中国中药杂志

2017, v.42(17) 3332-3340

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川芎转录组SSR分析与EST-SSR标记的开发
EST-SSR identification,markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences

袁灿;彭芳;杨泽茂;钟文娟;牟方生;龚一耘;戢沛城;蒲德强;黄海燕;杨晓;张超;
YUAN Can;PENG Fang;YANG Ze-mao;ZHONG Wen-juan;MOU Fang-sheng;GONG Yi-yun;JI Pei-cheng;PU De-qiang;HUANG Hai-yan;YANG Xiao;ZHANG Chao;Industrial Crop Research Institute,Sichuan Academy of Agricultural Sciences;Institute of Bast Fiber Crops,Chinese Academy of Agricultural Sciences;

摘要(Abstract):

该研究通过组装川芎根转录组数据获得24 422个unigene,随后对得到的unigene进行了SSR检测,共检测到4 073个SSR位点。对检测到的EST-SSR进行特征分析,结果显示单核苷酸重复最多,占41.0%。SSR所在序列功能注释结果显示在Nr中有2 201条序列能够被注释,同时SSR所在序列还被注释到49个GO分类和242个KEGG代谢通路中。利用SSR检测结果进行了EST-SSR标记开发,合成其中235对引物进行验证,74对扩增效果较好。利用74对EST-SSR引物对34个川芎资源进行遗传多样性分析,结果显示收集的川芎资源多样性较好,UPGMA聚类显示川芎资源分为两大类,聚类结果表现出一定的地域性,PCo A分析与UPGMA聚类结果类似。该研究首次对川芎进行EST-SSR分析和标记开发,对推动川芎资源遗传多样性研究、品种纯度检测、基因定位和分子育种等具有重要意义。
Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study,we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types,accounting for 41. 0%. In addition,the sequences containing SSR were functionally annotated in Gene Ontology( GO) and KEGG pathway and were assigned to 49 GO categories,242 KEGG pathways,among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently,genetic diversity analysis,UPGMA cluster analysis,PCo A analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCo A results,L. chuanxiong resources were clustered into two groups,which are believed to be partial related to their geographical distribution. In this study,EST-SSRs in L. chuanxiong was firstly identified,and newly developed molecular markers would contribute significantly to further genetic diversity study,the purity detection,gene mapping,and molecular breeding.

关键词(KeyWords): 川芎;EST-SSR;功能注释;标记开发;遗传多样性
Ligusticum chuanxiong;EST-SSR;functional annotation;development of molecular marker;genetic diversity

Abstract:

Keywords:

基金项目(Foundation): 四川省育种攻关项目(2016NYZ0036);; 四川省财政创新能力提升工程项目(2016TSCY-001)

作者(Author): 袁灿;彭芳;杨泽茂;钟文娟;牟方生;龚一耘;戢沛城;蒲德强;黄海燕;杨晓;张超;
YUAN Can;PENG Fang;YANG Ze-mao;ZHONG Wen-juan;MOU Fang-sheng;GONG Yi-yun;JI Pei-cheng;PU De-qiang;HUANG Hai-yan;YANG Xiao;ZHANG Chao;Industrial Crop Research Institute,Sichuan Academy of Agricultural Sciences;Institute of Bast Fiber Crops,Chinese Academy of Agricultural Sciences;

Email:

DOI: 10.19540/j.cnki.cjcmm.20170814.004

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