QTL Mapping Of Growth-related Traits And Linkage Disequilibrium Analysis In The Pacific Oyster Crassostrea Gigas

The Pacific oyster (Crassostrea gigas) is one of the most important commercialbivalve species cultured in China as well as in the world. Conventional selectiveimprovement has been actively performed; however, so far, its hereditary basis is stillwild type and there have been no stable strains which can be used in aquaculture.Insufficiency of excellent broodstock and low yield represent the major limitation toC. gigas farming industry in China. With the rapid development of molecular biology,marker-assisted selection (MAS) and integration of phenotypic selection in breedingstrategies would be more effective. In this study, we constructed genetic linkage map,mapped QTL associated with growth-related traits and estimated linkagedisequilibrium level in the Pacific oyster. These findings provide solid support for C.gigas molecular breeding.1. Construction of genetic linkage map for the Pacific oysterA sex-averaged linkage map was constructed by combining64genomic SSRs,42EST-SSRs and320AFLP markers in an F1full-sib family. A total of426markerswere assigned to11linkage groups, spanning558.2cM with an average interval of1.3cM and94.7%of genome coverage. Segregation distortion was significant for18.8%of the markers (P <0.05), and distorted markers tended to occur on somegenetic regions or linkage groups.Microsatellite markers are inherited as co-dominant, which are reproducible andhigh polymorphism. They are easily transferred among populations and laboratories,and one of ideal joining markers to construct a consensus map. In order to improvethe number of microsatellite markers on the map of the Pacific oyster, the consensusmap of C. gigas was first constructed using JoinMap4.0based on commonmicrosatellite markers among six mapping populations. The consensus map contained161microsatellite markers, spanning10linkage groups. The map length and averagegenetic distance is respectively615.4cM and3.8cM. The number of loci on linkagegroup ranged from10to24and the genetic length of linkage group varied from47.3to73.3cM. At present, this consensus map is the densest microsatellite markers basedmap of C. gigas. Among different mapping populations, the grouping of markers is consistent; however, the order of markers is a little different, which likely attributed topolymorphism for chromosomal rearrangements in the natural population of C.gigas.2. QTL mapping of growth related traits for the Pacific oysterSex-averaged linkage map was used to scan QTL associated with growth relatedtraits and sex. Most growth-related quantitative traits were highly significantly (P <0.01) correlated, and principle component analysis obtained four principlecomponents. QTL analysis identified three significant QTL for two principlecomponents, which explained0.6%-13.9%of the phenotypic variation. One QTL forsex was detected on linkage group6, and the inheritabilities of sex for parental allelesand maternal alleles on that locus C15are39.8%and0.01%, respectively.3. Linkage disequilibrium analysis in the Pacific oysterLinkage disequilibrium (LD) has received considerable attention recently becauseof its usefulness in facilitating the mapping of the actual genes responsible for variationof economically important traits through association mapping. The feasibility andefficacy of association studies is strongly dependent on the extent of LD, whichdetermines the density of markers and experimental design for an association analysisin the population under study. In this study, we firstly characterized the extent of LDin a wild population and a cultured mass selection population of the Pacific oyster. Atotal of88wild and96cultured individuals were sampled to assess the level ofgenome-wide LD by using53microsatellites. For wild population, no significantassociations between syntenic marker pairs was observed, while three for culturedpopulation, LD decay was12.7cM, indicating that strong artificial selection might bea key force in substantial increase of genome-wide LD in cultured population. Thedifference of LD between wild and cultured populations showed that associationstudies in the Pacific oyster can be achieved with reasonable marker densities atrelatively low cost by choice of association mapping population. Furthermore, numbersof rare alleles and the frequent occurrence of LD between nonsyntenic lociencouraged the joint of linkage analysis and LD mapping when mapping genes in theoyster. The information on the linkage disequilibrium in cultured population obtainedin this study will be useful for future association mapping in the oyster.