Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing.
Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing.
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DOI：
10.1038/srep20549
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发表时间：
2016-02-08
影响因子：
4.6
通讯作者：
Liu Z
中科院分区：
文献类型：
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作者：
Zhou Q;Luo D;Ma L;Xie W;Wang Y;Wang Y;Liu Z
西伯利亚披碱草(Elymus siBiricus L.)是一种多年生自我受精的牧草，在畜牧业和环境养料中发挥着重要作用。然而，关于该物种的转录和基因组信息非常有限，这阻碍了遗传和育种研究。在本研究中，通过Illumina配对末端测序从11个不同的组织样本中获得76,686,804个干净的读数，并将其存入NCBI SRA数据库(SRX574376)。从从头组装获得的94,458个Unigene序列中鉴定出8,769个EST-SSR。此外，成功设计了1,078对引物，随机选取500对对15份西伯利亚野百合种质资源进行了遗传多样性分析。共有112对引物具有多态性，其多态信息含量(PIC)值在0.39~0.81之间，具有较高的信息量。此外，利用这112对多态引物对13种披碱草属植物进行了遗传转化，发现55个EST-SSR标记在13种披碱草属植物中表现出多态性。这项研究收集了老芒麦的全球序列数据，新开发的标记将对促进老芒麦及其近缘种的遗传多样性具有重要价值。
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.