In the past 15 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL) identification and marker assisted selection (MAS). However, results have been modest. This has been due to several factors including difficulty in gene identification and long time consuming methods. GAIN-SPEED aims at demonstrating in wheat the potential of combining genomics resources, particularly the chromosome’s first draft sequence, the next generation sequencing and array technologies and association mapping to develop an original strategy to accelerate the QTL cloning. This project is proposed with a companion project, 3Bseq, submitted to the Plant Genomics call 2009, whose objective is to produce a fully annotated genomic sequence of the largest bread wheat chromosome, the chromosome 3B, anchored to genetics maps. GAIN-SPEED will draw on the sequence produced to generate molecular markers on targeted regions to speed up marker assisted selection (MAS). This marker development will be processed using Nimblegen Sequence Capture technology that enables targeted sequencing of thousands of exons or contiguous genomic loci of up to 5Mb in a single experiment. That will allow us to develop large amount of SNP markers on gene rich regions containing putative candidate genes for our traits of interest. Using the next generation of genotyping platforms, these markers will be genotyped on an association panel that will help us to select more precisely the markers associated with the traits of interest and better define the zone carrying the QTL. The most associated SNP will be the start point to screen recombinant inbred lines and generate material useful for fine mapping approach. This project doesn’t aim to map based clone QTL but it will therefore lay the foundation of faster and more efficient MAS, through the fine mapping of important QTL, bringing together fundamental research developed in the companion project and industrial interests.