candidate genes for drought tolerance: approaches used in ......candidate genes for drought...
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Candidate genes for drought tolerance:approaches used in ADOC
(allele diversity of orthologous candidate genes)
Breakout discussions, 15 september 2006
Dominique This
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What are candidate genes?
• Definition (Varshney, 2006, trends in plant Science):A gene that has been identified as related to a particular trait
(phenotype, disease or condition).
Two categories- positional: might be associated with a trait, based on the
location of a gene on a chromosome (QTL and map-based cloningapproaches)
- functional: whose function has something in commonbiologically with the trait under investigation (transcriptomics, expression genetics…)
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From Varshney et al, 2005
An integrative approach
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Why using a candidate geneapproach in allelic diversity?
• Perfect (functional) molecular markers for cropimprovement, unravelling the metabolicpathways controlling agronomical traits
• Make benefits from decades of fundamentalresearch in plant physiology and molecularbiology (integrative approach)
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In our case: constraints• Should apply to the maximum of crop species (common
pathways)
• Should benefit from the scientific expertise present in the community and interct with other projects
• Should be of practical value for breeding schemes
• Limited number of sequences / cost…
• No specific target region
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How we choose our candidate genesfor drought tolerance…
• Huge amount of bibliography on the subject– preferably multiple evidence of a role in drought tolerance
(expression, mutant, QTL…) in different plants
• Share experience between partners / important traits (breeding) and genes under investigation in otherprograms (much of the answer is there)
• Discussions and potential associations with genespecialists that we know well…(makes the functionalinterpretation easier, avoid mistakes)
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From Vinocur & Altman, 2005
Josette Masle,Recent paper in Nature on ERECTA
ICRISAT, CIAT: ongoing work on DREBgenes
Michel Zivy, JM Ribaut: ASR / maize
Tim Setter, Michael Dingkuhn, John Bennett: sugar metabolism and sink strength(SS, SPS, invertases)
CIP / potato: microarrays data(SS, LEA, …)
Manypossibilitiesthroughoutresponsemechanismto stress
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Pathwaychosen
• Sucrose metabolism
• Impact on:– Osmotic adjustment– Sink-source regulations
and phenotyping plasticity– Sugar signalling– Water use efficiency– Quality and carbohydrate
production (grain, rootand tubers…)
Salerno, 2003
Enzymes: SS, SPS, InvertasesFunctional candidates
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Transcription factors: ASR genes(ABA - stress - ripening -induced)
Jeanneau et al., 2002, Biochimie, 84:1127-1135
positional candidate gene for leaf senescence and ASI. May regulate sucrose transport in some plants. Functional candidate too (transgenes, expression)
But nothing in crucifers?
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DREB1A and DREB2A
From From Agarwal et al, 2006
Functional candidate genes(binding to Drought ResponseElements). More general?Positional?
Expression
Transgenic
plants
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ERECTA and ERECTA-like genes
From Masle et al, 2005, Nature
From Shapk et al, 2005, Science
ERECTA: positional candidate gene for WUE on chr 2 in Arabidopsis thaliana(what in other species?)
ERECTA and ERECTA like genes: functional candidates for stomatal patterning, transpiration efficiency…(mutants, complementation…)
Link with sucrose metabolism ?
Signal transduction
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Problems encountered• Dealing with gene families in 7 crops
• Orthologous relationships not easy to assess. Sequenceavailability? Annotation problems? Subfunctionalization?
• Choosing a subset across crops: Based on QTL data? Functional analysis? Link with other projects?
• Polymorphism in coding region or promoter?• Substrate specificity vs expression?
• What about other genes?• Did we miss the most important ones?
• Usefulness in association mapping?• Would anonymous markers well spread be enough?
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Additional questions
• Bibliographic survey– Should we exchange this information? – In which form?
• Interaction with other projects?– Some SP1 projects. Other crops interested: Exchange primers?– Rice mutants. For all of them? What in other crops?– Failure in grain formation. Cross interest for ‘root and tubers’
crops? – Maize association mapping. Common genes?– SP4 project (Samart Wanchana). How to interact efficiently?