especially if you have some background or interest in modelling, maths or computer science. I also encourage you to talk with me about including some modelling work in any other plant biology Honours project you are developing with another supervisor, especially if you are interested in adding invaluable and sought-after modelling skills to your repertoire! Tactical and Strategic Decisions in Agro-ecological Systems – Dealing with Risk, Variability, Uncertainty

and Tradeoffs in a Changing Climate (in conjunction with CSIRO)

This project will investigate the tradeoffs, risk, variability and uncertainty in agro-ecological systems with the aim of identifying strategies for dealing with them most effectively. The project will use existing models and possibly develop these models further. These issues are of particular relevance in a time of conflicting demands (between agricultural production, carbon sequestration and conservation for example) changing climate and increasing climate variability. Biosecurity and Biological Invasion (with Plant Biosecurity CRC)

Invasive weeds, insects and diseases can have huge negative impacts on both natural environments and agricultural industries. Models of how these spread and colonise new environments can help us predict their impact, design efficient surveillance strategies and make decisions about effective management and response to new incursions.

Modelling the Evolution of Resistance (in conjunction with AHRI, CRC Plant Biosecurity and/or DAFWA)

Understanding what factors lead to the evolution of resistance in weeds, pathogens and insect pests, and how this resistance can be delayed or avoided is one of the most important challenges facing agriculture, and computer models are an essential tool in gaining this understanding. This project will involve using existing simulation models of population dynamics and the development of resistance. The models will be used to simulate previously conducted field trials and experiments in order to validate the models and/or prioritise areas for future improvement and/or to investigate and evaluate possible management strategies for avoiding and/or delaying the development of resistance. Modelling Weed Seedbank Dynamics and/or Crop-Weed Competition (in conjunction with DAFWA, GRDC)

This project will involve using existing simulation models of weed seedbank dynamics, such as the Weed Seed Wizard and RIM. The models will be used to simulate field trials that have been conducted around Australia, in order to validate the models and prioritise areas for future improvement. The focus of the project will depend on the background and interest of the applicant – no prior expertise in modelling is required. Modelling the Interactions between Physiology, Structure and Environment

The beautiful and intricate structures of plants (from seagrass, to wheat, to frangipanis) are a result of complex and dynamic interactions between inbuilt rules of morphogenesis, physiological processes and environmental influences. Can models give us insight into how these structures emerge, how they are optimised to take advantage of their environments, and how we can make use of them in agriculture and restoration?

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ASSOCIATE PROFESSOR MEGAN RYAN

Agriculture Central Wing; Ph 6488 2208; Email: megan.ryan@uwa.edu.au

Areas of interest

� Phosphorus (P) dynamics in pastures and revegetated areas in the Peel Harvey region

� Ability of native legumes to remediate hydrocarbon contamination of soil

� Herbaceous native plants with novel P nutrition

� Arbuscular mycorrhizal fungi and plant P nutrition

� New annual and perennial pasture legumes

PROJECT TITLE: Effect of lowering the concentration of soil available P on competition among pasture species of differing P requirements and common pasture weeds. BACKGROUND – P reserves are diminishing and there is an urgent need to reduce P use in farming systems. In pastures, P fertiliser use could be reduced through replacing current pasture legumes (ie subclover) with species with a lower critical P (ie species that reach maximum yield at a lower P level eg serradellas). However, it is unknown how a change in soil P would affect competition at germination among these legumes and other pasture species and weeds. This project would look at the competition between subclover, serradella, annual ryegrass and capeweed under a range of soil P levels.

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PROFESSOR ERIK VENEKLAAS Room 2.104 Agriculture Central Wing; Ph 6488 3584; Email: Erik.Veneklaas@uwa.edu.au

Plant Physiological Ecology

My main interest is in how plants are affected by their environment (e.g. climatic and soil conditions), but also how plants affect their environment (e.g. invading weeds affecting native plant communities, revegetation effects on rehabilitated land, positive effects of companion crops and rotational crops, legumes mobilising soil P). The main factors of interest in SW Australia are water and mineral nutrients (especially P). Below is a list of possible topics, but I also welcome your own ideas! Do contact me if you want to know more! Ecophysiology of native species under stress

• Decline of SW Australian eucalypts (Eucalyptus wandoo). Our State Centre of Excellence for Climate Change, Woodland and Forest Health offers various opportunities to do research projects into tree declines that are occurring in woodlands and forests of the region, and appear to be related to reduced rainfall. Projects may include tree water relations, nutrition, pathology, competition, modelling, etc. For scholarship info see website (http://www.treehealth.murdoch.edu.au/index.html). Collaborations with Pieter Poot and Michael Renton. Martin Bader, Jerome Chopard and several others outside UWA.

• Samphire ecophysiology at the Fortescue Marshes in the Pilbara: drought, flooding, salinity. Tissue tolerance, water use and C balance, root dynamics, population dynamics, ecohydrology Collaboration with Tim Colmer.

• Fitness differences between different provenances of native species, and their crossbred offspring, exposed to abiotic stress. Collaboration with Siegy Krauss and Hans Lambers.

Plant water relations and ecohydrology

• Ecological engineering and ecohydrology: achieving defined hydrological outcomes through optimal combinations of plant species and soil conditions. Collaboration with Christoph Hinz and Hans Lambers.

• Dryland crops: water use efficiency and drought tolerance.

Photosynthesis and transpiration of native plants

• Sclerophyllous leaves: are they physiologically and biochemically different or just a different way of ‘packaging’ photosynthetic tissue?

Plant nutrition

• Phosphorus economy of native plants: relationships between P acquisition efficiency, P use efficiency, growth and dominance status in native ecosystems. Collaboration with Hans Lambers, Kingsley Dixon and Francois Teste.

• Phosphorus use efficiency of crops.

• Timing and placement of cluster roots – costs and benefits in terms of C and P.

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ASSOCIATE PROFESSOR THOMAS WERNBERG School of Plant Biology & Australian Institute of Marine Biology, UWA Oceans Institute, Fairway, Ph. 6369 4047, thomas.wernberg@uwa.edu.au

ECOLOGY OF MARINE PLANTS ON REEFS AND IN ESTUARIES; CLIMATE CHANGE AND

INVASIVE SPECIES Thomas Wernberg’s main research interests are ecological interactions involving marine plants on and around subtidal reefs and in estuaries (e.g., the Swan River). His research has a strong empirical focus and relies on field and laboratory observations and experiments to tease apart the causes of species distribution in nature. He is particularly interested in the nexus between physiology, ecology and biogeography, and the need to understand current and future patterns of global change (climate change, invasive species, eutrophication). Most, but not all, of his projects will require an ability to scuba dive, and many projects will require willingness to participate in field trips to remote coastal areas (e.g., temperate south coast, tropical northwest coast). Projects will be co-supervised by one or more of his current collaborators – Prof Gary Kendrick (UWA), Dr. Dan Smale (UWA), Andrew Heyward (AIMS), Martial Depcynski (AIMS), Dr. Mat Vanderklift (CSIRO), and Dr. Mads Thomsen (Danish National Research Institute). Project Ideas

1. Ecology of macroalgae in coral reef lagoons; 2. Distribution and diversity of coastal macroalgae in the Kimberley region; 3. Influence of climate on reproduction, recruitment, growth, productivity and mortality of canopy

algae; 4. Temperature adaptation in marine macroalgae (ecophysiology); 5. Combined effects of multiple stressors on macroalgae (e.g., temperature, pH and eutrophication); 6. Consequences of ocean climate on seaweed-herbivore interactions; 7. Biogeography of marine macroalgae; 8. Comparative ecology and ecophysiology of invasive and non-invasive Caulerpa species; 9. Interactions between an invasive snail (Battilaria australis), algae and seagrasses in the Swan River.

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ASSOCIATE PROFESSOR GUIJUN YAN Room 2.129 Agriculture Central Wing; Ph 6488 1240; Email: guijun.yan@uwa.edu.au

PLANT CYTOGENETICS, MOLECULAR GENETICS, PLANT BREEDING AND

CONSERVATION OF PLANT BIODIVERSITY

Research interests My main research focuses on the understanding of interspecific and intergeneric genome relationships and genome interactions of wide hybrids using cytogenetic and molecular approaches. In collaboration with my colleagues, I worked on the breeding, genetics, identification of barriers to wide hybridization, cytoevolution, chromosome inheritance, molecular evolution, molecular phylogenetics and molecular marker-assisted breeding of Ziziphus, Actinidia, Chamelaucium, Verticordia, Boronia and Leucadendron. Currently, I am interested in understanding the reproductive biology, molecular genetics and cytogenetics of Proteaceous plants, Brassica and field pea wide hybridisation and barley and wheat genomics and proteomics. I strongly believe that the best way to conserve biodiversity is to bring the plants to cultivation through collection, selection and breeding. Project Ideas 1. Reconstruction of phylogenetic relationships in plants Selected publications in this area: George N, Byrne M, Maslin B, and Yan G (2006) Genetic differentiation among morphological variants of

Acacia saligna (Mimosaceae). Tree Genetics and Genomes 2:109-119 Yan G, F Shan, JA Plummer (2002) Genomic Relationships within Boronia (Rutaceae) as Revealed by

Karyotype Analysis and RAPD Molecular Markers. Plant Systematics and Evolution 233: 147-161

2. Any projects related to cytogenetics and molecular cytogenetics of plants Selected publications in this area: Shan F, G Yan, and JA Plummer (2003) Cyto-evolution of Boronia genomes revealed by fluorescent in situ

hybridisation with rDNA probes. Genome 46: 507-513 Shepherd KA, G Yan (2003) Chromosome number and size variations in the Australian Salicornioideae

(Chenopodiaceae) – evidence of polyploidisation. Australian Journal of Botany 51: 441-452

3. Any project on wide hybridisation and overcoming wide hybridization barriers Selected publications in this area: Liu H, Yan G and Sedgley R (2006) Interspecific hybridization in the genus Leucadendron through embryo

rescue. South African Journal of Botany 72:416-420 Astarini IA, Yan G and Plummer JA (1999) Interspecific hybridisation in Boronias. Australian Journal of

Botany 47: 851-864

4. Molecular fingerprinting of plants Selected publications in this area: Yuan H, Yan G, Siddique KHM and Yang H (2005) RAMP based fingerprinting and assessment of

relationships among Australian narrow-leafed lupin (Lupinus angustifolius L.) cultivars. Australian

Journal of Agricultural Research 56:1339-1346 Pharmawati M, Yan G and Finnegan PM (2005) Molecular variation and fingerprinting of Leucadendron

cultivars (Proteaceae) by ISSR markers. Annals of Botany 95: 1163-1170 5. New endeavors –Genomics, proteomics and fast generation of broad acre crops

Selected publications in this area: Yang H, Lin R, Renshaw D, Li C, Adhikari K, Thomas G, Buirchell B, Sweetingham M, Yan G (2010)

Development of sequence-specific PCR markers associated with a polygenic controlled trait for marker-assisted selection using a modified selective genotyping strategy: a case study on anthracnose disease resistance in white lupin (Lupinus albus L.). Molecular Breeding 25: 239-249

Ma J, Yan GJ, Liu CJ (2011) Development of near-isogenic lines for a major QTL on 3BL conferring Fusarium crown rot resistance in hexaploid wheat. Euphytica 183:147–152

Shahidul Islam, Wujun Ma, Rudi Appels, Bevan J Buirchell, Junhong Ma, Guijun Yan (2011) Diversity of seed storage protein among the Australian narrow-leafed lupin cultivars (Lupinus angustifolious L.). Crop and Pasture Science 62: 765–775

Zheng Z, Wang HB, Chen GD, Yan GJ and Liu CJ (2013). A procedure allowing up to eight generations of wheat and nine generations of barley per annum. Euphytica 191: 311-316.

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OTHER ORGANISATIONS AFFILIATED WITH THE SCHOOL OF PLANT BIOLOGY

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BOTANIC GARDENS & PARKS AUTHORITY

KINGS PARK’S 2015 PLANT BIOLOGY HONOURS & MASTERS PROJECT OPTIONS Kings Park and Botanic Garden is a national leader in conservation biology and restoration ecology research, providing a unique "one-stop-shop" that delivers practical research outcomes for biodiversity conservation and ecosystem restoration. The staff comprises >45 research scientists and postgraduate students in the core integrated disciplines of conservation genetics, propagation science, seed science, germplasm storage, restoration ecology and orchid conservation. For further information see: www.bgpa.wa.gov.au/science Facilities: Equipment, computers, laboratories, office space, expertise and administration are available in the Biodiversity Conservation Centre (BCC) at Kings Park and Botanic Garden.

RESEARCH AREA: “Restoration Ecology and Restoration Ecophysiology” 1. Optimising seedling establishment in mine site restoration. The ability of seedlings to establish in restoration sites is dictated by their interaction with abiotic stresses such as drought and soil compaction. This project will use novel approaches to understand Banksia woodland species tolerance to these stresses. Working in collaboration with industry partners outcomes from this project will underpin future restoration processes. Supervisor: Dr. Jason Stevens (phone: 9480 3639, email: jason.stevens@bgpa.wa.gov.au) 2. Climate change impacts on biodiverse plant communities The increasing prevalence of drought in combination with higher temperatures is leading to large shifts in plant community structure in Western Australia’s biodiverse plant communities. New technology now exists that shows (in real time) plant water use in response to these environmental drivers. This will lead to an unprecedented understanding of plant water use and help us to define environmental thresholds for some of our native plants. Opportunities exist to explore climate impacts on intact vegetation communities or in restored ecosystems. Supervisor: Dr. Jason Stevens (phone: 9480 3639, email: jason.stevens@bgpa.wa.gov.au) 3. Quantifying plant community attributes for restoration of Banksia woodland in urban bushland

fragments This project will use both historical records, and quantitative analysis of modern vegetation survey data, to assess and select Swan Coastal Plains Banksia Woodland communities as reference targets for ecosystem restoration, as well as to accurately quantify restoration targets (e.g. species richness, community composition, special scales of monitoring) – of sites fragmented through urbanisation, cleared of pine plantations and/or rehabilitated following mining. Supervisor: Dr Ben Miller (phone: 9480 3631, email: ben.miller@bgpa.wa.gov.au) For information on other Conservation Biotechnology projects please contact: Dr. Jason Stevens (phone: 9480 3639, email: jason.stevens@bgpa.wa.gov.au)

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RESEARCH AREA: “Rare Plant Biology - Conservation Biotechnology” 1. Correlating cell membrane composition with tolerance to cryogenic treatments The aim is to study the factors that determine the ability of various plants to survive cryogenic storage, with a focus on recalcitrant and endangered species of relevance in post-mining rehabilitation. The preservation of cell membrane structure is essential for the survival of tissues subjected to cryogenic storage at very low temperatures. Plant sterols and phospholipids are known to regulate membrane fluidity and permeability and the unsaturated degree of these fatty acids appears to be closely associated with abiotic stress resistance in plants. Free fatty acids, produced during water stress by action of lipases on polar lipids, may be stored in neutral lipids (triacylglycerols) in order to avoid oxidation by free radicals and reactive oxygen species and, hence, their abundance and type may influence post-cryogenic survival. This project will characterise the species-dependent composition of biological membranes, which will help to provide a rationale for observed differences in tissue survival upon thawing, and will be the basis for future molecular modelling and biophysical studies of membrane structure and dynamics.

Supervisors: Dr. Eric Bunn (phone: 9480 3647, email eric.bunn@bgpa.wa.gov.au), Assoc. Prof. Ricardo L. Mancera 2. Evaluation of oxidative stress markers in cryotolerant and cryosensitive plant species The aim is to study the factors that determine the ability of various plants to survive cryogenic storage, with a focus on recalcitrant and endangered species of relevance in post-mining rehabilitation. Oxidative stress markers are detectable in cryopreserved cells from many species and it has been demonstrated that tissues with high catalase and low superoxide dismutase activity show increased tolerance to cryostorage. Elevated levels of antioxidant activity have also been correlated with a reduction in the production of hydroxyl radicals. Low temperature stress can also stimulate ethylene biosynthesis, a response that has been correlated with senescence and plant stress, which can also be utilised as an indicator of post-cryogenic storage membrane damage. This project will determine the significance of stress markers for cryosensitive and cryotolerant Australian plant native species during cryogenic storage.

Supervisors: Dr. Eric Bunn (phone: 9480 3647, email eric.bunn@bgpa.wa.gov.au), Assoc. Prof. Ricardo L. Mancera 3. Evaluation of plant tissue responses to a range of cryogenic solutions The aim is to study the factors that determine the ability of various plants to survive cryogenic storage, with a focus on recalcitrant and endangered species of relevance in post-mining rehabilitation.Relatively little is known about how cryogenic solutions promote survival after liquid nitrogen storage and their specific mode of action. The most commonly used cryoprotectant, the plant vitrification solution 2 (PVS2), has been successfully applied to many different Australian species. While other solutions are successful on a number of plants, only PVS2 yields high survival following liquid nitrogen immersion. The exact reason for this lack of survival is currently unknown, despite the fact that the composition of the different solutions is relatively similar. All these solutions have glycerol, ethylene glycol, sucrose and DMSO as their core components, which are believed to aid cell membrane stabilisation during cooling through interactions with membrane structures, promoting cell desiccation by increasing the osmotic potential extracellularly, and replacing intracellular water so that cellular volume is not substantially altered during desiccation. This project will investigate the changes that occur in the shoot tips of cryosensitive and cryotolerant Australian plant native species upon cooling with liquid nitrogen in the presence of different cryogenic solutions.

Supervisors: Dr. Eric Bunn (phone: 9480 3647, email eric.bunn@bgpa.wa.gov.au), Assoc. Prof. Ricardo L. Mancera 4. Smoke and sex – using the smoke chemical as a propagation tool? The recent discovery by UWA and Kings Park scientists of the active smoke chemical (karrikinolide) is a triumph of Australian science. Karrikins are a new class of naturally-occurring plant growth-promoting compounds and research has now established that they can stimulate plant tissues grown in vitro. Recent research has found in vitro cultured somatic embryos derived from Baloskion tetraphyllum (Restionaceae) were stimulated to grow and develop more rapidly when exposed to karrikinolide. However, little else is known about the effects of Karrikins, their active concentration or other responsive species or tissues. This project aims to discover and document the effects of karrikinolide on embryogenic callus derived from Lepidosperma spp. Supervisors: Dr. Eric Bunn (phone: 9480 3647, email eric.bunn@bgpa.wa.gov.au) Dr. Shane Turner (phone: 9480 3639, email: shane.turner@bgpa.wa.gov.au)

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5. Saving the sedges – researching mass propagation of Australian native sedges. An honours project will be offered on developing tissue culture-based mass propagation techniques for the dryland Cyperaceae (sedges) species Mesomalaena pseudostygia, Mesomalaena tetragona and Schoenus

grandiflorus. This project will investigate methods of mass-producing plants through specialised plant tissue culture techniques, concentrating on the challenging area of seed embryo extraction and culture. Supervisor: Dr. Eric Bunn (phone: 9480 3647, email eric.bunn@bgpa.wa.gov.au)

6. Propagation and storage biology of the critically endangered species Androcalva perlaria

(Sterculiaceae). Androcalva perlaria (previously Commersonia sp Mt Groper) is poorly studied species known to occur from less than 5 sites along the South coast of Western Australia. Little is currently known about its propagation biology and storage requirements, aspects which are critical to securing its long term future. This project will therefore investigate key features of the seed biology of this species and will also assess the applicability of plant tissue culture for its mass propagation. In addition, the response of seeds and somatic tissues (shoot cultures and shoot tips) to various forms of long-term storage such as maintenance at 10 °C, 5 °C, -18 °C and -196 °C (cryostorage) will also be assessed. Supervisor: Dr. Shane Turner (phone: 9480 3639, email: shane.turner@bgpa.wa.gov.au) For information on other Rare Plant Biology - Conservation Biotechnology projects please contact: Supervisor: Dr. Eric Bunn (phone: 9480 3647, email eric.bunn@bgpa.wa.gov.au)

Research area: “Conservation Genetics” 1. Restoration genetics How far from a restoration site can seed be collected whilst still maintaining the genetic integrity of the local population? At what point is there a negative impact on restoration success? How can we best delineate the scale of the local genetic provenance when dealing with highly diverse plant communities? And when do other considerations, such as seed source population properties, become more important than local provenance issues? Within this project, there is enormous scope for population genetic studies using a range of molecular markers such as microsatellites, as well as powerful new tools coming on line through development with next generation sequencing technologies. Other opportunities exist with ecological studies, pollination studies and landscape characterisation studies across a broad range of species – individually or as an integrated study, to contribute to better outcomes in bushland rehabilitation. This project will focus on banksia woodland communities in the Perth metropolitan area. Supervisors: Dr Siegy Krauss (Siegy.Krauss@bgpa.wa.gov.au); 2. Assessing functionality in restored Banksia populations. Ecological restoration of diverse native plant communities is an increasingly important conservation action. However, the functionality of restored populations through the delivery of pollinator services for seed production is increasingly recognized as critical for the long term viability of these restored communities. This project builds on previous research in restored Banksia woodland communities to assess functionality through a combination of field and molecular lab work. Bird and insect pollinators in restored populations will be contrasted to those in natural populations, and paternity assignment performed on seed from restored and natural populations to assess realized patterns of pollen dispersal, and the integration between restored and natural populations. This ecological genetic study will lead to improved guidelines for the ecological restoration of functional and resilient plant populations. Supervisors: Dr Siegy Krauss (Siegy.Krauss@bgpa.wa.gov.au) 3. Pollination ecology and reproductive biology of rare acacias. Acacia karina is a narrow endemic, restricted to a handful of populations on ironstone in the mid-west of WA. Some of these populations are to be impacted by mining activities, and an understanding of the levels and structuring of genetic variation, and the processes impacting on this genetic variation, are required for management and conservation. This project applies newly developed microsatellite markers for the detailed assessment of realized mating patterns through an analysis of paternity, to generate new data on outcrossing rates and pollen dispersal. In addition, fieldwork during its flowering period will generate new data on pollinators, pollinator movement and behaviour, and the reproductive biology of A. karina. These data will

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be interpreted in the context of assessing impacts of mining activities on the long-term viability of this species, and contribute novel information on the reproductive biology of acacias generally. Supervisors: Dr Paul Nevill (Paul.Nevill@bgpa.wa.gov.au); Dr Siegy Krauss (Siegy.Krauss@bgpa.wa.gov.au) 4. Local adaptation and outbreeding depression among native triggerplant (Stylidiaceae) populations Triggerplants (Stylidium) are model systems to address vital issues in seed sourcing for ecological restoration such as local adaptation and outbreeding depression. This project builds on more than 5 years of research in establishing second generation seed following large scale cross pollination manipulations and provenance field trials by Dr Kristina Hufford. In this project, you would utilize these seed to establish plants in reciprocal field trials in the Darling Range, and monitor the success of these plants for an assessment of home-site advantage and outbreeding depression. The question to be answered is whether the evidence for outbreeding depression found in the first generation offspring continues into the second generation. In addition, there is the opportunity to assess population genetic variation among these source populations with microsatellite markers. Ultimately, these data will contribute to genetic provenance maps for seed collection and improved outcomes for bushland restoration. Supervisors: Dr Siegy Krauss ((Siegy.Krauss@bgpa.wa.gov.au)); Dr Erik Veneklaas 5. Mating systems in Pilbara spinifexes Desert spinifexes (Triodia spp.) are the dominant species in arid hummock grasslands across almost a quarter of Australia, and are therefore key species for restoration. Mating systems (eg. inbreeding or outcrossing strategies) are a primary driver of genetic variation within and between populations, and a critical factor in planning and monitoring restoration success in mining rehabilitation. Mating systems are especially important to consider in seed farming, now being investigated as a potentially reliable seed source for spinifex to mitigate extreme seasonal fluctuations which limit seed availability for industry. For example, if plants are strictly outcrossing, small scale seed farm or rehab plots may not produce enough outcross pollen to permit viable seed production, or produce highly inbred seed which reduces survival rates. This project will investigate mating systems in Pilbara spinifex using newly developed molecular markers, to answer some fundamental questions about arid Australia’s most important plant. Supervisors: Dr Matt Barrett (Matt.Barrett@bgpa.wa.gov.au); Dr Siegy Krauss (Siegy. Krauss@bgpa.wa.gov.au). 6. Genetics of Seagrass Seagrasses belong to a large group of marine flowering plants, adapted for an entirely submerged life. They produce flowers and seeds, with pollen and seed dispersal occurring within the water column. Seagrass meadows also exhibit extensive vegetative (or clonal) reproduction. The meadows are extremely productive ecosystems and play a vital role in providing fish nurseries and stabilising seabeds and coastal shorelines. Extensive decline in seagrass meadows has been documented around Australia, and globally, with experimental restoration efforts requiring donor plant material. Ecological, morphological, and molecular tools are being used to addresses a range of issues relating to population structure, mating systems, seed dispersal, and recruitment to contribute to the long-term success of restoration efforts. Microsatellite DNA markers are specifically being used to answer questions relating to clonal diversity, gene flow among meadows and the role ocean currents play in pollen and seed dispersal. Several options for projects are available, and can be developed around student skills and interests.

Supervisors: Dr Elizabeth Sinclair (elizabeth.sinclair@uwa.edu.au), Dr Siegy Krauss, Dr Gary Kendrick 7. Genetic patterns in Pilbara riparian species using next-generation sequencing (NGS) approaches The Pilbara in northwestern Australia is an ancient biophysical region and an important zone of biodiversity and endemism. Our understanding of patterns of biotic diversity in the region is limited and in this project you will use next-generation sequencing (NGS) approaches to study genetic patterns in widespread Pilbara riparian tree species. Supervisors: Dr Paul Nevill (paul.nevill@bgpa.wa.gov.au); Dr Siegy Krauss (siegy.krauss@bgpa.wa.gov.au) All of these projects are supported by external funds. For information on other Conservation Genetics projects please contact: Dr. Siegy Krauss (phone: 9480 3673, email: siegy.krauss@bgpa.wa.gov.au)

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RESEARCH AREA: “Seed Banking and Seed Science” 1. Use of seed enabling technology to improve the establishment of agricultural and NRM important

perennials Australian native plants have been identified as having a large potential for pasture/cropping systems, agro-forestry and land remediation. However, the need to lower the cost of production or land rehabilitation by improving plant establishment success. Kings Park has strategically developed many germination enhancement treatments that aim to reduce the amount of seed usage and produce more vigorous plants thus assisting these industries in becoming more economically viable. A range of projects are being offered working on a wide variety of herbaceous and woody native perennial species as well as native grasses for direct seeding. Topics include general seed biology, refining seed enabling technology and use of seed coating to improve delivery and establishment success. Supervisor: Dr. Jason Stevens, (phone 9480 3639, email: Jason.stevens@bgpa.wa.gov.au 2. Hydrochory, strandlines and genetic structure in riparian trees The importance of water in seed dispersal (hydrochory) and emergence timing are poorly understood in riparian species. In this study combining seed ecology and molecular approaches you will examine key questions in the dispersal ecology of co-occurring Pilbara riparian species.

Supervisors: Dr Lucy Commander (phone: 9480 3622, lucy.commander@bgpa.wa.gov.au); Dr Paul Nevill (paul.nevill@bgpa.wa.gov.au) 3. Seedling emergence – does speed really matter? Seed germination is the most risky event in a plant’s life as seeds need to germinate at a suitable place and time for seedling survival. Germination can be particularly risky in arid areas, as low and variable rainfall could result in insufficient moisture for seedling survival and establishment. Predictive germination is a concept which describes the cuing of seed germination using environmental factors favourable to seedling survival. Germination speed and germination with the required amount of soil moisture are two mechanisms used for predictive germination. Fast germination allows a competitive advantage, however it is associated with higher risk, as moisture may not be available for long enough to allow for seedling establishment. This study will use perennial and annual species of arid Australia to assess the use of predictive germination models for determining risk-taking and risk-averse species to provide insights into species co-existence in variable environments and community composition in restoration. Supervisors: Dr Lucy Commander (phone: 9480 3622, lucy.commander@bgpa.wa.gov.au); Dr David Merritt david.merritt@bgpa.wa.gov.au For information on other Seed Banking and Seed Science projects please contact: Dr David Merritt (phone: 9480 3639; email: david.merritt @bgpa.wa.gov.au)

RESEARCH AREA: “Pollination Biology”

1. The effects of habitat fragmentation on pollination systems on the Swan Coastal Plain Western Australia is recognised as a biodiversity hotspot through the combination of high floristic diversity and pervasive anthropogenic threats. Critical to conservation of this flora is an understanding of reproductive strategies, particularly pollination. Yet remarkably pollination systems have been studied in very few insect pollinated plants including many of our most well known wildflowers. This project aims to resolve pollination systems in a range of species naturally occurring in floristically diverse urban remnants and the effects of habitat fragmentation and habitat modification on pollinator communities.

Supervisors: Dr Ryan Phillips (phone: 9480 3682, email ryan.phillips@bgpa.wa.gov.au Mr Myles Menz (email myles.menz@bgpa.wa.gov.au) Prof. Kingsley Dixon (email kingsley.dixon@bgpa.wa.gov.au) 2. Bee pollination of pea plants and the potential for competition with feral honey bees Western Australian pea plants (Fabaceae) are characterized by high species diversity and a range of striking floral colour patterns. The majority of species are believed to be pollinated by native bees and, more recently, the feral honey bee (Apis mellifera). However, most aspects of this interaction remain largely

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unstudied including the foraging specificity of native bees, the relative importance of Apis mellifera for pollination, differences in foraging behaviour between bee species and the consequences for pollen movement. This project will investigate these issues by focusing on winter flowering pea plants in the Darling Range (Hovea and Davesia).

Supervisors: Dr Ryan Phillips (phone: 9480 3682, email ryan.phillips@bgpa.wa.gov.au); Mr Myles Menz (email myles.menz@bgpa.wa.gov.au); Prof. Kingsley Dixon (email kingsley.dixon@bgpa.wa.gov.au)

RESEARCH AREA: “Orchid Biology”

1. Microhabitat requirements for the germination and survival of the endangered spider orchid Caladenia huegelii Caladenia huegelii, the Grand Spider Orchid, is a rare and endangered species restricted to the Swan Coastal Plain. While C. huegelii was probably once common in its restricted range, it is now highly threatened by clearing for agriculture and ongoing urbanization. A multidisciplinary research program has shown that C. huegelii not only has very low reproductive success but relies on a single species of mycorrhizal fungus for germination and annual growth. Fortunately, propagation techniques are well developed, creating the opportunity for reintroductions into the wild. This project will primarily involve a microhabitat study of both the location of adult plants and sites where germination occurs with the aim of better managing the species and optimizing the reintroduction process. Further, we will aim to establish if orchids have more specific habitat requirements during germination than as adult plants. The project will also involve comparison with common co-occuring Caladenia which utilize different species of mycorrhizal fungi. This will enable investigation of the interaction of fungal species and microhabitat in the formation of symbiosis.

Supervisors: Dr Belinda Newman, (phone: 9480 3682, email belinda.newman@bgpa.wa.gov.au) Dr Ryan Phillips (email ryan.phillips@bgpa.wa.gov.au); Mr Myles Menz (email myles.menz@bgpa.wa.gov.au); Prof. Kingsley Dixon (email kingsley.dixon@bgpa.wa.gov.au) 2. Impacts of population size and co-flowering species on reproductive success in the pea plant mimic Diuris brumalis The Orchidaceae is remarkable for having a high diversity of deceptive pollination strategies. In many cases the orchid produces a showy display indicative of a nectar producing plant – yet no such reward is provided to the pollinator. Donkey orchids (Diuris) have long been thought to mimic pea plants (Fabaceae), thereby luring pollinators to their nectarless flowers. However, this theory has recently been questioned on the basis that Diuris do not necessarily co-occur with the pea plants they are believed to mimic. This study aims to confirm the sharing of pollinators between Diuris and pea plants and then test if the presence of pea plants has a positive benefit on reproductive success of Diuris. The relationship of reproductive success and population size will also be investigated to test if deceptive pollination strategies are more successful for small populations.

Supervisors: Dr Ryan Phillips (phone: 9480 3682, email ryan.phillips@bgpa.wa.gov.au) Mr Myles Menz (email myles.menz@bgpa.wa.gov.au) Dr Belinda Newman, (email belinda.newman@bgpa.wa.gov.au) Prof. Kingsley Dixon (email kingsley.dixon@bgpa.wa.gov.au) 3. Ecological drivers of niche occupancy and symbiosis formation in the rare and threatened orchid, Caladenia lodgeana Caladenia lodgeana is a rare spider orchid restricted to the Collie Basin in the south-west of Western Australia. A large-scale, regional mycorrhizal baiting study revealed that formation of a symbiosis between the orchid and fungi was occurring primarily within established orchid populations and rarely outside of them. This raises the question as to why sites outside of the orchids current range don’t appear to support formation of a mycorrhizal symbiosis? Are the fungi of co-occurring spider orchids able to outcompete the C. lodgeana compatible fungi? This study would focus on baiting for the mycorrhizal fungi of C. lodgeana and other co-occurring spider orchids within and outside the range of C. lodgeana populations. Comparative studies of germination and habitat variables will help determine the ecological drivers of niche occupancy and symbiosis formation. The results of this study will aid in future reintroduction efforts and will also form

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part of an integrated research program focused on the conservation of the rare and threatened spider orchid, C. lodgeana.

Supervisors: Dr Belinda Newman, (phone: 9480 3682, email belinda.newman@bgpa.wa.gov.au) Dr Ryan Phillips (email ryan.phillips@bgpa.wa.gov.au) Mr Myles Menz (email myles.menz@bgpa.wa.gov.au) Prof. Kingsley Dixon (email kingsley.dixon@bgpa.wa.gov.au)

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THE CENTRE FOR PLANT GENETICS AND BREEDING (PGB)

PGB is a Research Centre at in the School of Plant Biology and has collaborative links with the Department of Agriculture and Food, Western Australia, CSIRO, Murdoch University and also international organizations. We aim to link the theory and practice of genetic improvement of a range of crop and model plant species with research and education in plant breeding, thereby providing an opportunity for translational research from model plants to crops. We contribute to national and international efforts to enhance world food and feed security by addressing problems and priorities through strategic scientific research and development, linked to an applied base. PGB’s research focus includes cereals, legumes (grain and pasture) and oilseeds in the following areas:

• Germplasm development (wide-crosses to introgress desirable traits, pre-emptive breeding and screening for physiological traits, exotic pests and diseases, germplasm collection and characterisation using agronomic, morphological and molecular data, development of core collections and agro-ecological evaluation of crop germplasm).

• Breeding technologies such as development of double haploids and rapid generation protocols New crop development.

• Improved adaptation to abiotic (climatic and edaphic) stress.

• Developing new pasture species for a wide range of soil types and environments.

• Nitrogen fixation, global warming potential and sustainability of production systems with legumes.

International Linkages The Centre has built a network of international linkages with standing agreements for research cooperation and exchange of germplasm with several countries and specific project-based linkages with many others (including international agricultural research centres).

What can PGB offer to Undergraduate and Post-graduate training in legume science?

• Collaborative partners and associates with diverse skills in basic and applied aspects of crop research and development.

• Crop related projects in partnership with the industry.

• Scientists with wide experience and strong linkages with international agricultural centres and national agricultural system (Indian sub-continent, West Asia and North Africa, Central Asian Republic, South America and China).

A selection of the many project ideas developed by PGB scientists and associates and available for students to consider as honours or fourth-year projects is presented on the following pages.

For further information contact individual researchers directly or: Centre for Plant Genetics and Breeding (PGB), Faculty of Natural & Agricultural Sciences, The University of Western Australia (M080), 35 Stirling Highway, Crawley WA 6009 Phone: 61 8 6488 2505 Fax: 61 8 6488 1140 Email: william.erskine@uwa.edu.au Website: http://www.pgb.plants.uwa.edu.au/

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PROFESSOR WILLIAM ERSKINE

Room 1.149 CRC Wing; Ph 6488 1903; Email: William.Erskine@uwa.edu.au

LEGUME VARIATION, GENETICS & BREEDING My interests are in the variation, genetics and breeding of food, forage and pasture legumes. In a changing climate and with fertilizer costs spiralling, legumes will increasingly return into grain production systems to underpin long-term sustainability through nitrogen fixation in association with rhizobium reducing the need for synthetic fertilizer produced from fossil fuel, and through their action as a disease and weed break for cereals. I am happy to supervise students in aspects of legume improvement, often co-supervised with others, in aspects of the reliability of production. These include, for example, legume variability in response to major biotic and abiotic stresses, seed quality and nitrogen fixation efficiency and all aspects of broadening the genetic base of legume improvement. Characterise large and small seeded legumes for breeding for water logging tolerance. (with Dr Imran Malik)

Background

Waterlogging is wide spread problem in the world. Waterlogging of soil results from combination of factors such as excess rainfall, poor soil drainage and water storage capacity of the soil. Irrigation may also cause waterlogging depending on the soil type. Duration and intensity of waterlogging is creasing with the effect of climate change. The average area adversely affected by waterlogging per year is 1.8 million ha in Western Australia. A series of physical, chemical and biological changes take place soon after the onset of waterlogging event. All these changes take place due to the disappearance of molecular O2 from the soil. Grain legume species differed in their response to waterlogging. Field experiments demonstrated variation among the large and small seeded Field pea (Pisum sativum) in their waterlogging tolerance at germination. Grass pea (Lathyrus sativus) is reputed for waterlogging tolerance among the legumes; by contrast, Lentil (Lens culinaris) is susceptible to waterlogging. Considering all these evidences it is important for breeding purpose to evaluate responses of large and small seeded legumes to waterlogging and subsequent recovery.

Project aim: Evaluate tolerance of large and small seeded legumes to waterlogging at germination and response at recovery.

Materials and Methods: The experiment will be carried out at UWA in Glass house and/or in phytotron. Ten grain legumes of different seed size will be grown in waterlogged (reduced) soil for 10 d and then pots will be drained to allow recovery for 10 d. At the same time 10 legumes will be grown in drained soil to compare responses. Two harvests will be made as follows: i start of the recovery (10 d after sowing) and ii. end of the experiment (20 d after sowing).

The project will focus on measuring impacts of soil waterlogging on roots and shoots of the legume seedlings. Measuring O2 movement from shoot to root can also be possible within the project.

The project will give opportunity the student to learn new techniques and to understand the importance of physiological traits relevant to overcome abiotic stress for breeding purpose.

Association mapping of key phenotypic traits (to be discussed ... could be resistance to clover scorch

disease or Red-legged Earth Mite, Hard-seededness, or other morphological traits etc) to molecular

markers using the HAPMAP developed for the subterranean clover CORE collection. (With Dr Parwinder Kaur) Association genetics is a powerful tool for genetic analysis relating SNP markers to phenotypic data and also data on climate of collection locations. MSc/PhD Project to possibly include:

• Phenotyping the CORE collection of 97 lines

• Correlation analyses among phenotypic traits and with climatic data of collection location

• Association mapping: Correlation between traits and markers

• Development of PCR markers for phenotypic traits for industry use and Marker Assisted Breeding programs

Contacts: Professor William Erskine (william.erskine@uwa.edu.au) and Dr Parwinder Kaur (parwinder.kaur@uwa.edu.au)

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ASSISTANT PROFESSOR JANINE CROSER Room 1.141 PBG; Ph: 6488 7951/ 0422702382 Email: janine.croser@uwa.edu.au

Biotech & BioFuels Research topics currently available for Honours/4th year projects in 2015: � Be part of the solution to the peak oil crisis - Camelina sativa is an alternative oilseed with very high

levels of Omega-3 and promise as a low-input biofuel feedstock. We have imported a range of exciting lines from Russia which need to be further characterized. We can offer projects in C. sativa related to genetics (molecular mapping; genome size determination), plant breeding (crossing and mutation for improving oil qualities), agronomy (classical field trials to determine performance of lines under diverse growing conditions) and biotechnology (development of doubled haploids). We also need to further explore its application in industry, cosmetics and healthfoods and can provide targeted projects in these areas.

NB. Camelina was the research subject of the WA regional finalist of the BioGENEius competition for 2010.

� Test tube breeding…In vitro flowering of a range of oilseeds – flowering and seed set can be induced

in vitro from stem cuttings without rooting. This enables us to fast-track breeding by reducing generation time. Factors such as temperature, light spectrum and length of exposure and culture medium are all important in protocol development. An excellent opportunity to develop a protocol with significant industry outcomes within the timeframe of a fourth year project.

� Why use exotics when the locals may be just as good? Tissue culture of native legumes – investigate

the potential for using biotechnology tools for plant improvement in some of Australia’s native pasture legumes – especially those with promise for adaptation to broad acre farming systems (spp. Cullen, Kennedia, etc.). In collaboration with Dr Megan Ryan and Mr Richard Bennett (UWA).

If you are interested in any of these topics, or have suggestions related to these areas (cell biology/ in vitro culture/ utilisation of novel species), please send me an email or drop by my office for a chat.

RESEARCH ASSIST PROFESSOR PING SI Room 1.159 Central Agriculture wing; Ph: 6488 1233; Email: ping.si@uwa.edu.au Honours/MSc Projects in 2015:

Herbicide tolerance in grain legumes Herbicides are one of very important elements of modern agriculture. They have played very important role in weed management, thus increasing crop production. Improving herbicide tolerance means increase in food security. We have grain legumes (narrow-leafed lupin) mutants with increased herbicide tolerance. They are excellent materials to investigate the mechanisms of tolerance.

• Mechanisms of non-target-site metribuzin tolerance in lupin mutants Metribuzin affects photosynthesis of plants. We have several genotypes (mutants and wild types) of three distinctive levels of metribuzin tolerance (highly tolerant to susceptible). They are excellent genetic materials to answer questions like: Do these different tolerance levels relate to different photosynthetic rates? Do external environments have impact on them? In collaboration with Associate Professor Qin Yu of AHRI, School of Plant Biology.

Si, P. Pan, G and Sweetingham M (2011) Semi-dominant genes confer additive tolerance to

metribuzin in narrow-leafed lupin (Lupinus angustifolius L.) mutants. Euphytica 177, 411 -418. DOI 10.1007/s10681-010-0278-9

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Si P. Buirchell, B. and Sweetingham, MW. (2009) Improved metribuzin tolerance in narrow-leafed lupin (Lupinus angustifolius L.) by induced mutation and field selection. Field Crops Research, 113, 282-

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• Genetic variation in lupin germplasm with tolerance to a number of herbicides Higher tolerance and multiple tolerance to diverse range of herbicides are required for the effective weed

management. The lupin germplasm is very diverse and it offers great opportunity to identify tolerant accessions. This is an excellent honours project and we have published 4th year project in scientific journal.

Si, P. Sweetingham, MW. Buirchell, B. Bowran, D. and Piper T. (2006) Genotypic variation on metribuzin tolerance in narrow-leafed lupin (Lupinus angustifolius L.). Australian Journal of Experimental Agriculture, 46, 85-91 Si, P. Yan, G, Kemsan, MA and Adhikari KN (2012) Genotypic variation of metribuzin and carfentrazone-ethyl tolerance among yellow lupin (Lupinus luteus L.) germplasm. New Zealand Journal of Crop and Horticultural Science 40, 43-54. Adapting lupin to cooler winter conditions Improvement in lupin’s early growth cold temperature would improve lupin adaption into cooler winter growing regions. Narrow-leafed lupin has been well adapted to the northern crop growing regions with warmer winter temperature. In collaboration with Dr Jens Burgess, CSIRO. Si, P. and Thurling, N. (2001) Genetic improvement of pre-anthesis growth of turnip rape (Brassica

rapa L.) at low temperature. Australian Journal of Agricultural Research 52, 653-660

PROFESSOR TANVEER KHAN Room 1.151 Central Agriculture wing; Ph: 6488 1233; Email: tanveer.khan@uwa.edu.au

Histo-pathological studies in chickpea host resistance to Ascochyta rabiei (ascochyta blight disease)

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THE COMMONWEALTH SCIENTIFIC AND INDUSTRIAL RESEARCH ORGANISATION (CSIRO)

ADJUNCT ASSOCIATE PROFESSOR PHIL WARD Senior Research Scientist, CSIRO Plant Industry, Floreat Park, WA; Ph: 9333 6616; Email: Phil.Ward@csiro.au Research Interests My research revolves around water use by plants: how water use is impacted by the environment; and how it impacts on the environment. Current research projects include:

• Water balance of conservation farming systems (with Dr Ken Flower and WANTFA). How does stubble retention, as part of a conservation farming system, affect evaporation from the soil, infiltration into the soil, deep drainage to groundwater, and crop water use efficiency?

• Measuring crop root growth in WA soils (with Dr Yvette Oliver, CSIRO and Mr David Hall,

DAFWA). Western Australian soils pose some significant challenges for crop root growth, such as soil compaction, soil acidity, and transient salinity. Previous research on overcoming soil constraints has shown inconsistent results, but actual measurements of root growth and water and nutrient uptake have rarely been undertaken, so our current understanding of these effects is limited.

• Water repellency and stubble retention (with Dr Margaret Roper, CSIRO, and Dr Steve Davies,

DAFWA). The theory of water repellence suggests that its severity should increase under stubble retention. However, farmers report that symptoms of water repellency are often less severe after adopting stubble retention. Can this be explained by patterns of soil water distribution?

In addition to the work described above on agricultural systems, I have also worked on native ecosystems, including Banksia woodland and mallee heath (with Prof Hans Lambers and Dr Erik Veneklaas), measuring water use at the ecosystem level. Possible Projects

• Impact of stubble orientation on evaporation from the soil during early crop growth. One of the ways to improve crop water use efficiency is to reduce water loss by evaporation from the soil surface. Can stubble retention assist in reducing evaporation, and will this increase water use efficiency? This project would involve field work at the existing trials (managed by WANTFA) located at Cunderdin and Mingenew. Measurements would include evaporation rate and soil water content in some of the treatments at the sites for the first few months of crop growth (May-July).

• Does pasture cropping reduce the incidence and severity of wind erosion? One of the major proposed benefits of pasture cropping on the sandplain areas of WA is the potential for the higher levels of ground cover to reduce the incidence and severity of wind erosion. However, there is currently no data to support this assertion. In this project, you would take erosion measurements on farmer sites in the Northern wheat belt. Measurements would be most suited to April and May, but could be conducted at any time.

• How does soil disturbance affect water repellency? Farmers are currently experimenting with soil disturbance ranging from minimal to complete soil inversion, and each level of soil disturbance has the potential to change the way that water repellency is expressed, sometimes in unexpected ways.

• Dead roots as potential wicks. Recent research has shown that in sandy soils, evaporation over summer might actually be higher from areas where stubble is retained compared with areas where stubble is removed. This finding is contrary to expectations. Can dead roots act as continuous soil pores, transmitting water to the soil surface? This project will involve glasshouse research, using a tracer in water to determine patterns of water movement in pots containing dead wheat plants.

I am also happy to discuss other project ideas related to soil water or plant water use.

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ADJUNCT ASSOCIATE PROFESSOR BRUCE WEBBER Research Scientist, CSIRO Ecosystem Sciences, Underwood Ave, Floreat Ph: 08 9333 6802; Email: bruce.webber@uwa.edu.au; Web: www.uwa.edu.au/people/bruce.webber PLANT ECOPHYSIOLOGY, PLANT-ANIMAL INTERACTIONS, BIOGEOGRAPHY, INVASION

ECOLOGY & CLIMATE CHANGE Research interests: My current interests relate to the management of invasive plants taking into account rapid global change drivers. I focus on understanding risks and impacts associated with invasive species and aim to provide evidence based assessments for influencing adaptation responses (management and policy) to global change. My work includes assessing variation in the invasive ability of plants, the interaction of these plants with their surrounding ecosystem, potential distribution studies based on modelling climatic and ecophysiological parameters, and understanding the ongoing effectiveness of biological control methods.

Students would have access to a suite of facilities at UWA and at the CSIRO CELS site in Floreat, according to the needs of the chosen project. Projects would involve collaborations with John Scott (www.csiro.au/people/John.K.Scott), Hans Lambers (www.uwa.edu.au/people/hans.lambers) and Melinda Trudgen. For further information or to propose alternative project ideas, please don’t hesitate to get in touch. Some specific projects for consideration this coming year are: Germination and establishment ecology of invasive sea spurge (with Dr John Scott) For plants, coastal foredunes are a highly mobile environment in which to establish and grow. Yet the exotic Mediterranean sea spurge is able to colonise this environment readily, resulting in a highly modified foredune community in many parts of southern Australia. As part of our broader work on characterising the invasion of sea spurge in Australia, this project will bring a plant ecophysiological perspective to investigating the mechanisms and processes that allow sea spurge to germinate, establish and then dominate. Ecosystem transforming processes associated with bridal creeper invasion (with Prof Hans Lambers) Areas colonised by bridal creeper, a weed of national significance, have increased soil nutrients and exhibit post-colonisation loss of native species. A change in decomposition rates is also associated with the weed invasion. The project will examine the ecosystem changing processes associated with invasion by bridal creeper both in the laboratory and field, and test management options for restoring impacted ecosystems. Understanding how urban trees become invasive weeds (with Ms Melinda Trudgen) Non-native plants are an integral part of our urban environments, yet some of these species go on to become invasive weeds and threaten natural ecosystems. Rosewood (Tipuana tipu) is a street tree that has the potential to be highly invasive. Several projects are available to assess mechanisms which drive the shift from garden tree to invasive weed. These include investigating seed predation (animal frugivory; are lawn mowers a new urban ‘predator’?), or the effects of competition on germination and seedling establishment. The role of bracken fern in ecosystem restoration (with Dr John Scott) Bracken (Pteridium esculentum) is one of the most widespread ferns in the world. While native to WA, it can form monocultures to the exclusion of other plant species, including exotic grasses and blackberry, the latter being the main invasive weed of river banks in south west WA. Bracken is fire prone, helps prevent erosion, may facilitate forest regeneration, but can halve Eucalyptus seedling survival. This project will assess by experiments and field observations the interaction between bracken, blackberry and riparian plant species regeneration in a south west WA context. The invasion ecology of blackberry (with Dr John Scott) A lack of knowledge on blackberry (Rubus anglocandicans) seed and seedling ecology is one of the main barriers to understanding the role of this major invasive species in riparian systems of south west Australia. The project will measure factors associated with seed germination and seedling establishment and growth using field experiments and observations. Seedling growth will also be studied in controlled temperature cabinets and with differing soil types and moisture regimes, providing data to underpin niche modelling. Climate change at regional scales (with Dr John Scott) Most of the modelling of climate change occurs at the national or state scale, but this is usually not the scale used for conservation planning. Planning for invasive plant management, ecosystem restoration and climate change at the regional requires a consideration of multiple interlocking questions. What are the vegetation characteristics that need to be considered? Which species are suitable for transplantation or control? How do regional scale and climate change scales overlap? These issues are being considered at a range of regional locations in WA with an opportunity to gain real experience in real-world climate change planning.

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DEPARTMENT OF AGRICULTURE AND FOOD WESTERN AUSTRALIA

ADJ. SENIOR LECTURER MANISHA SHANKAR Senior Plant Pathologist, Department of Agriculture and Food, South Perth Ph: 9368 3533; Email: mshankar@agric.wa.gov.au Phenotyping for seedling and adult plant resistance to yellow spot of wheat in a doubled haploid

mapping population fixed for 5BL locus The project deals with evaluation of seedling and adult plant response to yellow spot in controlled environment conditions. Good progress has been made internationally to understand resistance to yellow spot (causal fungus Pyrenophora tritici-repentis) of wheat and this work has helped identify the main resistance factor in Australian germplasm being toxin insensitivity at the 5BL locus, tsn1. Limited understanding exists on the extent of occurrence of tsn1 in Australian breeding material and yet there appears to be considerable variation in response to yellow spot resistance among tsn1 carrying lines that could, when understood, provide significant opportunity to enhance expression of resistance in Australian germplasm, additional to the moderate resistance achieved with the 5BL tsn1 locus. Phenotyping for seedling and adult plant resistance to stagonospora nodorum blotch of wheat in a

doubled haploid mapping population Stagonospora nodorum blotch, caused by Phaeosphaeria nodorum (E. Muller) Hedjaroude, is a severe leaf pathogen throughout many wheat growing areas. Experiments comparing yields from fungicide-protected and unprotected plots show 30-50% reduction in yield due to the disease in Western Australia. Resistance has been associated with excessive plant height and late development and is often quantitative making recovery of well-adapted highly resistant types difficult. This project aims to evaluate resistance in a wheat doubled haploid population under controlled environment conditions both at seedling and adult plant stages. The eventual aim is to identify marker-trait associations and provide information on chromosomal regions contributing resistance to Stagonospora nodorum in wheat.

ADJ. ASSOC. PROF. DANIEL REAL Department of Agriculture and Food Western Australia, Pasture Science Group, 3 Baron-Hay Court, South Perth, WA 6151 Ph: 9368 3879 Email: daniel.real@agric.wa.gov.au Research Interests As a participant of the Future Farm Industries CRC, my research interest is in perennial forage legume breeding. Specific projects can be developed to suit student’s interest within our breeding program in Tedera (Bituminaria bituminosa var. albomarginata). For further details please contact me by email: daniel.real@agric.wa.gov.au

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DEPARTMENT OF PARKS AND WILDLIFE

The Department of Parks and Wildlife has the lead responsibility for conserving Western Australia’s biodiversity and the protection, sustainable use and enjoyment of the State’s natural environment. It provides a clear focus on key biodiversity conservation priorities, such as the recovery of threatened plants and animals, mitigation of threatening processes, such as introduced pest plants, animals and diseases, fragmentation and climate change, and sustainable use of our natural resources. We manage 27 million hectares covering the State’s national parks, marine parks, conservation parks, State forests and timber reserves, nature reserves, marine nature reserves and marine management areas. The department is also responsible for fire preparedness and pest animal and weed control on 89 million hectares of unallocated Crown land and unmanaged reserves.

The Plant Science and Herbarium Program is one of six thematic science programs within the Science and Conservation Division. Key research activities are focused on developing an improved understanding of factors and processes that are critical for the conservation of the State’s plant diversity, and taxonomic and molecular taxonomic studies on the State’s flora. Research outcomes are incorporated into conservation management to ensure the persistence of rare and threatened species, ameliorate key threats such as dieback and weeds, develop threatened species reintroduction methodologies and improve our understanding of genetic and ecological factors that are vital for the long term viability of plant species.

RESEARCH THEME: Genetic and ecological consequences of small population processes, rarity

and habitat fragmentation

Genetic and ecological consequences of habitat fragmentation and population viability in key

species in the Dongolocking area of the Wheatbelt and the Swan Coastal Plain

This project will build on studies already underway in this area that aim to understand and quantify how genetic and demographic processes interact to influence the viability and long-term conservation value of native plant populations in remnant vegetation, and relate this to easily measured landscape and population parameters. This information can then be used to identify and prioritize high viability remnants for in-situ conservation and assess the value of small remnants in maintaining connectivity in the landscape by facilitating pollen movement and thus gene flow. The project also aims to test conservation genetics theory regarding the genetic deterioration of small fragmented populations but focuses on common species rather than rare species. This is important since it is the more abundant species that are the critical components of landscapes with regard to maintenance of broader ecosystem function such as hydrology and nutrient cycling, as well as provision of habitat for other native organisms. This project will involve the use of molecular genetic and field base ecological and demographic techniques.

Further Information: Dr David Coates, Ph 9219 9048 dave.coates@dpaw.wa.gov.au Dr Margaret Byrne, Ph 9219 9078 margaret.byrne@dpaw.wa.gov.au Dr Colin Yates, Ph 9219 9079 colin.yates@dpaw.wa.gov.au

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How does population size and isolation affect pollinator visitation, flowering, pollination, seed

production and seedling fitness in the rare Acacia woodmaniorum

The recently discovered Acacia woodmaniorum is endemic to the Banded Ironstone Formation (BIF) ranges of Western Australia. The rare species is known from an area of only 40km2 and may be placed under threat from future mining operations. The project will investigate various aspects of pollination biology, including the determination of key pollinators and what affect population size and isolation has on flowering, pollination, seed production and seedling fitness. Information on these aspects of pollination biology will further inform us about the patterns of pollen dispersal, that ultimately influence patterns of genetic variation in this species. The research is important for the ongoing management of natural populations that ensures any impacts from mining activities are minimised. This project will involve field based ecological and demographic techniques as well as glasshouse based work and will tie in with a larger study on fine scale genetic structure and patterns of gene flow in A. woodmaniourm.

Further Information: Dr David Coates, Ph 9219 9048 dave.coates@dpaw.wa.gov.au Dr Melissa Millar, Ph 9219 9083 melissa.millar@dpaw.wa.gov.au Genetic and ecological consequences of rarity in the critically endangered ghost wattle Acacia sciophanes

Acacia sciophanes is an extremely rare species covering a geographic range of less than 7 km. It is currently listed as threatened and ranked as Critically Endangered occurring in a heavily fragmented landscape where much of the native vegetation has been cleared for agricultural production. It develops into a diffuse, openly branched, wispy shrub up to 2.3 m tall and is closely related to a more common species Acacia anfractuosa that occurs over a range of some 200km. Previous studies indicate that it is characterised by reduced genetic diversity and increased inbreeding in its two populations but there is no clear evidence for inbreeding depression and reduced reproductive output influencing the viability of these populations. The aim of this project will be to expand previous mating system, genetic diversity and ecological studies to determine which key factors if any will limit the viability and long term survival of this species. This project will involve the use of molecular genetic and field base ecological and demographic techniques

Further Information: Dr David Coates, Ph 9219 9048 dave.coates@dec.wa.gov.au Dr Colin Yates, Ph 9219 9079 colin.yates@dec.wa.gov.au Pollen dispersal and gene flow among fragmented populations of Eremaea pauciflora in the

wheatbelt

Gene flow is a fundamental element of evolutionary processes maintaining cohesion of species. Pollen dispersal is a major component of gene flow in shrubs in south-west WA and recent studies have shown that pollen dispersal can be very extensive even in fragmented landscapes. This project will investigate the patterns of pollen dispersal in the Myrtaceous shrub Eremaea pauciflora in the Dongolocking region and complements previous ecological work on reproductive biology on the species in this area. Highly polymorphic microsatellite markers have been developed for the species to facilitate paternity assignment of seed crops. Knowledge of pollen dispersal is important for management of remnant populations and rehabilitation programs.

Further Information: Dr Margaret Byrne, Ph 9219 9078 margaret.byrne@dpaw.wa.gov.au Dr David Coates, Ph 9219 9048 dave.coates@dpaw.wa.gov.au

Dr Colin Yates, Ph 9219 9079 colin.yates@dpaw.wa.gov.au

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Species patterns in orchids in a fragmented landscape

Orchids are very species-rich in Western Australia, and many are restricted and threatened. Orchid taxonomy in fragmented landscapes is made more difficult by the fragmentation – many pieces of the puzzle are lacking. In particular, some populations that appear to constitute distinct species may not have appeared distinct before clearing, when the full range of variation would have been evident. Anecdotal evidence suggests that changes in the ecology of remnants (e.g. through changed fire regimes and local extinction of fossorial mammals) may be promoting clonality in orchid populations, further adding to the apparent distinctness of some taxa. This project will assess detailed population-level patterns in a number of orchid taxa in the fragmented wheatbelt, to assess species boundaries and taxonomic distinctiveness.

Further Information: Dr Kevin Thiele, kevin.thiele@dpaw.wa.goc.au

RESEARCH THEME: Molecular taxonomy and phylogeny

Phylogenetic and phylogeographic studies on highly endemic plants on the Banded Ironstone

Formation ranges

The Banded Ironstone Formation (BIF) ranges of Western Australia have a unique flora and fauna, with high species endemism on many ranges, particularly those on the boundary of the transitional rainfall zone. An understanding of the evolutionary history of species on these ranges will provide important information for assessing conservation value and making informed decisions on sustainable development. This project will build on current studies suggesting plants on BIF ranges have high genetic diversity but significant differentiation between ranges due to historical isolation. This project will address these issues with two approaches: (i) assess phylogeographic structure and population genetic diversity to identify historical and contemporary processes driving persistence within plant species; (ii) develop molecular phylogenies for targeted genera that have endemic species on the BIF ranges and search for congruent patterns of radiations or independent origin to elucidate any common history for the ranges.

Further Information Dr Margaret Byrne, Ph 9219 9078 margaret.byrne@dpaw.wa.gov.au Dr David Coates, Ph 9219 9048 dave.coates@dpaw.wa.gov.au

Assessing historical and contemporary evolutionary processes in foundation species for

landscape restoration in the midwest of Western Australia

Expansion of mining operations across the midwest region of Western Australia will see significant investment in landscape restoration over future decades. To be successful, restoration must consider the role genetic diversity plays in providing resilience and future adaptive potential to species in altered landscapes. This project will assess historically divergent lineages and contemporary processes of gene flow that shape genetic structure in a number of foundation species for which future restoration will be required. This information will be used to design appropriate seed sourcing regimes that optimise levels of genetic diversity and genetic connectivity across the restoration landscape.

Further Information Dr Margaret Byrne, Ph 9219 9078 margaret.byrne@dpaw.wa.gov.au Dr David Coates, Ph 9219 9048 dave.coates@dpaw.wa.gov.au Dr Melissa Millar, Ph 9219 9083 melissa.millar@dpaw.wa.gov.au

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Phylogeny of the small-flowered Myrtaceae

The small-flowered Myrtaceae (tribe Chamelaucieae) are an extremely species-rich group in Western Australia, including many important and spectacular genera such as Chamelaucium, Darwinia, Thryptomene and Baeckea. Many new species and some new genera are currently being described through revisionary work in progress by Barbara Rye and Malcolm Trudgen at the Western Australian Herbarium. This project will develop a phylogeny for the group using both molecular and morphological data, for the purpose of testing generic, infrageneric and subtribal classifications in the Chamelaucieae.

Further Information: Dr Kevin Thiele, kevin.thiele@dpaw.wa.gov.au Visualising, exploring and traversing the Tree of Life

The Tree of Life is a branching tree-structure used to represent phylogenetic relationships among all the world’s organisms. The Tree is both an integrative and explanatory structure – all known information about organisms can be placed at some level on the Tree of Life. New programs and initiatives in biodiversity informatics (such as the Atlas of Living Australia and the Encyclopedia of Life) seek to develop sophisticated, web-based tools for deploying information about organisms. The Tree of Life is increasingly seen as an ideal structure for exploring, visualizing and traversing the information webs envisaged by these projects. But our current methods for representing it are primitive and underwhelming. This project seeks a unique person – someone with an interest in evolutionary biology but who also is skilled in computer programming and gaming technologies – to explore new ways of representing the Tree of Life and develop and test prototype streaming Tree of Life Navigators.

Further Information: Dr Kevin Thiele, kevin.thiele@dpaw.wa.goc.au Taxonomic revision of the Philotheca spicata (Rutaceae) complex Philotheca spicata (Pepper and Salt) is an attractive, pale pink-flowered, sub-shrub endemic to south-west Western Australia. Preliminary molecular analysis of Philotheca spicata shows that this species is genetically distant from other members of the genus and that it represents an ancient evolutionary lineage. Philotheca spicata has a widespread distribution between Eneabba and Walpole and is morphologically variable across its range, with some variation correlated to geographic location and/or habitat. A geographically restricted informal subspecies, P. spicata subsp. Moore River National Park (G. & D. Woodman Op 47), is currently recognised. A revision of the species complex using a combined morphological and molecular approach is required, to determine the taxonomic and conservation status of the phrase-named subspecies and the distinctness of the various morphotypes.

Further Information: Dr Ryonen Butcher, ryonen.butcher@dpaw.wa.gov.au

RESEARCH THEME: Climate change adaptation

Adaptive variation across climate gradients

Projected climate change for south-western Australia is for hotter and drier conditions and climate adaptation strategies are suggesting gene migration ahead of changing climate as a means of ‘priming’ populations for future climates. However, we have little understanding of whether widespread species are adapted to conditions across the climatic gradient they occupy or whether they have high plasticity in being able to respond to different climates. Recent development of powerful nest generation genomic tools enables assessment of adaptive versus plastic responses in a way that has not been possible previously. This project will use new genomic methods to determine the adaptive and plastic responses of key plants, such as eucalypts and acacias, across the south-west climate gradient to provide information to guide assisted migration and restoration programs.

Further Information: Dr Margaret Byrne, Ph 9219 9078 margaret.byrne@dpaw.wa.gov.au

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Evolutionary history and identification of refugia

Refugia have intrinsic conservation value because they facilitate the local persistence of species and genotypes when regional conditions are unsuitable, and foster evolutionary processes that may lead to diversification. Phylogeographic analyses can identify the presence of refugia that are characterised by genetic signatures of high diversity, with low diversity in areas of expansion, or patterns of localised persistence. This project will combine cpDNA sequence analysis with paleo-distributional modeling to investigate evolutionary patterns in areas of topographic complexity or projected climate stability that are likely to have acted as refugia in the past and may do so under projected climate change. Further Information: Dr Margaret Byrne, Ph 9219 9078 margaret.byrne@dpaw.wa.gov.au Dr Colin Yates, Ph 9219 9079 colin.yates@dpaw.wa.gov.au

RESEARCH THEME: Seed biology and reintroductions of threatened flora

Assessment of temperature thresholds for seed germination in south west Western Australian

species in relation to climate change scenarios

Current climate models predict rising temperatures and declining winter rainfall across much of fire-prone southern Western Australia. These changes have the potential to impact on the Region’s rich plant diversity. One plant characteristic that may respond to climate change is germination, with some species possibly vulnerable to even modest changes in temperature. Successful regeneration after disturbance such as fire may be adversely affected. This project would see the screening of selected SW WA species for their tolerance to a range of temperatures during germination and early seedling performance to provide a more precise understanding of the likely impact of predicted rising temperatures on these critical periods in a plants life cycle.

Further Information: Dr Anne Cochrane, anne.cochrane@dpaw.wa.gov.au Development of guidelines for use of artificial disturbance in flora management and

threatened species recovery

The process of plant colonisation and establishment in many areas has been altered through human intervention and the management of threatened flora is increasingly relying on artificial disturbance to stimulate recruitment. Despite knowing that many threatened species require disturbance for recruitment, application of artificial disturbance treatments often fail to achieve their desired outcome. The nature, frequency and timing of disturbance are important for successful recruitment but using limited seed resources of threatened flora from ex situ collections in field investigations can be wasteful. With limited seed resources, it may be more appropriate to germinate seed under controlled conditions (eg temperature, moisture, predators) and plant the resultant seedlings. In the light of this, it would be prudent to establish disturbance guidelines based on surrogate common species as a priority. This project would investigate the nature of artificial disturbance that would provide the most effective result for recruitment and survival for plant species and to provide guidelines for their use in flora management and threatened species reintroduction.

Further Information: Dr Anne Cochrane, anne.cochrane@dpaw.wa.gov.au Good things come in small packages: seed biology of the triggerplants

Stylidium (the triggerplants) is a large and iconic plant group with more than 250 species in Western Australia, a significant proportion of which are rare, geographically restricted or poorly known. The genus is the subject of ongoing taxonomic research and seed banking efforts within DEC, however, to date there has been little research conducted on aspects of seed biology and morphology. This project will investigate the germination characteristics, and seedling growth forms of both common and rare, and annual and perennial species of Stylidium. It will provide information fundamental to the conservation and management of threatened triggerplants.

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Further Information: Dr Andrew Crawford, andrew.crawford@dpaw.wa.gov.au Dr Anne Cochrane, anne.cochrane@dpaw.wa.gov.au Dr Juliet Wege, juliet.wege@dpaw.wa.gov.au

Determining success criteria for reintroductions of threatened plants

Plant reintroductions are now recognised as a key management tool for preventing the extinction of species in the wild. They involve the planting of seed, seedlings or vegetatively propagated plants into an area where the plant formerly or currently occurs or to a new safe location. Plant reintroductions aim to create and maintain viable self sustaining populations, yet developing criteria that can readily assess this objective is difficult, particularly in long lived woody shrubs that make up many of Western Australia’s Critically Endangered Plants. This project will assess the use of novel techniques that may include eco-physiological approaches, use of molecular markers to estimate mating systems and population viability analysis as possible indicators of long term reintroduction success.

Further Information: Leonie Monks, leonie.monks@dpaw.wa.gov.au Dr Colin Yates, Ph 9219 9079 colin.yates@dpaw.wa.gov.au Dr David Coates, Ph 9219 9048 dave.coates@dpaw.wa.gov.au Dr Margaret Byrne, Ph 9219 9078 margaret.byrne@dpaw.wa.gov.au

RESEARCH THEME: Control and management of Phytophthora dieback

The use of high intensity phosphite techniques to control Phytophthora cinnamomi (Dieback)

Determination of the biology and epidemiology of Phytophthora cinnamomi, the major threat to the flora in the South Coast Region is important for implementing appropriate management options for the control of this pathogen. Further, understanding of the efficacy of high intensity phosphite for the control of P. cinnamomi would provide more options for the management of infested areas. The aim of this project is to advance our understanding of disease biology and epidemiology of P.

cinnamomi in the native plant communities within the National Parks of the South Coast Region of Western Australia and to demonstrate the use of novel phosphite control techniques to reduce the impact of P. cinnamomi within the Threatened Ecological Communities of the Stirling Range National Park and Bell Track infestation in the Fitzgerald River National Park.

Further Information: Dr Chris Dunne, chris.dunne@dpaw.wa.gov.au

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ADJUNCT ASSOCIATE PROFESSOR MARK BRUNDRETT Room 215 Botany Building; Ph 6488 2212; Email: mark.brundrettr@.uwa.edu.au ENDANGERED WHEATBELT ORCHIDS Quantify and understand habitat requirements and threatening processes impacting on a rare orchid in highly fragmented landscapes. Gain knowledge required for sustainable management and make direct contributions to recovery actions for an endangered species, while working in collaboration with DPaW and community groups. ECOLOGICAL IMPLICATIONS OF ORCHID FUNGAL ASSOCIATIONS Discover the role of highly specific fungal interactions on the dispersal of on rare and common orchid species by investigating the distribution of compatible fungi in soils. Help us to gain a greater understanding of the habitat requirements of orchids by studying their fungi. MYCORRHIZAL FUNGUS DIVERSITY IN A BIODIVERSITY HOTSPOT Investigate the diversity of the Glomalean fungi - the oldest group of true fungi, in our ancient landscapes (collaboration with Dr Susan Barker). Investigate diversity using a range of isolation and molecular techniques. Identify fungi with help from international collaborators. ECOLOGY OF MYCORRHIZAL ASSOCIATIONS Study ecological and functional aspects of mycorrhizal fungus associations in natural ecosystems, by investigating the relative dominance of plants with different types of mycorrhizal fungal associations in different habitats.

POLLINATION BIOLOGY OF WINTER FLOWERING ORCHIDS Determine if co-flowering orchids share pollinators and investigate why there are many similar looking taxa in genera such are Pterostylis (or are they really different)? Is there a link between winter orchids and fungus fruiting?

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THE UWA INSTITUTE OF AGRICULTURE The UWA Institute of Agriculture was established by the University of Western Australia (UWA) with a mandate to integrate agricultural and natural resource management, research, education, training and communication within and outside the university. The Institute is a partnership between the four schools within the Faculty of Natural and Agricultural Sciences (FNAS) and key agricultural, food and health, and biotechnology centres within and outside the Faculty within UWA. The UWA Institute of Agriculture works with the agricultural and natural resource management sector to improve workforce skills, and to generate new knowledge that will assist the industry’s participants to advance their individual aspirations, underpin local and regional prosperity, and exercise responsible stewardship of the environment. The Institute has five Programs: Integrated Land and Water; Animal Productions Systems; Plant Production Systems; Rural Economy, Policy and Development, and Education, Outreach and Technology Exchange. These programs are structured to be, where possible, interdisciplinary, intersecting across the varied strengths of the Faculty’s Schools, Centres and discipline groups. The Institute’s programs focus on key themes relevant to future agricultural, food industry and natural resource management needs. Its responsibility is to maintain position of UWA Agricultural Sciences and related natural resource management as the national tertiary leader in the discipline area and in the top 50 agricultural faculties in the world. HACKETT PROFESSOR KADAMBOT SIDDIQUE (kadambot.siddique@uwa.edu.au) Our group aims to gain a greater understanding of the physiology of crops, particularly wheat, in response to the environment and climate change so that we can identify traits for developing improved varieties. We are especially interested in mechanisms controlling plant water use. Water is fundamental to plant growth and productivity and yet it is usually the most limiting resource. Most of the water taken up by plants is lost to transpiration so there is a constant challenge in acquiring and keeping water, particularly in dryland cropping environments. Projects can involve lab, glasshouse or field work. If you have some ideas or you are interested in a relevant area not listed below, we are happy to discuss and develop a project with you. Some projects available include: Wheat root architecture and water transport capacity (in collaboration with Dr. Jairo Palta, CSIRO) Our previous research has shown that wheat roots absorb water preferentially within a few centimeters of the root tip. Wheat root systems with more branches and hence, more root tips should therefore have greater water transport capacity. To test this hypothesis, measurements of the hydraulic conductance and plant water relations of wheat genotypes with different root traits will be carried on plants grown is special root observation chambers. Brachypodium distachyon as a model for wheat water relations Brachypodium is an ideal model to study genes controlling water relations of cereal crops because it is a temperate grass species closely related to wheat and barley, and its genome has been sequenced. We have identified eight putative plasma membrane aquaporin genes in Brachypodium roots, some of which vary their expression diurnally in a pattern similar to changes in root hydraulic conductance. This project will test the role of aquaporins in regulating water flow through Brachypodium roots by inhibiting aquaporin activity. The function of the eight identified aquaporins will also be tested using heterologous expression systems (in collaboration with Prof. Steve Tyerman, University of Adelaide). Monitoring the water status of crops using novel magnetic probes This project will use new probes to monitor the water status of wheat plants in response to temperature and drought. Using two genotypes with contrasting transpiration efficiency, the project will identify the

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relationship between transpiration, leaf temperature and plant water status. We have funding for the student to visit with our collaborator in Germany, Prof. Ulrich Zimmermann who invented the probes. Hydraulic properties of leaves There is wide scope to develop a novel project in this field because of the limited research that has been conducted on Australian plants or crop species. Studies can include anatomical observations, hydraulic measurements and modeling.

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WINTHROP PROFESSOR WALLACE COWLING The UWA Institute of Agriculture, Room 2.102 Agriculture Central Wing; Ph 6488 7979; Email: wallace.cowling@uwa.edu.au

PLANT MOLECULAR GENETICS and PLANT BREEDING

Our group works towards sustainable plant breeding for changing environments – including the application of population genetics, genomics and evolutionary theory to improve crop disease resistance, stress tolerance and adaptation. A wide range of research is undertaken within the group, for example:

• Accelerating crop breeding through new methods enhanced by genetic or genomic information

• Incorporation and exploitation of genetic diversity in elite crop breeding programs

• Interspecific crossing in Brassica species to improve canola (Brassica napus)

• Development of a new hexaploid Brassica species for agriculture

• Heat and drought stress tolerance in Brassica rapa

• Mapping and identifying genes for blackleg disease resistance in canola

• Understanding the molecular basis of disease resistance and susceptibility in blackleg of canola

• Finding gene-specific markers for oil quality traits in canola, such as high oleic and low linolenic oils

• Gene identification in narrow-leafed lupin (Lupinus angustifolius)

• The genetic basis of heterosis (hybrid vigour) in canola.

Honours or MSc Project Ideas:

New breeding methods for genomic and genetic selection (with Assist Prof Matthew Nelson). We have developed a new early generation breeding system that incorporates genetic and genomic information – based on the animal model. This new method could revolutionise plant breeding.

“Dialing up” the right flowering time in canola. (with Assist Prof Matthew Nelson). We have discovered several genes in canola that interact with temperature and photoperiod to determine flowering time. Flowering time should occur at different times in each target region, and these alleles may be used to breed in the correct flowering time in each region.

Development and characterisation of an allohexaploid Brassica DH population (with Dr Sheng Chen) A golden opportunity exists to hasten the agricultural evolution of a new allohexaploid Brassica species. This new allohexaploid Brassica research was initiated in 2008. In this project, we will develop a double haploid population and characterize it at morphological, cytogenetic and molecular levels.

Studies on centres of origin and diversity in Brassica juncea (with Dr Sheng Chen) B. juncea is genetically diverse, with two main centres of diversity in India and China. Whole-genome molecular marker diversity analysis showed two major genetic subgroups of B. juncea. In this project, we will explore association mapping of genes of interest for key traits in a global collection of B. juncea.

Tolerance of Brassica rapa to heat and drought stress (with Dr Sheng Chen & W/Prof Neil Turner) Oilseed Brassica napus lacks heat and drought tolerance, and has narrow genetic diversity. Oilseed B. rapa (annual turnip rape or field mustard), one of the progenitors of B. napus, is genetically extremely diverse. This project will evaluate the effects of heat and drought stress on B. rapa. The aim is to develop effective and reproducible protocols for large-scale screening for heat and drought tolerance in B. rapa, and to find genes for heat and drought tolerance for incorporation into B. napus.

Centromere mapping in Brassica interspecific hybrids (lead by Assist Prof Matthew Nelson) Every chromosome of every eukaryote species has one functioning centromere that is crucial for cell division. Little is known of the location of centromeres in the genetic maps of most species, including Brassica species (e.g. canola). We have developed a model system using the interspecific hybrid F1 of

Brassica napus × B. carinata for mapping Brassica centromeres.

Characterisation of domestication genes in lupin (lead by Assist Prof Matthew Nelson) We are investigating genes underlying domestication traits such as early flowering, pod shattering and alkaloid content in narrow-leafed lupin. This project will draw resources from the lupin genome sequencing project (a collaborative project between UWA and CSIRO) and prior genetic mapping work in the group.

The molecular role of a canola blackleg resistance gene in canola (with Assoc Prof Susan Barker) We have located the region in the canola genome that contains a major resistance gene. Research within the group indicates that susceptibility to blackleg is an active response to the pathogen whereby plant cells die by programmed cell death. This project would define the function of the resistance gene in canola.

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WINTHROP PROFESSOR KARAM SINGH (karam.singh@csiro.au, 93336320) ASSISTANT PROFESSOR JONATHAN ANDERSON (jonathan.anderson@csiro.au, 93336103)

ASSISTANT PROFESSOR LARS KAMPHUIS (lars.kamphuis@csiro.au, 93336109) The CSIRO/UWA - Molecular Plant Pathology and Crop Genomics Group http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/WA-Crop-Genomics-Lab.aspx W/Prof Singh and his UWA/CSIRO colleagues study plant defence against insect pests and fungal pathogens. These projects are breaking new ground in plant biotic stress constraints, are world-class in science quality and are making important contributions to our understanding of plant-pathogen and plant-pest interactions. The group is also active in legume genomics including leading an effort to sequence the genome of narrow-leaf lupin, the major grain legume in Australia, and studying the human health benefits associated with lupin seed storage proteins. The group, which currently consists of 19 members, has excellent new laboratory and plant growth facilities, a bioinformatics team, and strong funding support. There are a number of potential Honours/postgraduate projects available around the following research areas that can be tailored to an individual’s strengths/interests.

1. Resistance to sap-sucking insect pests

Winthrop Professor Karam Singh http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/KaramSingh.aspx Dr Lingling Gao http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/LinglingGao.aspx Assistant Professor Lars Kamphuis http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/LarsKamphuis.aspx Sap-sucking insects, such as aphids, are major pests in agriculture causing direct feeding damage and transmitting over 50% of all plant viruses. The group has built up an excellent system to study sap-sucking insect pests involving the model legume Medicago truncatula and various aphid species including the model aphid, pea aphid. The combination of powerful genetic and genomic tools/resources on both the plant and aphid sides of the interaction enable cutting edge research and its’ application to agriculture. Two potential projects in this area are: 1a) Characterisation of loss of resistance to aphids mutant in the model legume Medicago truncatula: The legume Medicago truncatula cultivar Jester has resistance to three aphid species. A mutagenised Jester plant has been identified that has lost resistance to all three aphids. Resistance to aphids occurs through recognition by independent plants resistance genes for each aphid, which in turn triggers downstream defense responses in the plant. The identified mutant is compromised in resistance to three different aphid species making this a very interesting mutant, with a mutation in a gene that is essential in the downstream signalling cascade to mount a successful defense response to all three aphid species. Detailed characterisation of this mutant and the behaviour of the aphids including feeding behaviour and aphid settling in choice tests and aphid performance when given no choice of plant would shed more light on the resistance mechanisms that have been lost in this mutant plant. The characterisation of classical defense pathways in this mutant will also shed light on which major defense signalling pathways might be affected in this mutant, resulting in the loss of resistance to all three aphid species. The proposed research would expose the student to range of disciplines including physiology, molecular biology, biochemistry and basic bioinformatics, making this an interesting and exciting project. 1b) Characterisation of R gene mediated defences following aphid attack: Resistance to bluegreen aphid is controlled by a single dominant gene termed AKR (Acyrthosiphon kondoi resistance). A pair of near-isogenic lines has been generated which are either resistant (having AKR) or susceptible (lacking AKR) to bluegreen aphid. Potential projects using transcriptomics and/or metabolomics are available to identify key regulators and defence pathways recruited by the AKR resistance gene following recognition of the aphid. The proposed research would expose the student to range of disciplines including molecular biology, biochemistry, metabolomics, proteomics and basic bioinformatics, making this an interesting and exciting project.

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2. Resistance to fungal pathogens Winthrop Professor Karam Singh http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/KaramSingh.aspx Assistant Professor Jonathan Anderson http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/JonathanAnderson.aspx Dr Louise Thatcher http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/LouiseThatcher.aspx Fungal diseases are major problems for Australian agriculture. One such important pathogen, R. solani, causes substantial losses to wheat, barley, canola and various legumes in Australia. Internationally it is the second most important disease problem for the world’s largest staple food, rice. Another devastating fungal pathogen is Fusarium oxysporum, causal agent of Fusarium vascular wilt and able to infect over 100 plant species including grain legumes (e.g. chickpea, lupin) and oil seed crops (e.g. canola, cotton). Internationally, Fusarium wilt disease can cause losses of 10-100% in chickpea. Australia is currently free from isolates capable of infecting our major grain legumes (chickpea, lupin and lentil) however, the pathogen presents as a high biosecurity threat to these industries. The group uses powerful genomic and bioinformatic approaches on both the plant and pathogen side to unravel the mechanisms underlying resistance or susceptibility. 2a) Characterise host genes linked to fungal resistance using molecular and reverse genetic

approaches: The group has identified specific transcription factors and regulatory genes in both Arabidopsis and M. truncatula that are key mediators of plant defence responses to some fungal pathogens. Potential projects include functional characterisation through transgenic (knockout or overexpression) or mutant lines, and the identification of target genes and partner proteins using molecular and genomic approaches. The identification of regulatory sequences that allow the specific expression of the transcription factors in various plants is also a key component of producing plants with enhanced disease resistance. 2b) Identification of effectors/pathogenicity genes from R. solani or F. oxysporum genomes required

for virulence on a plant host: Pathogens employ a sophisticated system of proteins, called effectors, to interact with host proteins and manipulate the plant into susceptibility. Identification of these effectors can reveal the plant targets which may in turn be modified to confer resistance to the pathogen. The group has recently sequenced and assembled genomes for R. solani and F. oxysporum. Using a combination of powerful genetic resources, bioinformatics and molecular biology, putative pathogenicity effectors can be identified and their function in host manipulation investigated.

3. Novel regulators of biotic and abiotic stress induced responses in plants.

Winthrop Professor Karam Singh http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/KaramSingh.aspx Dr Louise Thatcher http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/LouiseThatcher.aspx The protection of cells from abiotic or biotic-induced stress is critical for an organism’s survival and a group of ubiquitous enzymes central to this protection are the detoxification family of glutathione S-transferases (GSTs). The research group of Winthrop Professor Singh conducted a genetic screen in the model plant Arabidopsis thaliana for mutants with altered expression of the early stress-responsive marker gene Glutathione S-Transferase Phi8 (AtGSTF8). Several novel mutants isolated from this screen confer altered responses to biotic and/or abiotic stress including increased thermo-tolerance and resistance to one or more fungal pathogens and insect pests. 3a) Characterise novel mutants: Several novel mutants have been cloned. Project areas include functional characterisation through the generation of knockout and overexpression lines, screening against diverse pathogens/pests and/or abiotic stresses (e.g heat, high light, salinity), the identification of interacting partners, and characterisation of transcriptomes under specific treatments. These projects will incorporate molecular, genomic and bioinformatic approaches.

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4. Human health benefits from lupin seed proteins

Winthrop Professor Karam Singh http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/KaramSingh.aspx Dr Rhonda Foley http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/RhondaFoley.aspx Assistant Professor Lars Kamphuis http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/LarsKamphuis.aspx The group is part of the Centre for Food and Genomic Medicine which links medical, food and plant researchers to tackle problems related to obesity and diabetes. The focus of the groups CFGM effort is on seed storage proteins of narrow leaf lupin (NLL) which are likely to be the constituents of the grain responsible for human health benefits relating to reduced risk of heart disease and appetite suppression. 4a) Lupin Seed Transcriptomics: Project areas include analysing gene expression during lupin seed development to identify key transcription factors controlling seed storage protein gene expression or using transcriptomics and phylogenetic studies comparing seed storage proteins between lupin species/cultivars and correlation of the different seed compositions and nutritional qualities.

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ASSOCIATE PROFESSOR CHRISTIAN NANSEN Animal Biology Building, Room 1.35 in the North Wing; Ph 6488 8672 Email: christian.nansen@uwa.edu.au

As recently employed at UWA (January 2012), I am in the process of developing an applied research program around arthropod (insects and mites) management and ecology. I am teaching AGRI4406 Integrated Pest Management, and I have a keen interest in introducing students to research methods and professional contacts that can make student more competitive on the job market. Behavioural responses by insects to surface treatments

Using Ethovision XT (www.noldus.com), we are interested in quantifying behavioural responses of different insects and mites to different agro-chemicals applied to crops. Some of these agro-chemicals are pesticides but only work (kill target pests) based on contact. So it would be a “problem” if these contact pesticides are repellent to the target pest. By offering individual insects a choice and characterize and quantify how much time they spent on different surface treatments, we can obtain valuable insight into the performance of these agrochemicals. This information is very valuable to both industry partners and farmers. This project has two components:

• Acquire quantitative behavioural data based on Ethovision XT.

• Conduct greenhouse experiments with insect pests on growing plants with/without experimental agrochemical treatments.

This project will provide the student with hands-on experience with: 1) Ethovision XT, 2) rearing of insects, and 3) plant-insect studies. Quantifying pesticide spray deposition in fields

It is well established that commercial pesticide applications in paddocks rarely lead to more than 5-10% spray coverage – and even less in the bottom of dense crop canopies. Thus, target pests are essentially presented with a choice of which about 90-95% of a leaf is without pesticide. Low spray coverage is believed to contribute significantly to the risk of target pest populations developing resistance to pesticides. In this project, we will develop a decision support tool farmers so that they can increase the likelihood of high spray coverage based on weather conditions. An example of such a develop a decision support is available at http://pilcc.tamu.edu/. This project is field based and will require travelling to farming regions and collect spray coverage data and weather data. We will quantify the spray coverage and use regression models to explain the spray coverage based on weather variables, spray characteristics, and canopy height. This project will provide the student with hands-on experience with: 1) field research in farmers paddocks, 2) website presentation of research data, 3) dissemination of research data to growers. Spatial and temporal association of mite communities in WA cropping systems Several soil mite species occur in pastures and canola fields and they are responsible for economic losses. This project is field based and will require travelling to farming regions in the southern WA. The overall objectives are to characterize spatial patterns in mite populations and to develop research-based sampling plans to be used by growers and crop consultants. Through field sampling and introduction into spatial statistics, the student will develop significant skill sets that are widely useful in both environmental and production habitats. This project is expected to produce a scientific publication and will link closely with current interest by grower groups, crop advisers, and GRDC (www.grdc.com.au) in pesticide resistance management in mite populations.