Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing.

Qiang Zhou,Wengang Xie,Dong Luo,Yu Wang,Zhipeng Liu,Yanrong Wang,Lichao Ma

doi:10.1038/srep20549

Abstract

Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. However, the transcriptomic and genomic information on this species is very limited, which hinders genetic and breeding studies. In the present study, 76,686,804 clean reads were generated from 11 different tissue samples of E. sibiricus by Illumina paired-end sequencing, and the reads were deposited into the NCBI SRA database (SRX574376). A total of 8,769 EST-SSRs were identified from 94,458 unigene sequences, which were obtained by de novo assembly. Moreover, 1,078 primer pairs were successfully designed, and 500 pairs were randomly selected to assess polymorphisms in 15 E. sibiricus accessions. A total of 112 primer pairs were polymorphic, and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness. Furthermore, these 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species, and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. This study collected the global sequence data for E. sibiricus, and the newly developed markers will prove valuable in facilitating genetic diversity in E. sibiricus and related Elymus species.

Highlights

Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance
Siberian wildrye (Elymus sibiricus L.) is the typical species of the genus Elymus, which is the largest genus in the Triticeae family, and there are approximately 150 species of this genus distributed in most temperate regions of the world[1]
The objective of this study was to achieve a valuable sequence resource and develop some high polymorphism EST-SSR markers that would allow a better understanding of the genetic diversity in both E. sibiricus and the Elymus genus, which may be useful in modern E. sibiricus breeding programs

Summary

Introduction

Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. A total of 112 primer pairs were polymorphic, and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness These 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species, and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. E. sibiricus has the characteristics of good palatability, high yield, rich in nutrients, and high digestibility, which are conducive to the growth and reproduction of domestic animals It has been widely used as an important forage grass in cultivated pastures and natural grassland, in the Qinghai-Tibet plateau, due to its excellent cold and drought tolerance, high forage quality, good adaptability to the local environment and important role in animal husbandry and environmental sustenance[3]. Compared with genomic-SSRs, EST-SSRs have a higher level of transferability across related species because EST-SSRs originate from the transcribed regions in genomes and possess conserved sequences among homologous genes[12]

Objectives

Methods

Results

Discussion

Conclusion