苏丹草转录组SSR分子标记开发及遗传多样性评价

doi:10.11686/cyxb2017420

草业学报 ›› 2018, Vol. 27 ›› Issue (5): 178-189.DOI: 10.11686/cyxb2017420

苏丹草转录组SSR分子标记开发及遗传多样性评价

朱永群¹, 彭丹丹¹, 林超文¹, 聂刚², 许文志¹, 黄琳凯², 罗付香¹, 彭建华³, 张新全^2*

1.四川省农业科学院土壤肥料研究所,四川成都 610066;
2.四川农业大学动物科技学院,四川成都 611130;
3.四川省农业科学院,四川成都 610066

收稿日期:2017-10-18 修回日期:2017-12-15 出版日期:2018-05-20 发布日期:2018-05-20
通讯作者: * E-mail: zhangxq@sicau.edu.cn
作者简介:朱永群(1980-),女,四川眉山人,副研究员。E-mail: Zyq80842@hotmail.com
基金资助:
国家牧草产业技术体系(CARS-35-36),四川省财政创新能力提升工程优秀论文基金(2014LWJJ-006),四川省财政创新能力提升工程(2016TSCY-005)和四川省饲草育种攻关(2016NYZ0039)资助

Development of SSR markers based on transcriptome sequence and analysis of genetic diversity in Sorghum sudanense

ZHU Yong-qun¹, PENG Dan-dan¹, LIN Chao-wen¹, NIE Gang², XU Wen-zhi¹, HUANG Lin-kai², LUO Fu-xiang¹, PENG Jian-hua³, ZHANG Xin-quan^2*

1.Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
2.College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
3.Sichuan Academy of Agricultural Sciences, Chengdu 610066, China

Received:2017-10-18 Revised:2017-12-15 Online:2018-05-20 Published:2018-05-20
Contact: * E-mail: zhangxq@sicau.edu.cn

摘要/Abstract

摘要： 苏丹草是一种高产优质的禾本科牧草,优质分子标记的缺乏成为苏丹草育种工作顺利开展的限制性因素。本研究基于高通量测序结果开发苏丹草EST-SSR标记,并对34份苏丹草和2份高丹草种质资源进行了遗传多样性分析,验证所开发的EST-SSR引物的可应用性。从苏丹草转录组的80686条序列中鉴定出17548个SSR位点分布在13574条序列中,分布频率为16.82%。一、二和三核苷酸重复分别占38.59%、19.18%和39.09%,SSR重复基元的重复次数分布在5~23次;开发的300对引物扩增成功率达73.67%,其中54对多态性引物在36份供试材料中共扩增出275条带,其中多态性条带有205条,多态位点百分率(PPB)为73.05%,多态信息含量(PIC)平均值为0.41,遗传距离的变化范围为0.3922~0.9020;聚类分析结果将36份供试材料分为3大类群,相同品种的材料大致聚为一类,材料间的聚类与地理来源呈一定的相关性。以上结果证明了利用苏丹草转录组数据开发SSR标记的可行性并揭示了供试材料间具有丰富的遗传多样性,为苏丹草及近源物种种质资源的多样性水平和变异分析以及分子标记辅助育种等研究提供依据。

关键词: 苏丹草, 转录组, EST-SSR标记, 遗传多样性

Abstract: Sudangrass (Sorghum sudanense) is a poaceous forage with comparatively high yield and quality, and a lack of molecular markers for quality has been a limiting factor for the sudangrass breeding. EST-SSR markers based on the transcriptome sequence of sudangrass were developed and used to study the genetic diversity of 34 accessions of sudangrass and 2 accessions of Sorghum and further to validate the applicability of SSR primers. A total of 17548 SSR sites were identified from 80686 unigenes. These SSR sites were distributed in 13574 sequences at a frequency of 16.82%. The mononucleotide, dinucleotide, and trinucleotide repeat categories were, respectively, 38.59%, 19.18% and 39.09% of the total SSRs. The number of repeat units of the SSRs ranged from 5 to 23. Randomly selected pairs of primers (n=300) were validated and the success rate of amplification was 73.67%, resulting in 54 pairs of effective primers generated, for a total of 275 alleles. Of these, 205 (73.05%) were polymorphic. The average genetic diversity, as measured by the polymorphic information content, was 0.41, and the genetic similarity coefficient ranged from 0.3922 to 0.9022. Tested materials were classified into three groups based on UPGMA cluster analysis, and the clustering results were found to be related to geographic origin. Results of our study suggest the development of SSR markers based on transcriptome data could be used to analyse the genetic diversity and identify variation of germplasm resources in sudangrass or similar species, contributing to marker-assisted breeding.

Key words: Sorghum sudanense, transcriptome, EST-SSR marker, genetic diversity

朱永群, 彭丹丹, 林超文, 聂刚, 许文志, 黄琳凯, 罗付香, 彭建华, 张新全. 苏丹草转录组SSR分子标记开发及遗传多样性评价[J]. 草业学报, 2018, 27(5): 178-189.

ZHU Yong-qun, PENG Dan-dan, LIN Chao-wen, NIE Gang, XU Wen-zhi, HUANG Lin-kai, LUO Fu-xiang, PENG Jian-hua, ZHANG Xin-quan. Development of SSR markers based on transcriptome sequence and analysis of genetic diversity in Sorghum sudanense[J]. Acta Prataculturae Sinica, 2018, 27(5): 178-189.

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苏丹草转录组SSR分子标记开发及遗传多样性评价

Development of SSR markers based on transcriptome sequence and analysis of genetic diversity in Sorghum sudanense

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