基于RAD-seq的荸荠SSR标记开发  

Development of Polymorphic SSR Markers in Chinese Water Chestnut based on RAD-seq

作　　者：何芳练 董伟清 邱祖杨 蒋慧萍 刘莉莉 陈琦 黄诗宇 He Fanglian;Dong Weiqing;Qiu Zuyang;Jiang Huiping;Liu Lili;Chen Qi;Huang Shiyu(Institute of Biotechnology,Guanxi Zhuang Nationality Autonomous Region Academy of Agricultural Sciences,Nanning,530007;Lipu Municipal Bureau of Agriculture and Rural Affairs,Lipu,546600;Nanning New Technical Entrepreneur Center,Nanning,530007)

机构地区：[1]广西壮族自治区农业科学院生物技术研究所,南宁530007 [2]荔浦市农业农村局,荔浦546600 [3]南宁新技术创业者中心,南宁530007

出　　处：《分子植物育种》2022年第1期210-217,共8页Molecular Plant Breeding

基　　金：广西创新驱动发展专项(桂科AA17204045-8)资助。

摘　　要：荸荠(Eleocharis dulcis)是一种重要的特色水生蔬菜,为开发用于荸荠遗传学研究的简单重复序列(SSR)分子标记,本研究基于RAD-seq技术对荸荠进行简化基因组测序,并进行SSR标记开发与引物设计。结果显示,共检测到5039个SSR位点,其中4127个SSR位点可利用并成功设计引物。在可利用的SSR位点中,三碱基重复基序类型所占比例最高,数量为1894个,占位点总数的45.89%;其次是二碱基重复基序类型,数量为1406个,占位点总数的34.07%。随机选取了100对引物进行有效性验证,扩增成功率为93%,从扩增成功的引物中选取83对引物对两个品种进行多态性检测,83对引物共得到232条条带,其中多态性条带为128条,具有多态性的引物为60对,多态性比率为72.28%。通过RAD-seq开发的荸荠SSR标记有效性和多态性较高,为后期荸荠种质资源的高效利用、品种的遗传改良及分子育种提供了基础。Chinese water chestnut(Eleocharis dulcis)is an important characteristic vegetable that grows in shallow waters.In order to develop simple sequence repeat(SSR)molecular markers for genetics research on Eleocharis dulcis,simplified genome sequencing by restriction-site associated DNA sequencing(RAD-seq),SSR search and primer design were performed.A total of 5039 SSR loci were detected,from which 4127 pairs of primer were designed.Among them,the proportion of tri-nucleotides motifs was the highest(1894),accounting for 45.89%of the total loci;followed by di-nucleotide with 1406,accounting for 34.07%.A total of 100 pairs of randomly selected primers were verified.93%of the primers were successfully amplified.To assess the polymorphism of these primers,two varieties of Chinese water chestnuts were used to amplify the SSR marker using 83 pairs of primers.The 83 pairs of primers generated a total of 232 fragments.A total of 128 fragments were polymorphic.60 pairs of primers out of 83 pairs generated at least one polymorphic band,and the ratio of polymorphic primers was72.28%.These SSR markers developed from RAD-seq were proved to be effective,which will provide a useful tool for genetic diversity research and molecular breeding in Chinese water chestnuts.

关 键 词：荸荠(Eleocharis dulcis) RAD-seq SSR 分子标记 

分 类 号：S645.3[农业科学—蔬菜学]