基于转录组测序的核桃(Juglans regia L.)SSR标记开发  

Development of SSR Markers for Walnut (Juglans regia L.) with Transcriptome Sequencing Data

作　　者：覃阳 全绍文 周丽 杨洁萍 牛建新 Qin Yang;Quan Shaowen;Zhou Li;Yang Jieping;Niu Jianxin(College of Agriculture,Shihezi University,Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization,Shihezi,832003)

机构地区：[1]石河子大学农学院特色果蔬栽培生理与种质资源利用兵团重点实验室

出　　处：《分子植物育种》2019年第20期6736-6742,共7页Molecular Plant Breeding

基　　金：国家自然科学基金项目(30560090);新疆重大科技专项(201130102-1-4)共同资助

摘　　要：本研究通过高通量测序技术结合MISA软件分析核桃转录组中SSR的分布类型及特点。通过Primer 3设计得到426对SSR引物,以来源于新疆林业科学院的10份核桃种质对随机合成的10对引物进行多态性筛选,并对核桃转录组数据进行了SSR位点搜索和分析,继而开发SSR标记。利用MISA软件在132 154条Unigenes共检测出63 400个SSR位点,分布于47 169条Unigene中,出现频率为47.97%,平均分布距离为2.55 kb。优势重复基序为单核苷酸、二核苷酸和三核苷酸,分别占总SSR位点的55.73%,34.48%和8.63%。二核苷酸重复基元中以AG/CT为优势重复基元,占二核苷酸重复的64.77%,三核苷酸重复基元以AAG/CTT为主。10对引物进行多态性验证分析结果显示:8对有效扩增引物中,7对引物在10份不同核桃种质中表现出多态性。以上结果表明,核桃转录组测序产生的Unigene信息可作为开发SSR标记的有效来源。开发的大批量SSR标记可为核桃种质资源遗传多样性分析和遗传图谱构建提供更加丰富可靠的标记选择。In this study, MISA software was used to screen and analyze the distribution types and characteristics of simple sequence repeats(SSRs) in the pericarp transcriptome of walnut which obtained by high-throughput sequencing technology. Then, the 426 SSR primer pairs were designed by Primer 3.0 software and 10 primer pairs of them were selected randomly to test polymorphism among 10 individuals which from Xinjiang Academy of Forestry Sciences to develop the SSR markers. 132 154 unigenes base pairs were analyzed by MISA software, and a total of 63 400 SSRs were identified from 47 169 Unigenes. The frequency of SSRs from these Unigenes was47.97%, and the mean distribution distance of loci was 2.55 kb. Meanwhile, the major types such as mononucleotide,dinucleotide and trinucleotide accounted for 55.73%, 34.48% and 8.63%, respectively. Furthermore, AG/CT was the predominant dinucleotide repeat type(64.77%), and the AAG/CTT was the predominant trinucleotide repeat type. The results of polymorphism analysis of 10 pairs of primers showed that among the 8 pairs of effective amplification primers, 7 pairs of primers showed polymorphism in 10 different walnut germplasms. The results indicated that the Unigenes generated from trasncriptome sequencing in walnut could be used as an effective source to develop SSR markers. Th e large quantities of SSR markers will provide reliable markers for map structure, genetic polymorphism analysis for walnut germplasm resource.

关 键 词：核桃(Juglans regia L.) 转录组 SSR标记开发 

分 类 号：S66[农业科学—果树学]