Transcript Jatropha curcas

International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Genetic Markers for Jatropha Biodiversity
Evaluation and Breeding
HONG Yan,
Group of Plant Biotechnology
[email protected]
• Introduction to jatropha
• Genetic markers, various
techniques
• Controlled pollination and genetic
mapping
• Our findings with SSR and AFLP
on jatropha genetic diversity
• Methylation sensitive diversity
• Implication / discussion
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
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“It has not been really domesticated….
will also require serious amounts of agronomic research”
Nature editorial
International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Breeding / domestication will increase productivity and
improve other agronomic traits
Maize
Wild plants vs domesticated ones
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
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Genotype and environment
• Morphology and agronomic traits are variable for jatropha
– Between varieties, also within varieties
– Variable performance of sibling plants under same growth conditions
proves the importance of genotype
• A few provenance trials* conducted in Africa found:
– Genotype-environment interaction (GxE)
– A great range of seed yield
– Various crude fat content from 18.4-42.3%
• Trait specific relative contribution remains to be further
investigated
*Heller 1996
International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Genetic Markers
• A gene or DNA sequence having a known location on a
chromosome and associated with a particular gene or trait
• Advantages of genetic markers:
– Profile of genetic markers will define a genotype
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Uniform at all tissues at all ages of the organism
allows early detection
developmentally stable and not affected by the environment
highly specific pattern can be developed for each individual
• Utilities:
– For biodiversity study
– To choose right parents for cross pollination
– Marker assisted breeding
– To differentiate plant varieties
– Quality control of plantation
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
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Comparison of Different genetic marker
techniques
Feature
Development cost
Running cost
Samples/day
Level of skill required
RFLP
medium
high
low
low
RAPD*
low
low
high
low
AFLP
low
medium
high
medium
Automation
Radioactivity
necessary
Reliability
Dominant or
codominant
Polymorphism
difficult
yes-no
yes
no
yes
yes-no
high
codominant
low-medium
dominant
medium
medium
high
dominant
(codominant)
medium
SSR
high
low
high
lowmedium
yes
yes-no
Sequencing
high
high
low
high
high
codominant
high
codominant
high
medium-low
yes
yes-no
*ISSR as an variant
Gustavo Caetano-Anolles and P.M.Gresshoff 1997
International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Genetic marker development and
biodiversity studies of jatropha
• Few reports with RAPD and ISSR techniques
– Potential problems of reliability and reproducibility
• Generally very low genetic diversity reported in local
populations analyzed
• No report on global jatropha genetic diversity
Basha 2007; Xiang 2007
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Controlled pollination for
breeding in TLL
– Self pollination: for
inbred lines and
evaluating heredity of
traits
– Cross pollination: to
generate hybrid seeds
between different
varieties, also with other
Jatropha species for
hybrid vigor and new
traits
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Interspecies jatropha hybrids
F1 hybrid plants
• Objectives:
– Genetic mapping
– Possible better traits
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
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Genetic marker
development in TLL
• >500 SSR loci were cloned
• >50 primer combinations of AFLP
analysis
• High throughput fluorescence marker
analysis with ABI 3730xl DNA
analyzer
• Both techniques are used together for
construction of genetic map of jatropha
with BC populations
Examples of SSR markers
Example of SSR allele detection
International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
SSR / AFLP evaluation of jatropha biodiversity
• Work in progress to analyze 192 samples from Asia, South
America and Africa
• Preliminary findings:
– SSR analysis showed very little diversity, most were homozygous
– EcoRI / MseI AFLP showed very little diversity, too (polymorphic
loci <5%, mean heterozygosity < 1%)
Monomorphic band pattern shown for most SSR loci
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
Low genetic diversity as detected by general AFLP analysis
HY
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
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Methylation
sensitive
AFLP AFLP analysis
Methylation
sensitive
PZ14A
SU6
MD42
MD44
E2/H3-HpaII
-methylation sensitive
X
E2/H3-MspI
-methylation insensitive
m5
m5
CCGG
GGCC
m5
Cut
CCGG
GGCC
m5
m5
No cut
International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
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Segregation of methylation
sensitive alleles
E1H2-376 E1H9-590 E4H5-91
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1
1
E4H3-253
1
MD24
Selfed
progenies 18,7
25,0
18,6
20,5
E1H2-376
MD24
1
TN02
0
F1 hybrids 7,10
Genotype Aa
E1H9-590
1
0
17,0
AA
E4H5-91
1
0
9,8
Aa
E4H3-253
1
0
10,7
Aa
International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Epigenetic diversity in jatropha
• Methylation sensitive AFLP
• Much higher diversity observed in methylation
sensitive AFLP analysis (polymorphic loci >60%,
mean heterozygosity >14%)
• Stable in various parts of a plant
• Heritable, follows Mendelian segregation
• Most diversity found within populations
• Biological significance not known yet
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
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DNA methylation in plant
• Best characterized epigenetic
modification
• Implicated in may important
biological processes
Interference of
DNA methylation
in Arabidopsis
by down regulate
MET1, a methylase
gene
Inheritance of methylation pattern
International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Discussion
• Reasons for the lack of biodiversity so far
– Technical or inherent?
• If low genetic diversity confirmed, issues to address:
– Genetic basis for phenotype?
– Breeding strategy?
– Any significance role of epigenetic in jatropha?
• Suggestions:
– A global survey of genetic diversity is important and critical
– International collaboration and verification is necessary
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International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
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Temasek Life Sciences Laboratory (TLL)
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A non-profit research institute owned
by Temasek holding, NUS and NTU
With 30 research groups, we work on
both basic and applied science
One center of excellence in the area of
plant tissue culture, genetic
modification, plant biology and
development study
Experience and mechanism to
collaborate and work with industry
A cluster with about 20 scientists
working on jatropha:
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Biodiversity and breeding
Genetic markers and mapping
Platform technology development
Phytochemistry
Genomics
Molecular and cell biology studies
Two experimental farms
1 Research Link, National University of Singapore,
Singapore 117604
Tel: +65 6872 7000
Fax: +65 6872 7007
http://www.tll.org.sg
International Consultation on Pro-poor Jatropha Development, Rome, Apr 08
HY
Jatropha International Congress
December 17 -18, 2008, Singapore
First Circular
Themes of the congress
1. Genetic resources
2. Breeding technologies and strategies
3. Genetics and Genomics
4. Biosynthesis of fatty acids and toxins
5. Tissue culture, propagation and transformation
6. Plantation management and pest control
7. Oil processing
8. By-product utilization
9. Investment and business models
10. Government policies and incentives
A True Event for Biofuel Research and Business
Organized by Temasek Life Sciences Laboratory
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