POST-DOCTORAL FELLOWSHIP 2006

Title :

Detecting selection signature by tracing back the best haplotypes in bread wheat breeding programs in France

Skills required : Quantitative and molecular Genetics of plant populations, algorithmic & programming.

Grant : PhD : 1900 €/month, senior 2200 €/month (raw). Length 24 months.

Beginning october or november, 2006

• Where : UMR Plant breeding and plant health, INRA-University, 234 av du Brézet, F63100 Clerrmont-Ferrand France (tel 00 33 4 73 62 43 09)

• Contacts : G. CHARMET charmet@clermont.inra.fr et F. BALFOURIER balfour@clermont.inra.fr

• Grant : PhD : 1900 €/month, senior 2200 €/month (raw). Length 24 months.

• Beginning october or november, 2006

Project presentation :

Bread wheat is one of the three major ceral crops worldwide, which provide a significant amount of food and feed in most countries. Bread wheat is also one of the first species to be domesticated, ~10 000 years ago, then genetically improved. Since the mid 19th century, its genetic variability has been exploited and allowed a continuous genetic progress in yield and adaptation. However, few retrospective analyses have been carried out to understand and quantify the effect of this historical selection on genetic variability (signature of selection). Such a knowledge would be very helpfull to optimize selection strategies in order to preserve the evolvability of the wheat germplasm in response to a changing environment. Indeed, retrospective analysis should allow to identify the chromosomic regions which have evolved under selection pressure. Signature of selection can be found by studying the evolution of allele/haplotype frequency and local pattern of linkage disequilibrium. These regions can be proposed as prioritary targets for alien transfer in breeding programmes, thus allowing a better exploitation of the huge collection of genetic resources of wheat and related species.

The proposed approach consists in tracing back, through the complete (as far as possible) pedigree of present elite lines, allelic combination at linked loci (i.e. haplotypes) which have been preferentially transmitted in response to selection pressure. Such an approach has already been proposed in human, although at a finer scale (gene sequence). The main objectives of the post-doc programme are:

• To adapt or develop a statistical test of non-neutrality based on the size of IBD-segments (identical by descent)

• To identify, with this test, chromosomic regions which have experienced selection pressure in the modern age of scientific breeding

• Trace back the origins of the best-fitted haplotypes by studying their coalescence through the pedigrees of present elite lines.

• Search new sources of variation for these meta-genes in genetic resources collections of wheat and related species.

The main steps to be achieved are

• The choice of target traits: yield, quality….

• A QTL meta-analysis to select a few chromosomic region on which dense marker genotyping would be carried on.

These first two steps have been achieved in 2006 by a master-degree

• Building up the pedigree of a selected set of present elite lines, up to landraces whenever possible (database mining)

• Dense genotyping using posymorphic markers (SSR, EST-SSCP…) in target regions.

• Statistical analyses of coalescence, local linkage disequilibrium, marker-trait association…

• BLUP estimates of haplotype effect in modern germplasm.

• Eventually, start a reflexion on developping algorithm and tools for choosi,g parents and crosses to cumulate the best haplotypes.