华细辛转录组SSR标记的开发及其在华细辛遗传多样性分析中的应用  

Exploration of transcriptome SSR markers and its application in genetic diversity assessment of Asarum sieboldii

作　　者：陈梦颖 戴瑞贤 范玉玲 刘忠[1] CHEN Meng-ying;DAI Rui-xian;FAN Yu-ling;LIU Zhong(School of Pharmacy,Shanghai Jiao Tong University,Shanghai 200240,China;School of Pharmacy,Fujian University of Traditional Chinese Medicine,Fuzhou 350122,China;School of Life Sciences,Beijing University of Chinese Medicine,Beijing 102488,China)

机构地区：[1]上海交通大学药学院,上海200240 [2]福建中医药大学药学院,福建福州350122 [3]北京中医药大学生命科学学院,北京102488

出　　处：《中国中药杂志》2023年第20期5519-5530,共12页China Journal of Chinese Materia Medica

基　　金：国家自然科学基金面上项目(32270384,31570325)。

摘　　要：为探索华细辛的遗传多样性,该研究基于转录组测序结果进行SSR标记的开发,并以来自不同地区的华细辛5个种群为分析样本,利用GenALEx 6.5、NTSYS 2.1和Structure 2.3.4等软件进行遗传多样性评估。结果显示,从华细辛转录组中筛选得到的16个多态性丰富且重复性好的SSR标记,以其两侧序列为模板设计引物,能够对华细辛5个种群的150个个体样本进行稳定扩增,共得到56个多态片段,平均每对引物扩增3.5个多态片段,变化范围为2~8个,检测到平均期望杂合度(H_(e))、Shannon′s多样性指数(I)、Nei′s基因多样性指数(H)、多态性信息含量指数(PIC)的均值分别为0.172、0.281、0.429、0.382。种群间遗传分化系数(F_(ST))均值为0.588,与分子方差分析(AMOVA)结果[华细辛种群间变异程度(69%)大于种群内变异程度(31%)]相一致,各种群的多态位点百分率(PPL)范围从大到小依次为SNJ>LN>SY>SZ>TB。主成分分析(PCoA)和UPGMA聚类分析进一步显示,华细辛个体样本均按地理分布进行遗传聚类,与Structure聚类分析结果一致。综上所述,从转录组中开发的SSR标记能够有效评估华细辛自然分布种群间的遗传分化程度和种群遗传结构,揭示华细辛遗传多样性较为贫乏,遗传变异主要体现在种群水平,以及种群间遗传分化程度与地理距离存在相关性。To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5,NTSYS 2.1,and Structure 2.3.4.The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome.Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations.On average,each primer amplified 3.5 polymorphic fragments,ranging from 2 to 8.The mean values of expected heterozygosity(H_e),Shannon′s diversity index(I),Nei′s gene diversity index(H),and the polymorphic information content(PIC) were 0.172,0.281,0.429,and 0.382,respectively.The mean population differentiation coefficient(F_(ST)) was 0.588,consistent with the analysis of molecular variance(AMOVA) results,which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%).The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ>LN>SY>SZ>TB.Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution,consistent with the results of the structure clustering analysis.In summary,the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations,revealing a relatively low genetic diversity in A.sieboldii,with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.

关 键 词：华细辛 转录组 SSR标记 遗传多样性 种群遗传结构 

分 类 号：S567.239[农业科学—中草药栽培]