Unravelling Hidden Variation in the Young Polyploid Wheat Genomes

Polyploid wheat species originated relatively recently and therefore, most genes are represented by more than one functional copy.  These duplicated genes act as a buffer to the rapid natural changes occurring in the large and dynamic wheat genomes. Gene redundancy also facilitates the generation of very high densities of induced mutations. We took advantage of this property to generate sequenced TILLING populations for tetraploid and hexaploid wheat. We developed an exome capture platform including 82,511 genes (286,800 exons) selected from multiple transcriptome analyses and used it to re-sequence the protein coding regions of 1,500 tetraploid and 1,250 hexaploid wheat EMS mutants. Using a stringent threshold, we detected and catalogued ~4 million induced mutations in tetraploid wheat and ~6 million in hexaploid wheat. This number of mutations is sufficient to generate truncations or deleterious amino acid changes in most wheat proteins (>30 mutations per kb, per population), facilitating their functional characterization. Since loss-of function mutations in one wheat homoeolog are frequently masked by redundancy in the other homoeologs, wheat breeders and natural selection often act on dominant mutations. This new resource will accelerate the identification of mutations in the different homoeologs and the generation of complete loss-of function mutations, unraveling previously untested genetic variation in wheat. A database searchable by BLAST and a visualization tool have been created and will be publicly available after publication. Access is currently provided upon request (>100 researchers are currently using this resource).