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. 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. 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.

中文翻译：

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Elymus sibiricus L 单位点和多位点基因组 SSR 标记的基因组调查测序、开发和表征

西伯利亚野麦（Elymus sibiricus L.）因其抗逆性强、营养价值高和易于栽培等优点，在青藏高原（QTP）的草地建立和牧场恢复方面引起了广泛关注。然而，由于缺乏 E. sibiricus 的基因组信息，阻碍了其遗传学研究和育种过程。在本研究中，我们进行了基因组调查，并基于下一代测序 (NGS) 开发了一套针对西伯利亚大肠菌的 SSR 标记。我们生成了 469.17 Gb 的干净序列，它是 6.86 Gb 估计基因组大小的 58.64 倍。我们组装了一个 4.34 Gb 的基因组草图，它具有 73.23% 的重复元件，0.01% 的杂合度和 45.68% 的 GC 含量。基于基因组序列，我们确定了 67,833 个 SSR 基因座，并从中随机选择了 400 个以开发标记。最后，30 个标记在种质之间表现出多态性，其中 10 个被鉴定为单基因座 SSR。这些新开发的标记与先前报道的 30 个标记一起用于分析 27 个野生西伯利亚 E. sibiricus 种质之间的遗传多态性。我们发现单基因座 SSR 在有效性上优于多基因座 SSR。该研究提供了在策略选择中进一步对西伯利亚 E. sibiricus 进行全基因组测序的见解。新开发的 SSR 标记将促进 Elymus 物种的遗传学研究和育种。我们发现单基因座 SSR 在有效性上优于多基因座 SSR。该研究提供了在策略选择中进一步对西伯利亚 E. sibiricus 进行全基因组测序的见解。新开发的 SSR 标记将促进 Elymus 物种的遗传学研究和育种。我们发现单基因座 SSR 在有效性上优于多基因座 SSR。该研究为在策略选择中对西伯利亚 E. sibiricus 的进一步全基因组测序提供了见解。新开发的 SSR 标记将促进 Elymus 物种的遗传学研究和育种。