The 10K+ SNP Maps of Flax

Canada is the largest producer of oilseed flax or linseed. Humans consume flax seeds or oil because of their many health benefits. With 55-57% omega-3 fatty acid, linseed is the richest plant source of this essential fatty acid. As part of the Genome Canada funded TUFGEN project, genomics resources such as the WGS sequence, ESTs, SSRs, SNPs, physical map and genetic maps have been generated. Here, we generated a high density genetic map combining SNPs and SSRs. A total of 96 individuals from CDC Bethune/Macbeth (BM), 88 from E1747/Viking (EV) and 78 from SP2047/UGG5-5 (SU) were sequenced using the Illumina platform. Genome coverage obtained through sequencing averaged 6.8× in BM, 13.8× in EV and 28.2× in SU. Using a modified AGSNP pipeline, 352,104 SNPs were discovered. For mapping purposes of this GBS strategy, we selected SNPs that were called in at least 60% of the individuals which totalled 12,613 in BM, 12,546 in EV and 8,209 in SU. Genetic maps for the three populations including the SSR markers were generated with Multipoint using a LOD of 8 and a maximum recombination frequency of 0.4. The combined SNP-SSR maps consisted of 12,957, 12,978 and 8,685 markers, respectively. A quarter of the SNPs showed segregation distortion. The three high density genetic maps will be used for QTL studies, marker assisted selection and map-based cloning. A consensus genetic map combining more than 10,000 SNPs and 700 SSRs is anticipated to be a notable resource for the flax community comparing advantageously with other major crops.