| The molecular genetic linkage map of bay scallop is essential for the identification and localization of quantitative trait loci (QTL) as well as for the maker-assisted selection program, which is great useful in enhancing breeding efficiency in this aquaculture important species. The purpose of this study includes four aspects. The first is to isolate lots of microsatellite DNA sequences by microsatellite-enrichment libraries. Second is to investigate the level of genetic differentiation between one wild population and three hatchery stocks of bay scallop. Third is to construct the genetic linkage map for bay scallop based on microsatellite DNA markers. The last is to localize some growth related QTLs by composite interval mapping.Microsatellite-enriched libraries, which enriched for (AC)15 and (AG)15 were constructed using the protocol of nylon membrane hybridization and colony hybridization. More than 1000 positive clones were sequenced, of which 516 were independent containing microsatellites after sequence alignment. The microsatellite sequences were divided into four categories: perfect repeats (49.0%), imperfect repeats (42.7%), and compound repeats (8.3%). Primers were designed and synthesized using sequence information from 382 clones. The polymorphisms of 15 markers were assessed with 38 individuals, and the results showed the number of alleles ranged from 3 to 7. The values of He and Ho ranged from 0.198 to 0.813 and 0.083 to 0.833 respectively. The results indicated that the method of screening microsatellite-enriched library is efficient and suitable to isolate a large number of microsatellite markers, and the markers developed will contribute significantly for the population genetic and linkage mapping study of bay scallop.Eight simple sequence repeats (SSR) were employed to investigate the level of genetic variation within one wild population and three hatchery stocks of bay scallop, and compare the degree of genetic differentiation between them. High polymorphism at the microsatellite loci was found within both wild and hatchery scallops. Compared to wild population, all the hatchery stocks showed less genetic variation as revealed in lower number of alleles and lower observed heterozygosity. The ZJ population lost 9 of out of 35 allels (25.7%) after 19 generations of isolation and genetic drift. Significant differentiation was found between the hatchery stocks and wild populations, and between the hatchery stocks. This study indicated that genetic compostion of cultured bay scallop population in China have been significantly affected by hatchery performance.We constructed sex-specific linkage maps for bay scallop (Argopecten irradians) based on 167 microsatellite DNA markers and one morphological character marker (shell color). Linkage mapping was performed on two unrelated families, and a composite linkage map for each sex was constructed by combining linkage information from the two reference families. The composite female map contained 118 markers in 16 linkage groups, spanning 761.0 cM; the male parent map had 126 markers in 18 linkage groups, covering 729.1 cM with an average interval 6.75 cM. Analysis of markers informative in both parents showed a higher recombination rate in the female parent, with an average female-to-male recombination ratio of 1.18: 1 between adjacent paired markers. Segregation distortion was asymmetrical between the sexes (9% in the female and 19% in the male), which supported the hypothesis that distortion resulted from heterospecific interactions between genome of the two subspecies of A. irradians.The location and effects of QTLs were estimated for five growth related traits in bay scallop based on two reference families. In total, 33 putative QTL (LOD > 2.0) were detected and mapped on sex-specific maps, including 8 for total weight, 6 for shell length, 6 for shell width,7 for shell height and 6 for shell weight. These QTLs were on LG1, LG3, LG4 and LG8 in family CC5 and on LG1, LG3, LG6, LG8 and LG9 in family CC10, explaining 5.5% to 29.2% of the trait variation. The common QTLs shared between two families would be very useful for improving growth related traits though marker-assisted selection in the future.
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