Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China.
Sichuan Academy of Grassland Science, Chengdu, 611731, China.
BMC Plant Biol. 2021 Jan 6;21(1):3. doi: 10.1186/s12870-020-02770-0.
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.
西伯利亚冰草（Elymus sibiricus L.）因其具有较强的抗逆性、高营养价值和易于栽培等优点，在青藏高原（QTP）的草地建立和牧场恢复方面引起了相当大的关注。然而，由于缺乏西伯利亚冰草的基因组信息，阻碍了其遗传学研究和育种进程。
本研究基于下一代测序（NGS）对西伯利亚冰草进行了基因组调查，并开发了一套 SSR 标记。我们生成了 469.17 Gb 的清洁序列，这是 6.86 Gb 估计基因组大小的 58.64 倍。我们组装了一个 4.34 Gb 的草图基因组，其中 73.23%的重复序列、杂合率为 0.01%，GC 含量为 45.68%。基于基因组序列，我们鉴定了 67833 个 SSR 位点，从中随机选择了 400 个进行标记开发。最终，有 30 个标记在品系间表现出多态性，其中 10 个被鉴定为单基因座 SSR。这些新开发的标记与之前报道的 30 个标记一起被应用于分析 27 个野生西伯利亚冰草品系的遗传多态性。我们发现单基因座 SSR 比多基因座 SSR 更有效。
本研究为西伯利亚冰草的全基因组测序策略选择提供了新的见解。新开发的 SSR 标记将有助于冰草属的遗传学研究和育种。
