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Characterization of novel EST-SNP markers and their association analysis with growth-related traits in the Pacific oyster Crassostrea gigas
- Wang, Jiulong, Li, Qi
- Aquaculture international 2017 v.25 no.5 pp. 1707-1719
- Crassostrea gigas, expressed sequence tags, fisheries, genetic improvement, genotyping, growth traits, heterozygosity, loci, marker-assisted selection, melting, oysters, phenotype, single nucleotide polymorphism, tail, variance
- The Pacific oyster Crassostrea gigas is one of the most commercially important and worldwide cultured fishery animals. To facilitate marker-assisted selection in genetic improvement of this species, 108 novel polymorphic single-nucleotide polymorphism (SNP) markers were developed from expressed sequence tags (ESTs) by high-resolution melting analysis. The association between the markers and growth traits in a fast-growing strain and validation in two cultured populations was analyzed. For the 108 SNP loci, the observed heterozygosity varied from 0.011 to 0.625 and the expected heterozygosity varied from 0.031 to 0.501. By selective genotyping method, special allele frequencies of nine SNP markers showed significant difference between the fast-growing strain and the commercial control population (P < 0.0001). The nine SNP loci were further validated in extreme phenotype tails of the commercial control population and an independent cultured population. Three markers, jl027, ji090, and jl615, were found to be significantly associated with growth traits in oysters (P < 0.01). The proportion of additive genetive variance explained by the three confirmed SNPs ranged from 0.27 to 2.23%. The putative functions of the ESTs containing the jl090 and jl615 markers indicated that they might be related to growth of C. gigas. The three confirmed SNPs associated with growth traits would have potential applications in future genetic improvement of C. gigas.