candidate genes for drought tolerance: approaches used in ......candidate genes for drought...
TRANSCRIPT
Candidate genes for drought tolerance:approaches used in ADOC
(allele diversity of orthologous candidate genes)
Breakout discussions, 15 september 2006
Dominique This
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…)
From Varshney et al, 2005
An integrative approach
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)
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
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)
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
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
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?
DREB1A and DREB2A
From From Agarwal et al, 2006
Functional candidate genes(binding to Drought ResponseElements). More general?Positional?
Expression
Transgenic
plants
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
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?
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?