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

BMC Plant Biology

Xiong Lei¹  Jian Yang¹  Yanli Xiong¹  Zhixiao Dong¹  Yi Xiong¹  Qingqing Yu¹  Xiao Ma¹  Wenhui Liu²  Shiqie Bai³  Wendan Wu⁴ 

[1] Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University;Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine;Sichuan Academy of Grassland Science;Sichuan Pratacultural Technology Research and Extension Center;

关键词: Genomic survey sequencing;    Elymus sibiricus L.;    Marker development;    Single-locus SSR;    Genetic diversity study;   

DOI  :  10.1186/s12870-020-02770-0

来源: DOAJ

【 摘 要 】

Abstract 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.

【 授权许可】

Unknown