A Novel Strategy to Assemble the Hexaploid Wheat Genome: Beyond Chinese Spring and Towards a Pan-Genome

Constructing a reference genome is a laborious task and represents an individual from a pool of genetic diversity within a species.  This is especially true for cultivated crop species which in many cases are complex products of hybridisation between wild relatives and further genetic introgressions. Crops have undergone selection through domestication and are being actively bred to generate better-performing varieties.  Given a method to generate accurate, reproducible genome assemblies at low cost, focus could shift from generating a single reference genome to generating assemblies from multiple cultivars of specific interest to breeders.  Being able to integrate and compare these multiple assemblies is key to modern breeding practices.

To assemble the hexaploid wheat genome we modified the DISCOVAR assembler previously used to assemble mammalian genomes.  During assembly, similar genomic regions are not collapsed together, essential when assembling a highly repetitive, polyploid genome.  We generated assemblies of two wheat cultivars, Triticum aestivum cvs. Chinese Spring CS42 and Cadenza. These assemblies give accurate representations of most of the genome space and show improved contiguity compared to previous whole-genome and chromosome assemblies.  We also present preliminary comparisons between the two cultivars.  

Using this method we plan to sequence elite lines and parents of mapping populations to quantify the extent of genetic diversity within bread wheat.  In the era of Triticeae pan-genomes we hope to maintain an integrated view of wheat diversity, where genomic variation becomes both a source of information for breeders and a more precise area of study.