Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China.
Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China.
Sci Rep. 2020 Apr 29;10(1):7259. doi: 10.1038/s41598-020-64037-w.
In order to identify candidate genes or loci associated with growth performance of the newly established common carp strain, Xinlong, we conducted a genome-wide association analysis using 2b-RAD technology on 123 individuals. We constructed two sets of libraries associated with growth-related parameters (weight, length, width and depth) measured at two different grow-out stages. Among the 413,059 SNPs identified using SOAP SNP calling, 147,131 were tested for GWAS after quality filtering. Finally, 39 overlapping SNPs, assigned to four genomic locations, were associated with growth traits in two stages. These loci were assigned to functional classes related to immune response, response to stress, neurogenesis, cholesterol metabolism and development, and proliferation and differentiation of cells. By overlapping results of Plink and EMMAX analyses, we identified three genes: TOX, PLK2 and CD163 (both methods P < 0.05). Our study results could be used for marker-assisted selection to further improve the growth of the Xinlong strain, and illustrate that largely different sets of genes drive the growth of carp in the early and late grow-out stages.
为了鉴定与新建立的草鱼品种“新隆”生长性能相关的候选基因或基因座，我们使用 2b-RAD 技术对 123 个个体进行了全基因组关联分析。我们构建了两组与两个不同养殖阶段测量的生长相关参数（体重、体长、体宽和体高）相关的文库。在使用 SOAP SNP 调用识别的 413059 个 SNPs 中，经过质量过滤后，对 147131 个 SNPs 进行了 GWAS 测试。最后，在两个阶段的生长性状中，有 39 个重叠 SNP 被分配到四个基因组位置。这些位点被分配到与免疫反应、应激反应、神经发生、胆固醇代谢和发育以及细胞增殖和分化相关的功能类别。通过 Plink 和 EMMAX 分析的重叠结果，我们鉴定出了三个基因：TOX、PLK2 和 CD163（两种方法的 P 值均<0.05）。我们的研究结果可用于标记辅助选择，以进一步提高新隆品种的生长性能，并说明在早期和后期养殖阶段，有很大不同的基因组驱动着鲤鱼的生长。
