MSc Plant Sciences Specialization F: Plant Breeding ... › upload_mm › 9 › 6 › 2 ›...

MSc Plant Sciences Specialization F: Plant Breeding

(Distance Learning)

Wageningen University

Course Descriptions (DRAFT 26-03-2015)

Wageningen University, part of Wageningen UR For quality of life

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PBR22803 Principles of Plant Breeding (Distance Learning)

Language of instruction: English

Teaching methods: 0.5 DT; 0.5 DG; 2.0 DEL

Contact person: R.E. Niks (niks001)

Lecturer(s): R.E. Niks (niks001)

Examiner(s): R.E. Niks (niks001)

Content:

This course introduces students to key principles of plant breeding. Different subjects are the importance of the

mode of reproduction of crops and the genetic consequences for selection. Various selection methods are

discussed. For an effective selection programme it is imperative to distinguish genotype from phenotype, since

only the genotypic differences are relevant to genetically improve the crop.

Learning outcomes:

After successful completion of this course students are expected to be able to:

- understand the advantages and limitations of plant breeding selection programmes

- understand the role of mode of reproduction of plants on the genetic composition of crops

- analyse genetic segregations

- analyse observations to separate genetic and non-genetic components of variation

- know the methods and perspectives of modifying genome numbers (ploidy levels) and DNA sequences

Activities:

The course consists of a number of e-learning modules that explain and illustrate the principles, and give

numerous exercises to the student to test his understanding. Feedback on correct and wrong answers is given.

Group assignments, self-tests and discussions are other activities in this course.

Literature:

Recommended: G. Acquaah, 2012. Principles of Plant Genetics and Breeding, 2nd Edition Wiley-Blackwell


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PBR23303 Plant Pathology and Disease Epidemiology (Distance

Learning)


Teaching methods: 0.5 DKC; 1.0 DT; 1.0 DG; 0.5 DEL

Contact person: Jan van Kan (kan001)

Lecturer(s): Jan van Kan (kan001) Wopke van der Werf (werf001)

Examiner(s): Jan van Kan (kan001) Wopke van der Werf (werf001)

Content:

The course focuses on the interactions of plants with attackers (viruses, micro-organisms, nematodes, insects,

parasitic plants), and beneficial organisms (symbiotic bacteria and fungi), as well as on interactions between

beneficial organisms and pathogens and their hosts at different integration levels, from molecules to ecosystems.

Learning outcomes:


- summarize molecular and physiological principles of interactions between plants and attackers;

- discuss the complexity of defence mechanisms that plants possess to (directly or indirectly) counteract attackers;

- compare different strategies and biochemical tools used by attackers to invade plants and reproduce - explain how symbiotic organisms interact with plants without triggering defence responses; - understand that the trophic lifestyle of an attacker is related to the way in which it uses its genetic toolbox - describe case studies of plant disease epidemics in time and space (field, regional, and continental scale) - apply key concepts in the population biology of plant diseases, such exponential growth, logistic growth, life

tables, relative rate of increase, and net reproductive ratio - describe the effect of host genetics, crop diversity and landscape diversity on the rate of spread and

population increase of plant diseases and pests - understand and apply basic probability models for sampling distributions of plant disease - formulate concepts for integrated management of plant disease on the basis of insight in epidemiology

Activities: Reading study material, video clips, self-assessments, participation in role-playing game

Literature: Available through the course website


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PBR31803 Genetics (Distance Learning)


Teaching methods: 0.5 DKC; 1.5 DT; 0.5 DG; 0.5 IS

Contact person: Herman van Eck

Lecturer(s): Herman van Eck and other lecturers

Examiner(s): Herman van Eck

Content:

This course gives an overview of the role of genetics in life sciences and the structural basis of genetics. Following

on this basis a series of more advanced topics is addressed, including extensions and exceptions to single locus

Mendelian inheritance, transposable elements and genome size, population genetics and evolution, complex traits,

genetic diversity, biosystematics, phylogenetics, and genome evolution.

Learning outcomes:


- analyse questions and problems on all aspects of Mendelian genetics, including deviations from standard

segregation ratios;

- apply quantitative and population genetics concepts to infer the effects of selection, non-random mating,

mutation, genetic drift on forward genetic screens

- describe the relation between genes, chromosomes and DNA and the concept of genome structure;

- understand evolutionary concepts explaining the origin of biological complexity, and processes shaping the

genome, such as horizontal gene transfer, genome duplications, hybridisations, transposition;

- apply quantitative and biosystematic approaches to evaluate genetic structure and diversity of populations, as

well as phylogenetic analyses

Activities:

Topics will be introduced and taught using knowledge clips (DKC). Students will read the textbook supplemented

with scientific articles (IS). In depth study of the topic is facilitated using Distance Tutorials (DT) using

Feedbackfruits and Peer to peer on line discussion.

Literature: Textbook Griffiths, An Introduction to Genetic Analysis 11th edition, and scientific papers


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PBR23803 Plant Biotechnology (Distance Learning)


Teaching methods: 0.7 DKC; 0.5 DT; 0.7 DG; 0.2 DEL; 0.9 IS

Contact person: Christian Bachem (Bache001)

Lecturer(s): Christian Bachem (Bache001), and other lecturers

Examiner(s): Christian Bachem (Bache001)

Assumed knowledge: Basic molecular biology and plant biochemistry

Content:

Plant biotechnology is a discipline that connects the new insights into genes and their products with the end

product that is destined for the market. As with other technological disciplines, plant biotechnology comprises a

mixture of many other scientific areas of biological sciences such as molecular biology, biochemistry, physiology

and genetics. In this course we will present information on the basics of classical plant biotechnology through to

advanced methods for modifying and improving plants and plant products. This will be done using knowledge clips,

exercises and study of a set textbook. In addition the participants will have the opportunity to apply the knowledge

gained during the course and use their own creativity in the form of an group assignment that will run throughout

the course. Another main feature of the course will be to analyse and assess the implications of this new

technology for wider society. The assignment will form a central part of the course and will be submitted in the

form of a written report and a presentation the latter will be reviewed and evaluated by fellow students. The

presentations and debates will form part of practical week at the WUR campus.

Learning outcomes:


1. Understand the scientific and technological components of what is and is not Plant Biotechnology

2. Understand the molecular biological basis of the key technologies comprising Plant biotechnology

3. Analyse literature an apply the findings to a biotechnological problem

4. Critically review the position of Plant Biotechnology in relation to society

5. Conceive, plan, write and present a project proposal for a plant biotechnological product

Activities:

1. Read the assigned chapters in the book

2. Watch the knowledge clips and additional learning material

3. Carry out on-line assignments

4. Peer to peer on line discussion

5. Plan and execute a project assignment

6. Prepare presentation and written report

7. Debate the placement of plant biotechnology in to societal and cultural contexts.

Literature: Textbook: Plant Biotechnology, Slater, Scott & Fowler 2nd ed. OUP. Additional academic literature

(PDFs) provided by tutor.


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PBR32303 Wageningen Weeks Part 1 (Distance Learning)


Teaching methods: 1.8 P; 0.8 T; 0.4 EO;

Contact person: Guusje Bonnema (bonne001)

Lecturer(s): Guusje Bonnema, Richard Visser and other lecturers

Examiner(s): Guusje Bonnema, Richard Visser

Content:

During this two week practical, students of the Distance Learning Specialization come to Wageningen and will meet

each other and Wageningen University staff for the first time. This practical period builds on the courses PBR-

22803 (Principles of plant breeding), PBR-31803 (genetics) and PBR-23803 (Plant Biotechnology) and the Skills

that are an integral part of this Distance Learning MSc. In the one day excursion we will visit two plant breeding

companies. This will be a vegetable breeding company, with application of genomics and Marker assisted selection

in breeding programs of many of their crops; special attention is given to their seed quality management. In

addition, an ornamental breeding company or crop breeding (potato) company will be visited, with different

breeding strategies. For the Skills training, students will have an interactive training and will present their Plant

biotechnology assignment and have a debate on societal issues related to plant breeding. The practicals are

designed to increase insight in genetic and breeding principles (heritability, epistasis, genetic diversity, segregation

ratio’s) and train skills in plant biotechnology research.

Learning outcomes:


- apply relevant laboratory techniques for assessing gene expression in transformed plants;

- make crosses in a diverse range of plants;

- understand the concepts genetic diversity, heritability and epistasis by phenotyping and genotyping plant

populations and fitting the outcome to genetic models;

- develop self-awareness of personal qualities and skills;

- present a group assignment using Powerpoint;

- participate in a debate about the (im)possibilities of plant biotechnology from a societal and a technical point of

view

- receive feedback from peers and supervisors, and skilfully provide feedback for your fellow students

Activities:

Excursion to two breeding companies and a technology lab; Practical experiments to apply knowledge from the

courses Principles in Plant Breeding, Genetics and Plant Biotechnology aimed to improve research skills and

practical skills, and deepen the understanding of theoretical concepts; Practical assignments to train

communication and personal skills; doing tests, give presentations, participate in debates, reflect on own

behaviour and that of your co-students and group

Literature: Available through the course website.


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MAT25303 Advanced Statistics for DL (Distance Learning)



Contact person: Gerrit Gort

Lecturer(s): Gerrit Gort, Bas Engel, Evert-Jan Bakker, Elly Korendijk

Examiner(s): Gerrit Gort ([email protected]), Bas Engel ([email protected])

Assumed knowledge: Basic Statistics

Content:

Statistical design and analysis of data using R; statistical methods for analysis comprise simple and multiple

regression, one-way and two-way analysis of variance (with and without interaction), analysis of covariance, chi-

square tests for contingency tables, logistic regression.

Learning outcomes:


- comprehend basic ideas of statistical inference, experimental design and data collection, such as random

sampling, randomisation and blocking, for experimental and observational studies

- determine an appropriate statistical model and associated statistical inference procedure, given the description

of the experiment and research question, for continuous data (in the context of linear regression, analysis of

(co)variance) and discrete data (in the context of goodness-of-fit and contingency tables for categorical data

and logistic regression for binary data and proportions)

- carry out the analysis, for a given problem, using the statistical program R, check model assumptions, interpret results, and formulate conclusions in terms of the actual problem

Activities: Study knowledge clips with theoretical assignments, practical assignments and case studies using R,

reporting on results.

Literature: Ott, RL, Longnecker M (2010) An introduction to statistical methods and data analysis (6th edition),

Brooks/Cole ISBN-10 0495109142; ISBN-13 9780495109143; BIB/1916191

mailto:[email protected]

mailto:[email protected])b


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PBR32803 Markers in Genetics and Plant Breeding (Distance Learning)



Contact person: Chris Maliepaard

Lecturer(s): Rients Niks, Jan-Kees Goud, Chris Maliepaard

Examiner(s): Chris Maliepaard, Rients Niks, Jan-Kees Goud

Assumed knowledge: Principles of Plant Breeding, Genetics, Statistics

Content:

In this course, the students will be made familiar with the use of molecular markers in genetic research and plant

breeding, the estimation of genetic distance based on marker genotype frequencies in different types of

segregating populations, the construction of linkage maps, the analysis of quantitative trait loci (QTLs) and the

discovery and application of markers in research and for selection in breeding programs, both for qualitative and

quantitative traits.

Learning outcomes:


- understand the concept of genetic markers in genetic research and breeding - understand the use of polymorphic markers in segregating populations - use sequence information for discovery of single-nucleotide polymorphisms (SNPs) and understand how these can be used as molecular markers for genetic mapping, QTL analysis and marker-aided selection - analyse genetic segregations, including cases where genetic linkage occurs - infer linkage/non-linkage and to calculate genetic distance from genotype frequencies in a segregating

population - use software to construct a genetic map from marker genotyping data in a segregating population and interpret the result - distinguish and contrast genetic and physical maps - map a gene involved in a qualitative trait in a mapping population - Understand the concept of QTL analysis using a genotyped mapping population, a linkage map for that population and a quantitative phenotypic trait scored in the population - distinguish and contrast QTL mapping procedures based on single marker analyses, interval mapping, composite interval mapping - perform QTL analyses using QTL mapping software and interpret the results - understand the principles of bulked-segregant analysis and selective genotyping - understand the application of molecular markers in indirect selection for phenotypic traits in breeding

programs

Activities: Study an E-learning module, individual and group exercises, application of software



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PBR33303 Quantitative and Population Genetics (Distance Learning)




Lecturer(s): Chris Maliepaard, Bas Zwaan

Examiner(s): Chris Maliepaard

Assumed knowledge: Genetics, Statistics, both at MSc level

Content:

In this course, students will learn concepts and applications of quantitative and population genetics. Applications

will be taught in exercises within the context of Plant Breeding, using statistical analyses.

Learning outcomes:

Quantitative genetics part:

- Comprehend and contrast the inheritance of qualitative vs. quantitative traits and the consequences for

plant breeding. The inheritance of monogenic vs. polygenic traits and the relationship to qualitative and

quantitative traits.

- Comprehend the importance of quantitative traits in breeding and possibilities and consequences for

selection over shorter and longer periods.

- Comprehend the concepts of additivity, dominance, incomplete (partial) dominance and overdominance in

single-locus and multi-locus genetic models. Comprehend the concept of epistasis and recognize different

forms of two-locus epistasis

- Comprehend how dominance and overdominance can be involved in the explanation of heterosis and

consequences for breeding (choice pure line or hybrid cultivars, maintaining heterozygosity in OPV,

inbreeding depression after sib mating or selfing).

- Calculate midparent value, (net) additive effect, (net) dominance effect and (means based) dominance

ratio from the means of a trait in basic generations such as BC1, F2, RILs, including parental generations

P1 and P2 and F1. Interpret results in terms of consequences for breeding.

- Comprehend the concepts of additive genetic variance, dominance genetic variance, dominance ratio and

their expectations in different breeding generations /research populations.

- Use quantitative genetics models and statistical methods to quantify additive genetic variance, dominance

genetic variance, (variance based) dominance ratio in basic breeding and research populations.

- Comprehend the concepts of genetic and environmental variance, narrow-sense and wide-sense

heritability. Understand that heritability estimates are specific for certain traits in certain populations

tested in certain environments with a certain experimental design but also have a wider interpretation

outside those specific contexts.

- Use quantitative genetics models and statistical methods to estimate variance components (genetic

variance, environmental variance, variance associated with G*E interaction) and to estimate wide-sense

and narrow-sense heritability.

- Comprehend the concepts of Selection Differential, selection intensity, Response to selection, genetic

correlation, indirect selection and Correlated Response to Selection, and the so-called breeders’ equation.

Understand how the response to selection may vary according to the heritability, the selection intensity,

the type of material, the stage at which the trait can be evaluated (before/after flowering!). Understand

indirect selection in terms of these concepts. Understand the relevance of response to selection in terms of

progress per time unit for selectable traits in a breeding program. Understand the relationship between

quantitative genetic theory of indirect selection and applications in indirect selection, notably in marker-

assisted selection of quantitative traits and/or genomic selection on breeding values of quantitative traits.

- Calculate response to selection and correlated response to selection, given a heritability estimate, intensity

of selection, selection differential.


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- Apply quantitative genetics theory and methodology to compare expected effectiveness of different

possible breeding strategies (e.g. breeding hybrid vs. pure line cultivar) under given assumptions and

limitations.

Population genetics part:

To be filled in.

Activities: Knowledge clips, individual and group exercises, online discussion, E-learning modules

Literature: Kearsey and Pooni Chapters 1 – 4.3, 15.5 to 15.8; Moose et al. 2004; Visscher et al. 2008


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PBR31802 Breeding for Quality (Distance Learning)


Teaching methods: 0.5 DKC; 0.8 DT; 0.2 DG; 0.5 IS

Contact person: Dr. AG Bovy

Lecturer(s): Dr. AG Bovy; Dr. L. Trindade

Examiner(s): Dr. L. Trindade

Assumed knowledge: Genetics, principles of plant breeding, molecular markers, mapping populations

Content:

Traditionally, producer traits such as yield and disease resistance have been the primary breeding targets in many

crops. In current agriculture, however, consumer-driven quality traits, such as flavour colour and nutritional value

have become increasingly important and the same holds for the production of specific plant compounds which can

be used as sources for bio-based applications. Breeding for Quality is directed at improving whole fruit/vegetable

characteristics and plant compounds, where flavour, colour, texture, absence of antinutritional factors or allergens,

and shelf-life are important breeding objectives. Breeding for Quality also comprises the efficient production of all

kinds of compounds, which are used as ingredients by the food, pharmaceutical, chemical, textile, paper, etc.

industries. Examples of such compounds are: carbohydrates (starch, fructans, cellulose), proteins (wheat gluten,

pea storage proteins), vegetable fats/oils (rape seed oil, cocoa fat), and secondary metabolites like flavours,

fragrances, and phytoestrogenic molecules. In breeding programs, the existing genetic variation is exploited to

increase the yield of (or enrich mixtures in) the target compounds. For this, it is necessary to understand the

metabolic routes leading to the synthesis of the desired compound, and to have knowledge on how these

compounds can be determined in the plant material

Learning outcomes:

- explain the major characteristics of various quality traits;

- define appropriate selection strategies for specific target traits;

- apply relevant analytic and statistical screening techniques for trait evaluation;

- use this knowledge to develop breeding strategies for improved resistance, tolerance and quality

Activities: Study knowledge clips with theoretical assignments, group activities, individual assignments and

literature



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PBR32302 Breeding for Abiotic Stress Tolerance (Distance Learning)


Teaching methods: 0.3 DKC; 1.7 DEL

Contact person: Gerard van der Linden

Lecturer(s): Gerard van der Linden

Examiner(s): Gerard van der Linden

Content:

Abiotic stress is the stress imposed on plants by the non-living environment. Abiotic stress is responsible for huge

yield losses in crops around the world. In this course we will assess the impact that abiotic stresses (drought,

salinity, nutrient deficiency) have on agricultural production, and provide you with knowledge and tools for

successful breeding for abiotic stress tolerance. The following questions will be addressed:

- What can agriculture do to minimize yield losses now and in a future where the climate changes, and input will be further restricted? - What are the requirements for successful breeding for abiotic stress tolerance? - How does a plant respond to abiotic stress, and which physiological and molecular mechanisms are important? - Which traits contribute to stress tolerance, how can these be measured and used for selection? How do modern genomics techniques contribute to abiotic stress tolerance breeding?

Learning outcomes:

After successful completion of this course students are expected to: - have acquired knowledge on how agriculture, crops and individual plants are affected by abiotic stress - have learned about main mechanisms that help plants to cope with abiotic stress - know about tools that can be used to monitor and understand the response and tolerance of plants to different abiotic stresses - be able to integrate the above knowledge for the design of a sensible breeding strategy for the improvement of abiotic stress tolerance in target crops.

Activities: Online lectures with video clips on specific subjects, short assignments



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PBR32802 Breeding for Resistance (Distance Learning)



Contact person: Vivianne Vleeshouwers (vlees001)

Lecturer(s): Vivianne Vleeshouwers (vlees001), Rients Niks (niks001), Yuling Bai (yulin001)

Examiner(s): Vivianne Vleeshouwers (vlees001)

Assumed knowledge: DL-Principles of Plant Breeding, DL-Plant Pathology

Content:

Biotic stress factors are among the main limitations for producing high quality and high quantities of vegetal

products. Resistance breeding focuses at the use of genetic resources for improving plant defence against these

stress factors. Biotic stress factors include pathogens and pests that infect or feed on crop plants. The present

course deals with defence mechanisms and strategies that protect host plants against pests and pathogens,

inheritance of resistance genes, and durable effectiveness of resistance genes.

Learning outcomes:


Explain the major characteristics of various resistance traits Discuss the various aspects of plant-pathogen interaction using the correct terminology Use the knowledge of plant-pathogen interaction to develop breeding strategies for improved and durably

effective resistance Choose the most appropriate screening and selection methods to develop cultivars with effective

resistance to pathogens and pests

Activities:

Study the textbook “Breeding Crops with Resistance to Diseases and Pests” Make exercises, some corresponding to certain parts of the book and other on line Make peer review assignments Study e-learning modules on the (lack of) durability of resistance and partial resistance

Literature: Niks RE, Parlevliet JE, Lindhout P, Bai Y (2011) Breeding crops with resistance to diseases and pests.

Wageningen Academic Publishers:198pp


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PBR33803 Germplasm and Seed Technology (Distance Learning)


Teaching methods: 0.5 DKC; 0.5 DT; 0.3 DG; 0.5 DEL; 0.2 IP; 1.0 IS

Contact person: Jan-Kees Goud (goud001)

Lecturer(s): Jan-Kees Goud (goud001), Herman van Eck (eck001) and others

Examiner(s): Jan-Kees Goud (goud001), Herman van Eck (eck001)

Assumed knowledge: Principles of Plant Breeding

Content:

This course introduces students to a number of important aspects of plant breeding, such as the process of domestication,

germplasm development and the importance of gene banks. Also, important practical aspects on bringing a cultivar to the

market are discussed, such as breeders’ rights and patents, and the design of seed and plant production programs.

Attention to financial aspects of breeding programs will also be given.

Learning outcomes:


1. explain the theory of domestication, the gene pool concept, and the process of germplasm development 2. explain the importance of gene banks and explain how they work

3. explain and discuss the principles of breeders’ rights and patents 4. understand how seed production programs are designed 5. evaluate planning and financial aspects of breeding programs.

Activities:

- Watch knowledge clips

- Study e-modules - Hand-in assignments - Watch DVD/YouTube movie and answer questions - Interact with peers and supervisors in discussions

Literature:

Book chapter(s): Acquaah, G, 2012, Principles of plant Genetics and Breeding, 2nd edition

Article: Zamir, D. 2001, Nature Reviews Genetics 2(12):983

DVD/YouTube: Seed hunter


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PBR34303 Genomics and Bioinformatics (Distance Learning)



Contact person: Christian Bachem (Bache001)

Lecturer(s): Christian Bachem (Bache001), Herman van Eck (Eck001)

Examiner(s): Christian Bachem (Bache001), Herman van Eck (Eck001)

Assumed knowledge: Basic knowledge of molecular biology and genetics

Content:

Genomics is a new area of research that relates to holistic study of the genome a the gene, transcript, protein and

metabolite levels. Due to the large amounts of data involved in this study computer tools are extensively used.

During the course we will present basic concepts genomics and introduce students to the problems of dealing with

and understanding these large datasets. We will discuss the basic architecture of the genome and the implications

for genome evolution. We will also deal with the structural and functional aspects of genomics from gene through

to metabolites. The course will help the students to analyse and understand the links and relationships between

genes and their various products. The course will comprise information packages in the form of knowledge clips

and these will be combined with a large number of exercises where the knowledge provided will be applied to

practical bioinformatics problems.

Learning outcomes:


1. Understand the organisation of plant genomes and how these evolved

2. Be able to explain the connections between gene, transcript, protein and metabolite

3. Have a basic understanding of the technologies that generate the various genomics data sets

4. Be able to analyse genomics data and retrieve biologically significant information from it

5. Gain an insight into the dependence and interactions between the different functional genomics levels

6. Have the ability to integrate information from genes to pathways to networks at an organism level

7. Understand and debate the potential role of genomics in a wider societal and cultural setting

Activities:

1. Read and understand the set texts and literature provided in the course

2. Watch and study the knowledge clips and other learning material

3. Follow the computer tutorials

4. Carry out the exercises and report the results

5. Participate in on-line debates and discussions

7. Carry out and submit assignments

Literature: Information will be primarily provided in the DL course material. Other information sources will be

actively retrieved from the providers of internet tools that will be used throughout the course


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PBR34803 Experimental Design and Data Analysis of Breeding Trials

(Distance Learning)




Lecturer(s): Chris Maliepaard, Gerrit Gort, Bas Engel, Marcos Malosetti

Examiner(s): Chris Maliepaard

Assumed knowledge: Statistics at MSc level

Content:

In this course, students are taught principles of experimental design of trials and statistical analysis of trial data

with a special emphasis to linear and generalized linear methods, mixed models, analysis of multi-environment

trials using different statistical methods.

Learning outcomes:


- Comprehend statistical principles underlying experimental designs for breeding trials with respect to

randomization, replication (including types of replicates and pseudo-replication), blocking, experimental

units, the use of controls, orthogonality, balance and efficiency, power.

- Comprehend the connections between these design principles and the models and model assumptions

underlying statistical analyses, most importantly linear regression and analysis of variance (distributional

assumptions, independence, equal variance; additivity or linearity of effects, single or multiple random

error terms)

- Apply these concepts when designing an experiment

- Explain, distinguish and characterize the following experimental designs: completely randomized design

(CRD), randomized complete block design (RCB), incomplete block designs (including resolvable designs:

lattice designs and alpha designs, row-column designs) and split-plot designs.

- Understand effects of missing values, data errors, outliers, uneven replication, confounding of effects, and

violations of distributional assumptions and assumptions of equal variance and independence.

- Understand statistical analysis methods, most notably single and multiple linear regression, one-way, two-

way and multi-factorial analysis of variance including interactions, analysis of covariance, post-hoc

pairwise comparisons with and without a multiple comparisons correction.

- Understand, distinguish, and apply the concepts of standard deviation, standard error of a parameter of

interest, standard error of the mean (SEM), standard error of a difference between means (SED) and least

significant difference (LSD) and their relationship with the residual variance estimated from an Anova or

regression analysis and with confidence intervals for parameters of interest (regression coefficients,

means, differences between means)

- Understand and explain R2 and adjusted R2 in the context of single and multiple regression analysis and

Anova

- Understand when generalized linear models (GLM) are more appropriate for data analysis than linear

regression or Anova

- Understand when linear mixed models (LMM) are more appropriate for data analysis than linear regression

or Anova

- Be able to perform different analyses using GLMs: logistic regression for binary data, threshold models for

multinomial or ordinal data, loglinear regression for counts

- Understand how and why distribution and link functions need to be specified in GLMs

- Understand the difference between fixed terms and random terms in a mixed model analysis, both

conceptually and in applications

- Specify a linear mixed model in fixed and random terms for a data analysis with unbalanced designs


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- Specify a linear mixed model in fixed and random terms for a data analysis with dependent observations

- Comprehend and apply linear mixed models in different contexts: estimation of variance components (e.g.

for heritability estimation), or quantify the relative importance of environmental and genetic contributions

to the variation in multi-environment trials; analysis of split-plot trials; account for

dependence/relatedness in full-sib and half-sib family analyses.

- Use a linear mixed model for the estimation of variance components

- Explain genotype by environment interaction as a concept in multi-environment trials in plant breeding

and in statistical terms

- Quantify, test and characterize genotype-by-environment interaction using different evaluation methods:

analysis of variance, mixed models, Finlay-Wilkinson regression, AMMI and GGE biplot

- Comprehend and discuss the concepts of stability, adaptability and (wide/specific) adaptation in plant

breeding in the context of Finlay-Wilkinson regression

- Understand the concepts underlying principal components analysis (PCA), including loadings and scores

plots, biplots and the effects of centering/scaling on PCA

- Perform a principal components analysis

- Be able to interpret a PCA biplot in terms of (approximate) correlations among variables (from the angles

of the loadings to the origin), in terms of distances among the objects (or clustering of separation of

objects in the PC-space), and in terms of relating objects to variables (according to relative positions of

the objects to the loadings vectors).

- Estimate heritability of traits from estimates of variance components obtained from Anova and mixed

models in genotype trials.

Activities: Knowledge clips, individual and group exercises, E-learning modules



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PBR35303 Wageningen Weeks Part 2 (Distance Learning)


Teaching methods: 1.8 P; 0.8 T; 0.4 EO

Contact person: Guusje Bonnema (bonne001)

Lecturer(s): Guusje Bonnema, Richard Visser and other lecturers

Examiner(s): Guusje Bonnema, Richard Visser

Assumed knowledge: Theoretical knowledge from the courses preceding the stay in Wageningen.

Content:

During this two week practical, students of the Distance Learning Specialization return to Wageningen to meet

again with each other and with Wageningen University staff. This practical period builds on the theory of the

preceding courses. The programme will include practicals, excursions, and plenary presentations and discussions of

the group work related to the Continuous Course and the course Design of Plant Breeding programmes.

Learning outcomes:


- assess quality criteria, by evaluating biochemical properties (lab test) and taste (student panels)

- assess influence of genotype and environment on biotic and abiotic stress responses

- assess chlorophyll content and evaluate role in stress response

- assess genetic variation and map QTL for traits

- understand the concepts genetic diversity, heritability and epistasis by phenotyping and genotyping plant

- present a plant breeding program using Powerpoint;

- define questions and recommendations as a group to breeding programs presented by others

- receive feedback from peers and supervisors, and skilfully provide feedback for your fellow students

Activities:

Excursion to breeding companies and/or a plant biotechnology lab

Practical experiments to apply theoretical knowledge from the preceding courses of the programme, aimed to

improve research skills and practical skills, and deepen the understanding of theoretical concepts

Practical assignments to train communication and personal skills; give presentations, participate in debates, reflect

on own behaviour and that of peers



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PBR35803 Design of Plant Breeding Programmes (Distance Learning)


Teaching methods: 0.5 DKC; 0.5 DT; 1.0 DG; 1.0 IP

Contact person: Guusje Bonnema

Lecturer(s): Guusje Bonnema and other lecturers

Examiner(s): Guusje Bonnema

Assumed knowledge: All preceding courses

Content:

This course is closely connected to the project part of the Continuous Course (YEI61812), and focuses on the

integration of knowledge on various aspects of plant breeding into a breeding programme for a specific crop. The

theoretical and practical aspects of plant breeding are taken into account and combined with some economic,

societal and environmental aspects.

Learning outcomes:

- integrate theoretical and practical knowledge in a design study for a breeding program;

- understand structure and connections between breeding methods, techniques and breeding goals;

- select parameters (parental choice, breeding strategy, population genetics, selection methods, traits of interest)

that are crucial for successful practical breeding;

- reflect on breeding methods and their presuppositions; question, adjust and estimate their implications;

- set up a breeding programme for a specific crop (all along the chain from defining the specific breeding goal(s)

until marketing the newly developed variety);

- justify the choices made in the breeding program;

- write a work plan and final report of the breeding program;

- present the work plan and final breeding plan to peers

Activities: Study knowledge clips on theoretical background, work on a group assignment to design a breeding

program, reporting on plans and results



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PBR36303 New Trends in Plant Breeding (Distance Learning)


Teaching methods: 0.5 DKC; 0.5 DT; 0.5 DG; 0.5 IP; 1.0 IS

Contact person: Jan-Kees Goud (goud001)

Lecturer(s): Vivianne Vleeshouwers (vlees001), Luisa Trindade (trind001), Edith Lammerts van Bueren

(lamme022), Olga Scholten (schol021), Robert van Loo (loo006), and Gerard van der Linden (linde027)

Examiner(s): Jan-Kees Goud (goud001)

Assumed knowledge: Principles of Plant Breeding, Breeding for Quality, Breeding for Tolerance, Breeding for

Resistance, Plant Pathology

Content:

This course aims at preparing students for a career in plant breeding industry or in science. Subjects treated are at a

higher integrational level, not only taking into account plant breeding aspects, but regarding all aspects involved, such as

environmental issues, products and chain issues, climate change and limiting resources. Subjects treated include new

trends and technologies in plant breeding, such as effector-based plant breeding, bio-based economy, climate resilience,

new crops, alternative cropping systems, breeding for low-input cropping systems, and breeding for symbiosis between

plants and micro-organisms.

Learning outcomes:


1. apply effector-based plant breeding for the selection of cultivars with resistance to plant pathogens 2. evaluate the challenges of the bio-based economy from the breeding perspective 3. assess morphological and physiological components relevant for the breeding of climate resilient plants

4. design breeding programs on alternative cropping systems, such as mixed cropping systems and low-input cropping systems

5. evaluate breeding possibilities in new crops 6. evaluate possibilities of breeding for symbiosis between plants and micro-organisms

Activities:

- Watch knowledge clips - Read articles - Hand-in assignments - Read scientific literature - Case study on novel breeding strategies, either focused on scientific research or on implementation in a commercial breeding program

Literature: Available through the course website. In addition, students need to search for relevant literature as

part of the case study.


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YEI61812 Continuous Course (Distance Learning)


Teaching methods: 3.0 DT; 9.0 DG

Contact person: Anja Kuipers

Lecturer(s): Guusje Bonnema, Truus van Woudenbergh, and others

Examiner(s): Guusje Bonnema, Truus van Woudenbergh

Content:

The continuous course has two major elements, skills building and a project.

Skills building focuses on the following skills:

1. Online study and communication skills (e.g. ICT, active cooperation in groupwork, intercultural communication,

giving and receiving feedback)

2. Academic skills (project management, information literacy, scientific writing, presentation skills, argumentation

skills, reflective learning)

The project relates to the content of the online specialisation itself, and also comprises training of specific content-

related skills. For the online specialisation Plant Breeding the project focuses on translating principles of plant

breeding into design, and on the synthesis and writing of a breeding programme that includes and connects all

relevant aspects on a multidisciplinary level. The project of the online specialisation Epidemiology and Public Health

focuses on intervention mapping, and writing a grant proposal.

Learning outcomes:


- perform a project in an international team;

- determine the project aims, develop a project plan and formulate tasks on the basis of disciplinary knowledge

and general academic skills and attitude;

- contribute to the execution of the project at an academic level by retrieval, selection and analysis of information;

- integrate relevant research-based information into scientifically correct written report, and present and defend

conclusions and recommendations in a professional and well-argued way;

- implement reflective learning by assessment of, and reflection on, personal functioning in a professional team;

- give and receive feedback in writing and verbally, based on assessment of the contribution of other team

members to team performance and execution of project tasks.

Activities: Tutorials and assignments for development of skills. Team meetings, literature study, proposal and

report writing, oral and online presentation

Literature:

Skills building: literature provided via Blackboard. Project: Specific literature available via Blackboard. In addition,

students need to search for relevant project related literature

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