Establishment Of Genomic Selection Technology In Shellfish And Its Application In Scallop Breeding

Scallop mariculture is one of the leading industries of sea-farming in China.Aiming at improvement of scallop production, multi-trait selection using best linerunbiased prediction (BLUP) has been introduced to scallop breeding. Withaccumulation of more and more genetic and phenotypic information, there is a needfor rapid and eiffcient utilization of this information to assist in scallop breeding.Genomic selection (GS)? in which selection decisions are made on genomic breedingvalues predicted from high-density single nucleotide polymorphic (SNP) markers，iswidely used in livestock animals and plants species. Recent researches demonstratedthat applying GS in breeding is revolutionizing the genetic improvement.Firstly, this paper proposed a method to construct the T matrix using thegenotypes of SNP molecular markers to assess the real kinship between full-sibindividuals of aquatic animals, and compared it with the C-matrix and the traditionalA-matrix in calculating the correlation coefifcient between individuals withsimulation data. Currently T matrix is not fully applicable to the algorithms thatestimate the heritability and breeding values, and the accuracy of genomic estimatedbreeding value (GEBV) calculated using T-matrix in genomic BLUP (GBLUP) waslower than the G-matrix one, but it could estimate the real correlation coefifcientbetween related individuals with genome-wide molecular markers in the range of(0.41,1.0), which could be a better description than the A-matrix one and theG-matrix one.Subsequently, this study considered two methods, MixP and gsbay，to carry outgenomic selection (GS) analysis using simulated data. The analysis resultsdemonstrated excellent performance and showed that both methods are able toobtain more accurate predictions of GEBV and marker effects in comparison withtraditional genomic selection methods based on GBLUP. The main advantage ofMixP and gsbay is to assume the prior distribution of single nucleotidepolymorphism (SNP) marker effects to be a mixture of two normal distributions inorder to improve accuracy and accelerate the analysis for the high-dimensional data.The study then upgraded the Analysis and Evaluation System for ShellfishGenetic Breeding by equipping it with GBLUP computing modules. And a new system, the Genomic Analysis and Evaluation System tor Shelltish Genetic Breeding, was build to apply genomic selection by calling MixP and gsbay.Afterwards, this study utilized the real data of a full-sib family with98Zhikong scallop (Chlamys farreri) individuals, with both genotype and phenotype records, to test the feasibility of the GS platform. The results indicated that gsbay is more robust, while MixP computes much faster, and both MixP and gsbay can be applied to the actual work of genomic selection:it is feasible to carry out GS in scallop breeding.