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

Zhixiao Dong,Xiao Ma,Wendan Wu,Qingqing Yu,Jian Yang,Xiong Lei,Yi Xiong,Wenhui Liu,Shiqie Bai,Yanli Xiong

doi:10.1186/s12870-020-02770-0

Abstract

BackgroundSiberian 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.ResultsIn 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.ConclusionsThis 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.

Highlights

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
The BLAST result showed that Triticum aestivum and Hordeum vulgare, as the closely-related species to Elymus, were the best matching species in all libraries
Reads of each library aligned with chloroplast genome of E. sibiricus showed lower than 5% matching rate, which indicated that the libraries were established without contamination

Summary

Introduction

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. Siberian wildrye (Elymus sibiricus L.), a model (2021) 21:3 breeding progress of this species compared to other Triticeae cereals such as wheat and barley. The mean nuclear DNA content (C-value) of E. sibiricus was determined by flow cytometry (FCM) as being 2C = 16.61 pg, approximately twice as large as the possible diploid progenitors from genus Pseudoroegneria (StSt) and Hordeum (HH) [6]. This complexity and huge genome size pose a great challenge to whole genome sequencing of E. sibiricus. Development of molecular markers based on genome survey sequencing and in silico analysis has become a practical tool for genetic study [7]

Methods

Results

Discussion

Conclusion