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

Abstract

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 microsatel-lite markers and the number of alleles in each locus ranged from 8 to 38 in the two populations. The aver-age 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 popula-tions 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 un-biased 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.