The Ten Genomes Project: Towards a Pan Genome of Wheat

Wheat (Triticum spp.) remains one of the last major crop species for which a fully assembled and annotated genome is not yet available. This has slowed identification of genes underlying phenotypic expression of agriculturally important traits. Recently, the International Wheat Genome Sequencing Consortium (IWGSC) announced the most comprehensive and contiguous assembly of the "Chinese Spring" hexaploid (2n=6x=42; AABBDD) wheat genome. This sequence will represent the gold standard reference of hexaploid wheat and is already paving the way for innovations in wheat biology and breeding. Another valuable resource is the pan-genome, which refers to the complete genomic composition of a species, including structural variation, copy number variation, and genes that maybe absent from a single reference genome. Several methods have been proposed to characterize the pan genome, including comparative analysis of complete de novo genome sequences from multiple lines. Here we report on highly contiguous assemblies of four elite wheat cultivars and their comparative analysis as a step towards characterizing the wheat pan-genome. Early results suggest that at least 6-8% of the genes show presence-absence variation in these cultivars. Two of the cultivars assemblies carry a 20 Mbp translocation on chromosome 2A representing the “Vpm-1” introgression from Aegilops ventricosa. This study represents novel insights into the pan-genome of elite cultivars and is expected to impact wheat biology research and breeding.