Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)
Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)
复制标题
红豆草（Onobrychis viciifolia）多态性 EST-SSR 标记的开发和同源四倍体基因组的表征
DOI：
10.7717/peerj.6542
复制
发表时间：
2019-03
期刊：
影响因子：
2.7
通讯作者：
Zhi-Peng Liu
中科院分区：
文献类型：
--
作者：
Shu-Heng Shen;Xu-Tian Chai;Qiang Zhou;Dong Luo;Yan-Rong Wang;Zhi-Peng Liu
背景红豆草(Onobrychis Viciifolia)是一种营养丰富、单宁含量高的四倍体豆科牧草。由于缺乏关于该物种的详细转录和基因组信息，红豆草改良的遗传和育种项目受到了严重阻碍。方法利用Illumina Pair-end测序技术，从14种红豆草组织中获得24,630,711个干净的读数，并存储在NCBI SRA数据库(SRX3763386)中。从这些干净的读数中，获得了77,764个Unigene序列，并通过从头组装鉴定了6,752个EST-SSR。共设计了2469对引物，随机选取200对对红豆草野生种质进行了遗传多样性分析。结果利用61个EST-SSR基因座对5个野生居群的40个红豆草个体进行进一步分析，每个座位的等位基因数在4~15个之间，期望杂合度在0.55~0.91之间。此外，通过对红豆草个体的EST-SSR条带数目进行计数，并对其中的三条或四条带进行测序，证实红豆草为同源四倍体。这一发现提供了关于这种植物的高水平信息。通过本研究，已成功开发出61个EST-SSR标记，可用于红豆草不同种质的遗传研究和群体遗传结构及变异的研究。
Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.
登录
查看更多内容
影响因子：
4.6
作者：
Zhou Q;Luo D;Ma L;Xie W;Wang Y;Wang Y;Liu Z
通讯作者：
Liu Z
影响因子：
2.1
作者：
E. T. Sottie;S. Acharya;T. McAllister;James E. Thomas;Yanan Wang;A. Iwaasa
通讯作者：
E. T. Sottie;S. Acharya;T. McAllister;James E. Thomas;Yanan Wang;A. Iwaasa
影响因子：
6.2
作者：
Wang, Shufen;Wang, Xiufeng;Wang, Fengde
通讯作者：
Wang, Fengde
影响因子：
3.5
作者：
PARKER, RJ;MOSS, BR
通讯作者：
MOSS, BR
影响因子：
5.4
作者：
Jena, Satya Narayan;Srivastava, Anukool;Sawant, Samir V.
通讯作者：
Sawant, Samir V.