基于转录组平台的蛤仔微卫星标记筛选  

Development of microsatellite markers in Ruditapes philippinarum using nextgeneration sequencing

作　　者：闫路路 秦艳杰[1] 闫喜武[1] 王琳楠[1] 毕成隆 张津源[1] 

机构地区：[1]大连海洋大学,水产与生命学院,辽宁省贝类良种繁育工程技术研究中心,大连116023

出　　处：《生态学报》2015年第5期1573-1580,共8页Acta Ecologica Sinica

基　　金：国家863计划(2012AA10A410-2);现代农业产业技术体系建设专项资金资助(CARS-48)

摘　　要：以菲律宾蛤仔转录组测序所得拼接序列为基础,采用MISA软件进行微卫星分析,对其中的145个微卫星位点进行引物设计,得到具有清晰扩增条带的微卫星位点58个。对大连庄河野生蛤仔群体的扩增结果表明,18个位点显示单态性,40个位点表现为多态性。该群体40个多态性微卫星位点得到的等位基因数在2—6之间,平均等位基因数为3.4250±0.9718,观测杂合度和期望杂合度分别在0.0000—1.0000和0.0615—0.7996之间,平均值分别为0.2727±0.2272和0.4739±0.1902,群体平均Nei指数为0.4664±0.1872。多态信息含量(PIC)在0.0586—0.7529之间,平均值为0.4148±0.1707,其中16个微卫星位点的PIC值大于0.5,为高度多态性,15个位点0.25<PIC<0.5,为中度多态性,其余9个为低度多态性。经Sequential Bonferroni校正的Hardy-Weinberg平衡检验,有10个位点尚未偏离平衡。基于转录组平台筛选微卫星标记的方法,在很大程度上推动了DNA分子标记的开发。研究开发的微卫星标记可用于蛤仔群体遗传学、遗传连锁图谱构建及其他相关研究,为蛤仔分子标记辅助育种及群体种质保护等工作提供技术支持。Ruditapes philippinarum has a high growth rate,short culture cycle,and is highly adaptable. Because of these traits,it is one of China＇s four major cultured shellfishes,and one of the world＇s major cultured shellfishes. Microsatellites known as simple sequence repeats are widely used to assess genetic diversity in farmed aquatic species populations,construct molecular genetic maps,and carry out gynogenesis,gene mapping,gene cloning,and paternity tests. These molecular markers have high stability and polymorphism,are site- specific and easily detected,and exhibit codominant inheritance and transferability of SSR primers. At present,the sustainable culture of Ruditapes philippinarum is threatened by having a single breeding method and difficulties with disease prevention,control,and treatment. We developed a series of microsatellite markers using a transcriptome-based platform to provide a foundation for genetic research in Ruditapes philippinarum. These markers may also be used for Ruditapes marker-assisted breeding. Genetic diversity measures the degree of variability of biological genetic information. DNA is the primary carrier of genetic information,so the diversity of DNA directly reflects the degree of genetic variation. The genetic diversity of a population can be represented by the number of alleles,heterozygosity scores,and polymorphism information content（ PIC）. We sequenced a large number of ESTs andscreened 145 potential microsatellites of trinucleotide repeats using MISA software. We successfully obtained clear,reproducible bands for 58 microsatellite loci. These were amplified in 32 wild clam individuals sampled from Zhuanghe,Dalian,Liaoning. A single allele was detected at 18 loci and another 40 were polymorphic（ number of alleles per locus ranged from 2 to 6,with an average of 3. 4250 ± 0. 9718）. The observed and expected heterozygosity was 0. 000—1. 000（ 0. 2727±0.2272） and 0.0615—0.7996（ 0.4739 ± 0.1902）,respectively. The average of the Nei index was 0.4664 ±0. 1872. Th

关 键 词：菲律宾蛤仔 转录组 微卫星 遗传多样性 

分 类 号：S917.4[农业科学—水产科学]