川芎转录组SSR分析与ESTSSR标记的开发(1)
[摘要] 該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ESTSSR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ESTSSR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ESTSSR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，PCoA分析与UPGMA聚类结果类似。该研究首次对川芎进行ESTSSR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。
[关键词] 川芎； ESTSSR； 功能注释； 标记开发； 遗传多样性
ESTSSR identification， markers development of Ligusticum chuanxiong
, 百拇医药
based on Ligusticum chuanxiong transcriptome sequences
YUAN Can1， PENG Fang1， YANG Zemao2， ZHONG Wenjuan1， MOU Fangsheng1，GONG Yiyun1， JI Peicheng1， PU Deqiang1， HUANG Haiyan1， YANG Xiao1*， ZHANG Chao1*
(1. Industrial Crop Research Institute， Sichuan Academy of Agricultural Sciences， Chengdu 610300， China；
2. Institute of Bast Fiber Crops， Chinese Academy of Agricultural Sciences， Changsha 410205， China)
, 百拇医药
[Abstract] Ligusticum chuanxiong is a wellknown 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. ESTSSR was detected and 4 073 SSR loci were identified. ESTSSR distribution and characteristic analysis results showed that the mononucleotide 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 ESTSSRs，74 primer pairs were ultimately proved to have high quality amplification. Subsequently， genetic diversity analysis， UPGMA cluster analysis， PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results， L. chuanxiong resources were clustered into two groups， which are believed to be partial related to their geographical distribution. In this study， ESTSSRs 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.
[Key words] Ligusticum chuanxiong； ESTSSR； functional annotation； development of molecular marker； genetic diversity, http://www.100md.com(袁灿 彭芳 杨泽茂 钟文娟 牟方生 龚一耘 戢沛城)
[关键词] 川芎； ESTSSR； 功能注释； 标记开发； 遗传多样性
ESTSSR identification， markers development of Ligusticum chuanxiong
, 百拇医药
based on Ligusticum chuanxiong transcriptome sequences
YUAN Can1， PENG Fang1， YANG Zemao2， ZHONG Wenjuan1， MOU Fangsheng1，GONG Yiyun1， JI Peicheng1， PU Deqiang1， HUANG Haiyan1， YANG Xiao1*， ZHANG Chao1*
(1. Industrial Crop Research Institute， Sichuan Academy of Agricultural Sciences， Chengdu 610300， China；
2. Institute of Bast Fiber Crops， Chinese Academy of Agricultural Sciences， Changsha 410205， China)
, 百拇医药
[Abstract] Ligusticum chuanxiong is a wellknown 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. ESTSSR was detected and 4 073 SSR loci were identified. ESTSSR distribution and characteristic analysis results showed that the mononucleotide 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 ESTSSRs，74 primer pairs were ultimately proved to have high quality amplification. Subsequently， genetic diversity analysis， UPGMA cluster analysis， PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results， L. chuanxiong resources were clustered into two groups， which are believed to be partial related to their geographical distribution. In this study， ESTSSRs 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.
[Key words] Ligusticum chuanxiong； ESTSSR； functional annotation； development of molecular marker； genetic diversity, http://www.100md.com(袁灿 彭芳 杨泽茂 钟文娟 牟方生 龚一耘 戢沛城)