A First Generation Haplotype Map of Wheat Genome

Progress in improving wheat, one of the major staple crops worldwide, is significantly delayed by the lack of comprehensive characterization of its genetic diversity. The complexity of the wheat genome resulting from its large size, highly repetitive DNA content (>90%), and two rounds of recent whole genome duplications represent a significant challenge for analysis. Here we developed the whole exome capture assay targeting 321 Mb of genic regions in the wheat genome and used it to re-sequence a set of geographically and genetically diverse hexaploid wheat accessions including founders of the nested association mapping population. We developed approaches for accurate read mapping and genetic variant identification in the allopolyploid genome. We generated a detailed catalog of variation in genic regions of each of the three wheat genomes including more than one million SNPs and indels. We constructed a dense diversity map and used it to assess the genome-wide patterns of genetic diversity and recombination, and identify tentative targets of selection. The developed resource will help to shape future efforts in the analysis of the wheat genome aimed at understanding the genetic basis of complex trait variation in wheat and detection of useful alleles for wheat improvement.