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Background  Siberian wildrye ( Elymus sibiricus  L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of  E. sibiricus  hampers its genetics study and breeding process.    Results  In this study, we performed a genome survey and developed a set of SSR markers for  E. sibiricus  based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild  E. sibiricus  accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness.    Conclusions  This study provided insights into further whole genome sequencing of  E. sibiricus  in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for  Elymus  species.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02770-0.

Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L