The refined flax genome, its evolution and application

Flax (Linum usitatissimum L.) is a self-pollinated annual species in Linaceae family and was domesticated ~7,000 years ago for its seed oil and/or its stem fibers. The haploid genome complement of flax is ~370 Mb in size and organized in 15 chromosomes (Ragupathy et al., 2011, Wang et al. 2012). The whole genome shotgun (WGS) sequence of flax cultivar CDC Bethune is assembled into 116,602 contigs (302 Mb) or 88,384 scaffolds (318 Mb) representing ~81% of the flax genome (Wang et al. 2012). We further refined the WGS assembly and sorted the scaffolds into 15 linkage groups by integration of the BAC-based physical map and its BAC end sequences (Ragupathy et al., 2011), the SSR-based consensus genetic map (Cloutier et al. 2012), and the high-density SNP and SSR based consensus map developed from three bi-parental populations using a genotyping-by-sequencing strategy. A total of 284 Mb of scaffold sequences were anchored to ~360 Mb FPC contigs, covering 95% of all predicted genes in the WGS assembly. The pseudo-molecule of the sorted draft genome contains ~359 Mb of sequences with linkage groups varying in sizes from 14.9 Mb (LG15) to 31.9 Mb (LG3). The comparative analysis of the draft flax pseudo-molecule and other evolutionally related species suggest that flax is a paleoploid that resulted from two genome duplication events (one recent event and one more ancient event) with recombinations and deletions of chromosome arms from its ancient species having a haploid chromosome number of 8. The updated draft flax pseudo-molecule (v1.0) has been employed in genome-wide SNP discovery and haplotype map construction, QTL identification and genome-wide association studies as well as genome-wide gene mining and fine mapping for economically important traits including yield, quality and disease resistance.