基于全长转录组数据的中国圆田螺微卫星特征分析与标记筛选  

Feature Analysis and Marker Development of Microsatellites for Cipangopaludina Chinensis Based on Full-length Transcriptome Data

作　　者：韦小凯 周康奇 邹欣汐 林勇 叶华[1] 罗辉[1] 覃俊奇 陈忠 黄姻 杜雪松 张彩群 潘贤辉 WEI Xiaokai;ZHOU Kangqi;ZOU Xinxi;LIN Yong;YE Hua;LUO Hui;QIN Junqi;CHEN Zhong;HUANG Yin;DU Xuesong;ZHANG Caiqun;PAN Xianhui(Southwest University,Chongqing 402460,P.R.China;Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture,Guangxi Aquatic Breeding Base,Guangxi Academy of Fishery Sciences,Nanning 530021,P.R.China)

机构地区：[1]西南大学,重庆荣昌402460 [2]广西壮族自治区水产科学研究院,广西水产遗传育种与健康养殖重点实验室,广西南宁530021

出　　处：《水生态学杂志》2025年第2期235-242,共8页Journal of Hydroecology

基　　金：国家重点研发计划项目(2022YFD2400700);广西创新驱动发展专项资金项目(AA17204080-5);广西特色淡水鱼产业创新团队项目(nycytxgxcxtd-2021-08);广西自然科学基金项目(2020GXNSFBA297067);广西科技基地与人才项目(AD21220010)。

摘　　要：通过高通量测序开发中国圆田螺多态性SSR标记,为田螺的种质利用及良种选育提供技术支撑。基于PacBio's SMRT测序获得中国圆田螺全长转录组数据,查找基因组微卫星(SSR)位点并分析其特征,共识别到8 058个SSR位点,1~6个核苷酸重复SSR均存在,其中二核苷酸重复SSR数量最多(4 647,57.67%),其次为三核苷酸重复SSR(1 274,15.81%)。在二核苷酸重复基元中以AC/GT的重复数最多,占总SSR位点数的34.82%。随机选择合成192对引物筛选获得22对多态性SSR引物,并使用这些标记对广西圆田螺群体进行遗传多样性分析。结果表明,有22个SSR标记扩增产物稳定,22个SSR标记共检测到102个等位基因,平均等位基因数(Na)为4.636,观测杂合度(H_o)和期望杂合度(He)均值分别为0.286和0.589,多态性信息含量(PIC)为0.247~0.844。在22个SSR位点中,高度多态性位点(PIC>0.50)有13个,中度多态性位点(0.25<PIC≤0.50)有8个,说明中国圆田螺群体遗传多样性较丰富。利用PacBio's SMRT测序技术开发中国圆田螺SSR标记不仅效率高,而且适用于中国圆田螺的资源评估。In this study,we developed polymorphic SSR markers for Cipangopaludina chinensis using high throughput sequencing and then screened the genomic microsatellite loci and analyzed their features.The aim of the study was to provide technical support for field snail germplasm utilization and breeding.The study was based on the full-length transcriptome data for C.chinensis,which was obtained through PacBio's SMRT sequencing.A total of 8058 SSR loci were identified and 1-6 nucleotide SSR repetition types were observed.Of these,dinucleotide repeat SSRs were the most common with 4647 SSR loci(57.67%),followed by trinucleotide repeat SSRs with 1274 SSR loci(15.81%).The AC/GT motif was the primary repeat unit among dinucleotide motifs,accounting for 34.82%of the total SSR loci.Then,192 pairs of primers were synthesized randomly to screen the polymorphic SSR primers using 10 different geographical populations of C.chinensis.A total of 22 pairs of polymorphic SSR primers were obtained,and the polymorphic SSR markers were used to analyze the genetic diversity of C.chinensis populations in different geographic regions of Guangxi Province.The amplification products of the 22 SSR markers were steady and 102 alleles were detected across all markers,with an average number of alleles(Na)of 4.636.The average observed heterozygosity(Ho)and expected heterozygosity(He)of the alleles were 0.286 and 0.589,respectively.The polymorphic information content(PIC)ranged from 0.247 to 0.844,with the average value of 0.547.Among the 22 SSR loci,13 were determined as highly polymorphic loci(PIC>0.50),and 8 were moderately polymorphic loci(0.25<PIC≤0.50),indicating high genetic diversity within the C.chinensis population.In conclusion,PacBio SMRT sequencing technology was an efficient means of developing SSR markers for C.chinensis,and the markers proved suitable for evaluating the C.chinensis resource.

关 键 词：中国圆田螺 转录组 微卫星 多态性标记 

分 类 号：S932.4[农业科学—渔业资源]