Regional Training Workshop on “National Plant Genetic Knowledge

Networks for Strengthening Regional Cooperation

and Knowledge Sharing”

29-30 August 2014CairoEgypt

Dina El-Khishin (Ph.D.)

Head of the Genomics, Proteomics

&

Bioinformatics Research Facility

Agricultural Genetic Engineering Research Institute (AGERI)

Giza

EGYPT

Dina El-Khishin (Ph.D.)

Head of the Genomics, Proteomics

&

Bioinformatics Research Facility

Agricultural Genetic Engineering Research Institute (AGERI)

Giza

EGYPT

Plant Genetic Resources

Challenges, Technology

and

the Future

“We live in a world that is becoming increasingly complex.

Unfortunately our styles of thinking rarely match this complexity”.

Garth Morgan’s book Images of Organization (1986)

Challenges

7

Global food security

New Techno log ies a re requ i red

Current position

Rate of crop improvement is slowing

Population is increasing (10 billion - 2030)

Declining land area available for food & concern over environmental issues

Agricultural Sector DevelopmentStrategic Goals

Optimizing crop returns per unit of land and water consumed.

Enhancing sustainability of resource use patterns and protection of the environment.

Bridging the food gap & achieving self reliance.

Expanding foreign exchange earning from agricultural exports .

Reduce the dependency on imported agricultural products (Seeds-Crops)

Improve the nutritional quality of food crops.

Reduce the use of agrochemicals & pesticides & their environmental risks.

Produce plants resistant to indigenous biotic and abiotic stress.

Produce more food

Biotechnology is required to:

Technical Networks Networks were found to reduce duplicative efforts among national institutions in several countries and to provide a cost-effective instrument for information exchange and institution building.

Ex. (AARINENA) Established Networks on: Date-Palm, Cotton, Olive, Medicinal Plants, Water Use Efficiency, Agricultural Biotechnology and Plant Genetic Recourses (PGRN).

Regional Agricultural Biotechnology Network (RABNET)

Aims to facilitate exchange of information

through the development of an information

system for the collection and dissemination of

information on advances in agricultural

b i o t e c h n o l o g y r e s e a r c h r e s u l t s .

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Regional Plant Genetic Resources Knowledge and Innovation Network Platform for Near East and North Africa [NENAPGRN]

The NENAPGRN network established as a partnership among all the different bodies and stakeholders in each of the participating member countries that are involved in any manner throughout the overall plant genetic recourses areas of research.

Agricultural Biotechnology

Network

This Network was established in December

2007 and hosted by AGERI –ARC , Egypt.

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Such networks have become important for strengthening rural development, food security & poverty reduction.

Initiated & supported through FAO, GFAR, ICARDA and NGO organizations .

They are a model for establishment of functional mechanisms for collaboration and enhancement of communication and exchange of experiences among different countries in one region and/or different regions of the world.

Molecular Markers,

Genomics

&

Plant Genetic Resources

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Molecular Tools for Variety Identification

Genetic markers

ClassMorphological

Biochemical

Molecular

Level of analysisPhenotype

Gene product

DNA sequence

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Applications for marker analysis• Population genetics - Investigations within a genus of centers of origin,

genetic diversity, gene flow, population structures and relationships among species.

• Phylogeny & Evolution - Descriptions of genetic relationships among species between different genera.

• Parentage analysis - Clone confirmation, seed orchard monitoring, and mating systems.

• Species I.D. - Molecular identification of species and their hybrids.

• Genome mapping - Constructing full coverage or QTL maps.

• Marker Aided Selection - following and manipulating QTLs, or single trait loci, through generations or across populations.

• Comparative mapping - Genome structure, framework maps, or transferring trait and marker data among species.

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DNA marker applications

(1) As genetic markers for mapping and tagging traits of interest.

(2) As indicators of genetic diversity.

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DNA markers as indicators of diversity

Diversity questions can be addressed at the species, population and individual level.

At the species level:

1-Define the distinctiveness of species.

2-Answers to problems concerning hybridization and polyploidy.

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At the population level:

1- Characterize diversity.

2-Resolve number of genetic classes.

3- Study genetic similarities.

4- Evolutionary relationships with wild relatives.

5- Conservation, germplasm and breeding line

characterization.

6- distribution of populations.

7- Genetic variation in and among populations.

8- Study gene flow or migration between populations.

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At the individual level:

1- Establishment of identities in cultivar, breed or clonal identification.

2- Paternity testing and forensics.

2nd International Symposium on Genomics of Plant Genetic Resources held in Bologna, Italy, 2010.

Objective of GPGR2 was to critically evaluate how the latest advances in genomics platforms and resources have enhanced our capacity to investigate plant genetic resources and harness their potential for improving crop productivity and quality.

This showed the increasingly pivotal role of genomics for characterizing germplasm collections, best managing gene banks, elucidating plant functions and identifying superior alleles at key loci for the selection of improved genotypes.

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One of the immediate applications of genomics and it's advanced technology is:

To assess the genetic diversity in germplasm collections.

To identify superior alleles at loci of interest by comparing trait variation and molecular polymorphisms.

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By combing through both germplasm banks and the multitude of plant genome resources, such as cDNA libraries and collections of ESTs and SSRs, to identify useful gene loci, and then moving these genes into crop improvement programs.

Using comparative genomics, to identify genes for similar traits in related species, and ultimately to build consensus gene maps of various crop species.

Finally, to develop an informatics platform to store and analyze the data generated.

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To this end newer techniques are used some of which:

Expressed Sequence Tags (ESTs)

Diversity Arrays ™ Technology (DArT) (Kilian,2002)

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Definitions

http://www.broadinstitute.org/education/glossary/genome

Genome an organism’s complete

heritable genetic material, Contains all the information

needed to build, Run, and maintain that organism

DNA SequencingDetermining the order of bases

(nucleotides) in a piece of DNAWhole genome sequencing:

determining the order of bases (nucleotides) in the whole genome DNA (or RNA)

How to sequence DNA?

• Sanger sequencing• Introduced at 1977• Automated capillary

electrophoresis• Up to 96 reactions in parallel• Up to 800 bases per reaction• High accuracy (99.999%)• Requires DNA cloning • Cost less than $1 per reaction

(Nat Biotechnol 2008, 26:1135-1145)

ABI 3730xl

The human genome project?

• 13 years

• Several dedicated

labs around the

world

• More than three

billion dollars!

• 46 chromosomes• 3 billions of bases

Again, How do we sequence DNA?

• Next generation DNA sequencing (NGS)

• Massively parallel sequencing• Tiny reaction volumes• No DNA cloning required• Good accuracy (99.99% with

some platforms)• Short sequence reads (50-500

bases)• Cost much less

(Nat Biotechnol 2008, 26:1135-1145)

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1000 Plant Transcriptomes Project

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EXAMPLES

INTERNATIONAL UNION FOR THE PROTECTION

OF NEW VARIETIES OF PLANTS (UPOV)GENEVA

WORKING GROUP ON BIOCHEMICAL AND MOLECULAR

TECHNIQUES AND DNA PROFILING IN PARTICULAR

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The power and benefits of NGS are particularly evident in species such as apple, potato or maize that suffer from low linkage disequilibrium while enjoying a high level of polymorphism, two features which require a highly detailed analysis at the DNA level to identify haplotype diversity in germplasm collections.

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A level of genetic resolution sufficient to

validate candidate genes and, in some

cases, even identify causal

polymorphisms can be attained by

association mapping, an approach

increasingly adopted to dissect the

genetic basis of target traits.

Characterization of germplasm collections.

Characterization at the genomic level is required for

⑴a more cost-efficient management of germplasm

collections, both in situ and ex situ,

(2) Understanding phylogenetic relationships among

species (Bolot et al., 2009),

(3) assembly of core collections suitable for association

mapping studies (Maccaferri et al., 2011)

(4) assessing genetic similarity among accessions sharing

common ancestors (Maccaferri et al., 2007).

Plant genetic resources (PGR) include cultivars, landraces, wild species closely related to cultivated varieties, breeder’s elite lines and mutants.

NGS with de novo assembly and resequencing has already provided a substantial amount of information, which warrants the coordination of existing databases and their integration into gene banks.

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Integration and coordination of genomic data into gene banks is very important and requires an international effort.

From the determination of phenotypic traits to the application of NGS to whole genomes, every aspect of genomics will have a great impact not only on PGR conservation, but also on plant breeding programs.

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