Genome-wide development of simple sequence repeats database for flax (Linum usitatissimum L.) and its use for genetic diversity assessment

Flax (Linum usitatissimum L.) is an important industrial crop and is widely cultivated in North America, Europe, and China for its fiber and oil. Identifying flax molecular markers is a vital step towards improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers have proven to be the most valuable type of genetic marker for molecular breeding and genetic diversity studies. However, the development of genome-wide SSRs in flax has not yet been reported, which limits their use in molecular breeding. In this study, we screened 25,871 SSR motifs from L. usitatissimum, mainly consisting of trinucleotide (52.8%) and dinucleotide (36.1%) repeats. Based on the 24,375 SSR motifs, 71,184 primers pairs of SSR markers were designed for the flax genome, covering the whole genome at a density of 225.3/Mb. Furthermore, 96 pairs of SSR markers from different chromosomes were used to assess a panel of 26 flax accessions obtained from different parts of the world. The 21 SSR markers exhibited polymorphisms across the 26 flax accessions, and the flax varieties were accurately clustered into two groups and two subgroups corresponding to their type (wild species or cultivar) and use (fiber or oilseed). This study demonstrates the potential value in analyzing genetic diversity in flax, and the large-scale development of SSR markers developed in this study will facilitate future molecular analyses in flax.