Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully explored in rainbow trout. A previously developed 50 K gene-transcribed SNP chip, containing ~ 21 K SNPs showing allelic imbalances potentially associated with important aquaculture production traits including body weight, muscle yield, was used for genotyping a total of 789 fish with available phenotypic data for bodyweight gain. Genotyped fish were obtained from two consecutive generations produced in the NCCCWA growth-selection breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform a genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with bodyweight gain. Using genomic sliding windows of 50 adjacent SNPs, 247 SNPs associated with bodyweight gain were identified. SNP-harboring genes were involved in cell growth, cell proliferation, cell cycle, lipid metabolism, proteolytic activities, chromatin modification, and developmental processes. Chromosome 14 harbored the highest number of SNPs (n = 50). An SNP window explaining the highest additive genetic variance for bodyweight gain (~ 6.4%) included a nonsynonymous SNP in a gene encoding inositol polyphosphate 5-phosphatase OCRL-1. Additionally, based on a single-marker GWA analysis, 33 SNPs were identified in association with bodyweight gain. The highest SNP explaining variation in bodyweight gain was identified in a gene coding for thrombospondin-1 (THBS1) (R2 = 0.09). The majority of SNP-harboring genes, including OCRL-1 and THBS1, were involved in developmental processes. Our results suggest that development-related genes are important determinants for growth and could be prioritized and used for genomic selection in breeding programs.

中文翻译：

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虹鳟鱼生长相关基因座的全基因组鉴定

增长是水产养殖的主要经济生产特征。生长性能的提高将减少鱼类达到市场规模所需的时间和成本。然而，虹鳟鱼尚未完全探究潜在的生长基因。先前开发的50 K基因转录SNP芯片包含〜21 K SNP，显示出与重要的水产养殖生产特性（包括体重，肌肉产量）潜在相关的等位基因失衡，用于对789条鱼类进行基因分型，并提供可利用的表型数据来增加体重。基因型鱼是从NCCCWA生长选择育种计划中连续两个世代获得的。加权单步GBLUP（WssGBLUP）用于执行全基因组关联（GWA）分析，以鉴定与体重增加相关的定量性状位点（QTL）。使用50个相邻SNP的基因组滑动窗口，确定了247个与体重增加相关的SNP。携带SNP的基因参与细胞生长，细胞增殖，细胞周期，脂质代谢，蛋白水解活性，染色质修饰和发育过程。14号染色体上的SNP数量最多（n = 50）。一个SNP窗口解释了体重增加的最高附加遗传方差（约6.4％），其中一个非同义SNP出现在编码肌醇多磷酸5磷酸酶OCRL-1的基因中。此外，基于单标记GWA分析，发现了33个SNP与体重增加有关。在编码血小板反应蛋白-1（THBS1）（R2 = 0.09）的基因中鉴定出最高的SNP，可以解释体重增加的变化。大多数SNP携带基因，包括OCRL-1和THBS1，参与了发展过程。我们的结果表明，与发育相关的基因是决定生长的重要因素，可以优先考虑并用于育种计划中的基因组选择。