The IWGSC Chromosome-based Survey Sequencing Initiative of Bread Wheat

Applying advanced genomics to wheat breeding will play a central role in securing affordable and nutritious food. Bread wheat (Triticum aestivum) has one of the largest (~17Gb) and most complex (allohexaploid, 6n=42, AA,BB,DD) genomes. While genome size varies in grasses, gene order, generally, is conserved along large chromosomal segments enabling comparative methods between related species. The IWGSC aims to establish a high quality, reference sequence of the wheat genome (cv. Chinese Spring) that is anchored to the genetic maps to provide high resolution links between the traits and the underlying variations in sequence and polymorphisms. A first goal has been to obtain physical maps of the individual chromosomes/arms. To anchor the physical contigs, survey sequences were achieved using NGS technologies for a majority of the chromosomes.The IWGSC then launched a short-term initiative to provide survey sequences of all 21 chromosomes. Sponsored by industry and government partners, the aim is to generate sequence and virtual order for most wheat genes.The sequences generated for each chromosome arm are assembled using the latest software tools. A first pass annotation is implemented over the draft assembly sequences where comparative genomics and colinearity with other grass genomes is used to derive a virtual gene order with an account of non-syntenic genes and pseudogenes. As sequences are generated independently for each chromosome, a second aim of this project is to characterise genomic variation between gene homoeologues (ie orthologous genes placed in different subgenomes), regulatory elements and repeat content.  An update of this initiative will be presented.