亚洲棉EST-SNP的挖掘及其在陆地棉中的验证

doi:10.11963/1002-7807.xpsxl.20170628

棉花学报 ›› 2017, Vol. 29 ›› Issue (5): 401-414.doi: 10.11963/1002-7807.xpsxl.20170628

• 研究与进展 • 下一篇

亚洲棉EST-SNP的挖掘及其在陆地棉中的验证

徐鹏，蔡继鸿，郭琪，张香桂，徐珍珍，沈新莲^*

江苏省农业科学院经济作物研究所/农业部长江下游棉花油菜重点实验室，江苏南京 210014

收稿日期:2016-10-17 出版日期:2017-09-15 发布日期:2017-09-15
通讯作者: xlshen68@126.com
作者简介:徐鹏（1981―），男，Semon528@hotmail.com
基金资助:
国家自然科学基金（31471545）；江苏省自然科学基金（BK20160580）；国家科技重大专项——转基因生物新品种培育（2014ZX08005-004-002）；棉花生物学国家重点实验室开放课题（CB2015A12）；江苏省协同创新中心

Development of EST-SNP Markers in Gossypium arboreum and Their Validation in G. hirsutum

Xu Peng, Cai Jihong, Guo Qi, Zhang Xianggui, Xu Zhenzhen, Shen Xinlian*

Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing 210014, China

Received:2016-10-17 Online:2017-09-15 Published:2017-09-15

摘要/Abstract

摘要： 【目的】随着不同棉种序列数据库的逐步完善以及高通量测序技术的发展，棉花单核苷酸多态性（Single nucleotide polymorphism，SNP）标记开发可利用的公共数据资源逐步增加。【方法】本研究基于陆地棉祖先基因组的现代种亚洲棉表达序列标签（Expressed sequence tag，EST）数据库，利用CAP3对亚洲棉EST数据库进行拼接。拼接获得7 187个重叠群（Contig），再利用QualitySNP软件进行SNP位点分析。【结果】在807条含有4条以上EST序列的Contig中查找到2 690个SNP位点。通过筛选次要等位基因频率大于30%的位点，获得953个可靠度较高的候选SNP，通过电子筛选，最终获得可用于陆地棉分析的SNP 149个，利用位点特异性聚合酶链式反应以及酶切扩增多态序列验证了EST-SNP的准确性。【结论】本研究证实基于亚洲棉EST数据库挖掘用于陆地棉研究的EST-SNP切实可行，并有望将EST-SNP用于陆地棉遗传图谱构建、重要性状的基因定位以及分子标记辅助育种。

关键词: 亚洲棉; 单核苷酸多态性; 酶切扩增多态性序列; 表达序列标签

Abstract: [Objective] With the development of the cotton genome sequence database and next-generation high-throughput sequencing techniques, the resources available for generating single nucleotide polymorphism (SNP) markers are gradually expanding. [Method] The Gossypium arboreum expressed sequence tags (ESTs) downloaded from the NCBI database were assembled into 7 187 contigs using the CAP3 program. Additionally, the QualitySNP program was used for SNP mining. [Result] A total of 2 690 SNPs were obtained from 807 contigs that consisted of more than four ESTs. We obtained 953 highly reliable candidate SNPs by screening for a minor loci frequency of more than 30%. Finally, a total of 149 candidate EST-SNPs that may be used in G. hirsutum were obtained through in silico screening. An allele-specific polymerase chain reaction and cleaved amplified polymorphic sequence molecular markers were used to validate the accuracy of the selected candidate SNPs in G. hirsutum. [Conclusion] The EST-SNP markers from G. arboreum may be used to analyze G. hirsutum. The obtained EST-SNP markers will be used to construct genetic maps, map important traits, and complete marker-assisted selection in G. hirsutum.

Key words: Gossypium arboreum; single nucleotide polymorphism; cleaved amplified polymorphic sequence; expressed sequence tag

中图分类号:

S562.03

徐鹏, 蔡继鸿, 郭琪, 张香桂, 徐珍珍, 沈新莲. 亚洲棉EST-SNP的挖掘及其在陆地棉中的验证[J]. 棉花学报, 2017, 29(5): 401-414.

Xu Peng, Cai Jihong, Guo Qi, Zhang Xianggui, Xu Zhenzhen, Shen Xinlian. Development of EST-SNP Markers in Gossypium arboreum and Their Validation in G. hirsutum[J]. Cotton Science, 2017, 29(5): 401-414.

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亚洲棉EST-SNP的挖掘及其在陆地棉中的验证

Development of EST-SNP Markers in Gossypium arboreum and Their Validation in G. hirsutum

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