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?