栉孔扇贝BES-SSR的开发及遗传多样性分析

通过分析栉孔扇贝BAC末端序列,发现大量微卫星DNA;随机选择14个多态性BES-SSR标记,在我国栉孔扇贝大连群体(DL)和青岛群体(QD)中验证标记的可用性,同时对这两个群体的遗传结构及其分化进行研究。结果表明,从17447条BESs中得到微卫星3374个,以四核苷酸重复为主(26.6%),五核苷酸重复次之(17.7%),六核苷酸重复最少(12.0%)。BES-SSR引物的扩增效率为77.3%(99/128),在作图亲本中的多态比例为33.6%(43/128),14个基因座在两群体中的平均等位基因数Na分别为18.9286和26.2143,平均有效等位基因数Ne为11.7505和17.0891,平均观察杂合度Ho为0.5100和0.4204,平均期望杂合度He为0.9156和0.9450,多态信息含量PIC分别为0.8940和0.9302,群体遗传多样性水平较高。两群体间的无偏遗传相似性系数为0.4879,遗传距离为0.7177,平均基因分化指数FST为0.0243,基因流Nm为10.0179,显示群体间遗传分化程度较弱,遗传变异主要来自于群体内个体之间,经Hardy-Weinberg平衡检验,两群体普遍存在杂合子缺失现象。研究表明,所开发的BES-SSR是高度多态位点,用于群体遗传多样性分析效果很好,显示BES是微卫星标记开发和应用的重要资源。

The development of BAC-end sequence-based microsatellite markers and analysis on population genetic diversity in Zhikong scallop (Chlamys farreri)

In this study, microsatellite markers were developed from the BAC-end sequences and used to analyze the genetic structure and genetic differentiation in two populations in Zhikong scallop (Chlamys farreri). A total of 3 374 microsatellites were identified from the 17 477 BAC-end sequences (BESs), of which tetra-nucleotide motifs were most abundant (26.6%), followed by penta-nucleotide motifs (17.7%) and hexa-nucleotide motifs were the least (12.0%). 77.3% SSRs were successfully amplified(99/128), and 43 SSRs(33.6%) were polymorphic in the parentage of mapping population. In order to apply these BES-SSR markers, 14 polymorphic SSRs were chosen to amplify and then analyze the genetic diversity in Dalian population and Qingdao population. A total of 395 alleles were obtained at the fourteen microsatellite markers and the number of alleles in each locus ranged from 8 to 38 in the two populations. The average number of alleles (Na) was 18.928 6 and 26.214 3 respectively. The average effective number of alleles (Ne) was 11.750 5 and 17.089 1 respectively. The mean observed heterozygosity (Ho) was 0.510 0 and 0.420 4. The mean expected heterozygosity (He) was 0.915 6 and 0.945 0. The data suggested both populations have high genetic diversities. The mean polymorphic information content (PIC) was 0.894 0 and 0.930 2, which were both greater than 0.5, indicating the fourteen loci were highly polymorphic. The unbiased genetic identity index was 0.487 9, and the genetic distance was 0.717 7. The coefficient of gene differentiation (FST) and gene flow (Nm) between two populations were 0.024 3 and 10.017 9 respectively. Low genetic differentiation was observed between the two populations, and the variance mainly came from individual difference. Significant deviation was detected by Hardy-Weinberg equilibrium test. There was heterozygote deficiency at all loci. The results showed BAC-end sequences were an effective resource for development of SSR markers for genetic and genomic researches.