海滨雀稗EST资源的SSR信息分析及EST-SSR标记开发

doi:10.11924/j.issn.1000-6850.casb16040046

中国农学通报 ›› 2016, Vol. 32 ›› Issue (30): 96-102.doi: 10.11924/j.issn.1000-6850.casb16040046

所属专题：资源与环境

海滨雀稗EST资源的SSR信息分析及EST-SSR标记开发

李华勇¹,王显生¹,王艳平¹,吴燕¹,沈奇¹,贾新平²

(¹江苏省农业科学院粮食作物研究所,南京 210014；²江苏省农业科学院园艺研究所,南京 210014）

收稿日期:2016-04-08 修回日期:2016-06-16 接受日期:2016-06-24 出版日期:2016-10-31 发布日期:2016-10-31
通讯作者: 贾新平
基金资助:
江苏省盐土生物资源研究重点实验室开放项目“基于转录组技术的海雀稗耐盐响应机制研究”(JKLBS2012003)；江苏省农业科技自主创新项目“主要大田作物种质资源的收集、鉴定与共享服务”(CX(14)2001)。

Analysis of SSR Information in EST Resources and Development of EST-SSR Marker in Paspalum vaginatum

Li Huayong¹, Wang Xiansheng¹, Wang Yanping¹, Wu Yan¹, Shen Qi¹, Jia Xinping²

(¹Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014; ²Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing 210014)

Received:2016-04-08 Revised:2016-06-16 Accepted:2016-06-24 Online:2016-10-31 Published:2016-10-31

摘要/Abstract

摘要： 本研究探讨海滨雀稗EST序列中SSR位点的分布特征，开发EST-SSR引物分析其在草坪草种质资源遗传多样性研究中的应用。利用SSRIT软件对81220条海滨雀稗EST序列进行SSR位点搜索，分析EST-SSR的分布和特点，并利用Primer 3.0软件设计50对引物，选择10份草坪草对引物进行有效性和多态性检测。结果表明，从13705条海滨雀稗EST序列中检测到了22721个SSR位点，出现频率为16.87%。三核苷和单核苷酸重复为主要类型，所占比例分别为31.71%和29.28%。在检测到的163种基元中，出现最多的重复基元是A/T，其次是CCG/CGG和AGC/CTG。选择合成了50对EST-SSR引物，以海滨雀稗‘Adalady’基因组DNA为模板进行PCR扩增，其中37对引物能扩增出条带。利用这些引物对10份草坪草品种进行多态性检测，其中12对引物的扩增结果具有多态性。利用开发的EST-SSR标记对10份草坪草进行聚类分析，可将其分为4类。利用海滨雀稗EST序列开发SSR标记是可行的，开发的EST-SSR标记能有效用于草坪草遗传多样性研究。

关键词: 甘薯, 甘薯, 根系, 生长, 分化, 农艺性状, 内源激素

Abstract: The objective of this study was to characterize SSR derived from the Paspalum vaginatum EST sequences and to develop EST-SSR markers for genetic diversities analysis. In total, 81220 EST sequences from Paspalum vaginatum were investigated using the software SSRIT, and the distribution and characteristics of EST-SSR were analyzed. Fifty primers were designed using the software Primer 3.0, and the validity and polymorphism of the primers were tested by PCR amplification of 10 turfgrass cultivars. The results showed that 22721 SSRs were identified from the Paspalum vaginatum 13705 EST sequences with a frequency of 16.87%. Analysis of EST-SSRs motifs revealed that tri-nucleotide and mono-nucleotide were the dominant motifs, accounted for 31.71% and 29.28%, respectively. A total of 163 EST-SSR motif types were mined, A/T was the dominant repeat motif, followed by CCG/CGG and AGC/CTG. Fifty primers of EST-SSRs primers were synthesized and 37 primer pairs could amplify clear bands using the DNA template of ‘Adalady’. The polymorphisms of the primers were tested by PCR amplification of 10 turfgrass cultivars, and 12 primer pairs showed polymorphism. The cluster analysis based on EST-SSR markers indicated that 10 turfgrass cultivars were grouped into four classes. These results showed that it is an effective and feasible way to develop EST-SSR markers from the Paspalum vaginatum EST sequences, and EST-SSR markers developed in the study could be used for genetic diversity analysis in turfgrass.

中图分类号:

S543

李华勇,王显生,王艳平,吴燕,沈奇,贾新平. 海滨雀稗EST资源的SSR信息分析及EST-SSR标记开发[J]. 中国农学通报, 2016, 32(30): 96-102.

Li Huayong,Wang Xiansheng,Wang Yanping,Wu Yan,Shen Qi and Jia Xinping. Analysis of SSR Information in EST Resources and Development of EST-SSR Marker in Paspalum vaginatum[J]. Chinese Agricultural Science Bulletin, 2016, 32(30): 96-102.

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海滨雀稗EST资源的SSR信息分析及EST-SSR标记开发

Analysis of SSR Information in EST Resources and Development of EST-SSR Marker in Paspalum vaginatum

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