Integration of Whole Genome Assemblies and Genetic Information in Hexaploid Wheat

Progress in sequencing technologies and the availability of sophisticated bioinformatics tools has had a direct impact on our ability to generate relatively complete genomics datasets for species characterised by complex genomes such wheat. The recently completed Chromosome Sequencing Survey (CSS) project is one example. The International Wheat Genome Sequencing Consortium (IWGSC) sponsored the CSS project with the aim to generating chromosome specific assemblies. These assemblies have already been key in providing the supporting reference backbone to develop downstream genomics applications such as exome capture assays and the analysis of epigenetic markers. This, however, only offers a partial view of the genome as the assemblies are highly fragmented with more than 10 million contigs and an average N50 of around 2.5 kb. The application of whole genome analyses such as genotype-to-phenotype association studies and the characterisation of genomic re-arrangements are not feasible with such a fragmented reference. We propose to generate a more contiguous draft reference for wheat by integrating anchoring data from a variety of sources with the CSS assemblies to provide a framework that will allows us to build long-range pseudomolecules representing the genome of the bread wheat. The generation of dense marker panels both trough physical and genetics maps approaches and whole genome sequencing libraries are a key to obtaining large scale anchoring data to order and orientate the CSS contigs. I will present an overview of the proposed strategy with results demonstrating the value of the approach.