基于不结球白菜转录组EST-SSR标记开发及多态性分析  

Development and Polymorphism Analysis of EST-SSR Markers Based on Transcriptome of Non-heading Chinese Cabbage(Brassica rapa ssp. chinensis)

作　　者：杨丹青 何晓丽 杜志杰 王树彬[1] 孙笠维 林义章[1] 邵贵荣 钟凤林[1,2] YANG Dan-Qing;HE Xiao-Li;DU Zhi-Jie;WANG Shu-Bin;SUN Li-Wei;LIN Yi-Zhang;SHAO Gui-Rong;ZHONG Feng-Lin(College of Horticulture,Fujian Agriculture and Forestry University,Fuzhou 350002,China;The Vegetable Institute of Fujian Agricultural and Forestry University,Fuzhou 350002,China;Fujian Jinpin Agricultural Technology Co.,Ltd.,Fuzhou 350002,China)

机构地区：[1]福建农林大学园艺学院,福州350002 [2]福建农林大学蔬菜研究所,福州350002 [3]福建金品农业科技股份有限公司,福州350002

出　　处：《农业生物技术学报》2020年第1期13-21,共9页Journal of Agricultural Biotechnology

基　　金：福州市科技项目(2018-G-37);国家青梗菜良种重大科研联合攻关项目(111821301354052283);福建省科技重大专项专题“高产、优质、抗逆、广适的设施蔬菜新品种选育与产业化”(2018NZ0002-2);福建省新世纪人才项目(KLa17011A)

摘　　要：由转录组测序信息获得的EST-SSR标记具有通用性好、保守性高、多态性丰富、共显性遗传等优点,广泛应用于植物种质资源的遗传多样性分析。本研究通过对不结球白菜(Brassica rapa ssp.chinensis)转录组高通量测序,挖掘SSR位点和开发EST-SSR标记,并进行引物的初步验证及其多态性分析。在不结球白菜转录组的48817条Unigene序列中共搜寻到17009个SSR位点,发生频率为18.44%,SSR分布频率为34.84%。不结球白菜SSR位点共包括212种重复基元。其中,单、二和三核苷酸重复为不结球白菜转录组SSR的主要类型,占SSR总量的98.31%。单核苷酸重复最多,占总量的39.70%,其优势重复单元为T/A(26.83%)。利用Primer Premier 3.0设计EST-SSR引物,在批量设计的引物中随机挑选40对进行合成并初步验证,25对引物在92份不结球白菜种质资源中均能扩增出预期大小的条带。其平均等位基因数3.72个,有效等位基因数(effective number of alleles,Ne)、Shannon’s指数(Shannon’s index,I)、多态性信息指数(polymorphism information content,PIC)和基因多样性(gene diversity,GD)分别为2.7108、0.9991、0.4884和0.5452。所获得的EST-SSR引物可为不结球白菜及芸薹属其他植物的遗传结构分析、种质资源利用及遗传图谱构建提供有效的分子标记。The EST-SSR markers obtained from transcriptome sequencing information have the advantages of good stability,high polymorphism,co-dominant inheritance,and simple operation,and are widely used in genetic diversity analysis of plant germplasm resources.In this study,high-throughput sequencing of the transcriptome of non-heading Chinese cabbage(Brassica rapa ssp.chinensis)was used to seek SSR loci and develop EST-SSR markers,and preliminary primer verification and polymorphism analysis were performed.A total of 17009 SSR loci were found in the 48817 unigene sequences of the transcriptional set of non-heading Chinese cabbage,with an occurrence frequency of 18.44%and a SSR distribution frequency of 34.84%.The SSR sites of non-heading Chinese cabbage contained 212 repeat elements whose SSR types were mainly concentrated on single,binary and trinucleotide repeats.Among them,single nucleotide repeats accounted for the most,accounting for 39.70%of the total,and the dominant repeating unit was T/A(26.83%).The ESTSSR primers designed by Primer Premier 3.0 soft were used to randomly selected for 40 pairs in batch design primers for synthesis and preliminary verification.Twenty-five pairs of primers could amplify the expected size bands in 92 non-heading Chinese cabbage germplasm resources.The average number of alleles was 3.72,and the effective number of alleles(Ne),Shannon’s index(I),polymorphism information content(PIC)and gene diversity(GD)were 2.7108,0.9991,0.4884 and 0.5452,respectively.The obtained EST-SSR primers could provide effective molecular markers for genetic structure analysis,germplasm utilization and genetic map construction of non-heading Chinese cabbage and other Brassica plants.

关 键 词：不结球白菜 EST-SSR 多态性 

分 类 号：S634.3[农业科学—蔬菜学]