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茶树EST-SNP分布特征及标记开发

  • 王丽鸳 ,
  • 张成才 ,
  • 成浩 ,
  • 韦康
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  • 中国农业科学院茶叶研究所,国家茶树改良中心,浙江 杭州 310008
王丽鸳(1978— ),女,浙江金华人,副研究员,主要从事茶树遗传育种和茶叶生物工程研究。

收稿日期: 2011-11-02

  修回日期: 2012-03-20

  网络出版日期: 2019-09-05

基金资助

现代农业产业技术体系建设专项资金(No. nycytx-23)、浙江省自然科学基金(X307603)、浙江省茶产业技术创新战略联盟专项资金

Characterization of EST-derived SNPs and Development of SNP-markers in Tea (Camellia sinensis)

  • WANG Li-yuan ,
  • ZHANG Cheng-cai ,
  • CHENG Hao ,
  • WEI Kang
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  • Tea Research Institute, Chinese Academy of Agricultural Sciences; National Center for Tea Improvement, Hangzhou 310008, China

Received date: 2011-11-02

  Revised date: 2012-03-20

  Online published: 2019-09-05

摘要

对NCBI网上公开的12757条茶树ESTs序列进行聚类,成功构建了茶树的独立基因(Unigene)数据库,发现茶树的EST序列冗余率约为68.2%。初步建立了茶树EST-SNP标记开发体系,明确了茶树EST中SNP的分布规律,茶树编码区的SNP发生频率约为0.58%,平均200bp就有1个SNP位点,并进一步推算出茶树基因组DNA序列的杂合率约为0.38%,平均300个碱基就可能出现1个杂合位点。从237个多基因聚类簇中发现了818个SNP候选位点,设计了25对SNP引物进行DNA重测序验证,发现EST-SNP候选位点的多态检出率为75%。

本文引用格式

王丽鸳 , 张成才 , 成浩 , 韦康 . 茶树EST-SNP分布特征及标记开发[J]. 茶叶科学, 2012 , 32(4) : 369 -376 . DOI: 10.13305/j.cnki.jts.2012.04.014

Abstract

By clustering the 12757 ESTs of tea downloaded from NCBI, a unigene database of tea was successfully built. It was found that the redundancy rate for ESTs from tea was approximately 68.2%. An EST-SNP exploiting system for tea was established preliminarily. The SNP distribution was identified. The occurrence frequency for coding region SNP in tea was appropriately 0.58%. It meant that there was average one SNP in every 200bp of tea ESTs. Furthermore, the hybrid rate for tea genome was deduced to be 0.38%, averagely one hybrid DNA site per 300bp. Totally 818 candidated SNP were exploited from 237 multigene clusters. Then 25 pairs of SNP primers were designed and 75% of these sites were validated to be polymorphism by DNA sequencing.

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