Key Note Speaker on “Knowledge Management in Plant Genetic Resources: Impact on Innovations, Challenges and Opportunities for Future Action.” © FAO: http://www.fao.org

1. Regional Training Workshop on
“National Plant Genetic Knowledge
Networks
for Strengthening Regional Cooperation
and Knowledge Sharing”
29-30 August 2014
Cairo
Egypt

2. 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

3. Plant Genetic Resources
Challenges, Technology
and
the Future

4. “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)

5. Challenges

7. 7
Global food security
New Technologies are required
Current position
Rate of crop improvement is slowing
Population is increasing (10 billion - 2030)
Declining land area available for food &
concern over environmental issues

8. Agricultural Sector Development
Strategic 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 .

9. 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:

10. 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).

11. 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.

13. 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.

15. Molecular Markers,
Genomics
&
Plant Genetic Resources

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Molecular Tools for Variety Identification
Genetic markers
Class
Morphological
Biochemical
Molecular
Level of analysis
Phenotype
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.

22. 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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27. 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 Sequencing
Determining the order of bases
(nucleotides) in a piece of DNA
Whole genome sequencing:
determining the order of bases
(nucleotides) in the whole
genome DNA (or RNA)

28. 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

29. The human genome project?
• 13 years
• Several dedicated
labs around the
world
• More than three
billion dollars!
• 46 chromosomes
• 3 billions of bases

30. 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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38. 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.

40. 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).

41. 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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