期刊
G3-GENES GENOMES GENETICS
卷 6, 期 5, 页码 1417-1426出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/g3.116.026971
关键词
single nucleotide polymorphisms; reduced-representation sequencing; distortion of segregation ratios; missing data imputation; growth-related traits candidate genes
资金
- National Basic Research Program of China (973 Program) [2010CB126402]
- National Natural Science Foundation of China [31530079]
- Earmarked Fund for Modern Agro-industry Technology Research Systems [CARS-48]
- Taishan Scholars Climbing Program of Shandong
Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing, genotyped from a C. gigas x C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL) for five growth-related traits were detected. These QTL could explain 4.2-7.7% (mean = 5.4%) of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16) were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata.
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