Gonzalez-Pena Dianelys, Gao Guangtu, Baranski Matthew, Moen Thomas, Cleveland Beth M, Kenney P Brett, Vallejo Roger L, Palti Yniv, Leeds Timothy D
United States Department of Agriculture, National Center for Cool and Cold Water Aquaculture, Agricultural Research Service Kearneysville, WV, USA.
Nofima Ås, Norway.
Front Genet. 2016 Nov 22;7:203. doi: 10.3389/fgene.2016.00203. eCollection 2016.
Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance. The GWAS analysis was performed using the weighted single-step GBLUP method (wssGWAS). Phenotypic records of 1447 fish (1.5 kg at harvest) from 299 full-sib families in three successive generations, of which 875 fish from 196 full-sib families were genotyped, were used in the GWAS analysis. A total of 38,107 polymorphic SNPs were analyzed in a univariate model with hatch year and harvest group as fixed effects, harvest weight as a continuous covariate, and animal and common environment as random effects. A new linkage map was developed to create windows of 20 adjacent SNPs for use in the GWAS. The two windows with largest effect for FY and FW were located on chromosome Omy9 and explained only 1.0-1.5% of genetic variance, thus suggesting a polygenic architecture affected by multiple loci with small effects in this population. One window on Omy5 explained 1.4 and 1.0% of the genetic variance for BW10 and BW13, respectively. Three windows located on Omy27, Omy17, and Omy9 (same window detected for FY) explained 1.7, 1.7, and 1.0%, respectively, of genetic variance for CAR. Among the detected 100 SNPs, 55% were located directly in genes (intron and exons). Nucleotide sequences of intragenic SNPs were blasted to the genome to create a putative gene network. The network suggests that differences in the ability to maintain a proliferative and renewable population of myogenic precursor cells may affect variation in growth and fillet yield in rainbow trout.
鱼片产量（FY，%）是虹鳟鱼养殖中一个重要的经济性状，会影响生产效率。尽管如此，FY在育种计划中却很少受到关注，因为难以对大量鱼类进行测量，且无法直接对育种候选鱼进行测量。虹鳟鱼高密度SNP阵列的最新发展为研究该性状的潜在遗传结构提供了所需工具。对一个为提高生长性能而进行选择性育种的家系虹鳟鱼群体的FY、孵化后10个月（BW10）和13个月（BW13）时的体重、去头胴体重（CAR）和鱼片重量（FW）进行了全基因组关联研究（GWAS）。GWAS分析采用加权单步GBLUP方法（wssGWAS）。来自三个连续世代299个全同胞家系的1447条鱼（收获时体重1.5千克）的表型记录用于GWAS分析，其中来自196个全同胞家系的875条鱼进行了基因分型。在一个单变量模型中分析了总共38107个多态性SNP，将孵化年份和收获组作为固定效应，收获体重作为连续协变量，动物和共同环境作为随机效应。开发了一个新的连锁图谱，以创建20个相邻SNP的窗口用于GWAS。对FY和FW影响最大的两个窗口位于Omy9染色体上，仅解释了1.0 - 1.5%的遗传方差，因此表明该群体中该性状受多个小效应位点影响的多基因结构。Omy5上的一个窗口分别解释了BW10和BW13遗传方差的1.4%和1.0%。位于Omy27、Omy17和Omy9上的三个窗口（与FY检测到的是同一个窗口）分别解释了CAR遗传方差的1.7%、1.7%和1.0%。在检测到的100个SNP中，55%直接位于基因（内含子和外显子）中。将基因内SNP的核苷酸序列与基因组进行比对，构建了一个推定的基因网络。该网络表明，维持成肌前体细胞增殖和可再生群体能力的差异可能会影响虹鳟鱼生长和鱼片产量的变异。
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