Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
School of Biological Sciences, The New Zealand Institute for Plant and Food Research Limited, Nelson 7010, New Zealand.
G3 (Bethesda). 2022 Mar 4;12(3). doi: 10.1093/g3journal/jkac015.
Growth is one of the most important traits of an organism. For exploited species, this trait has ecological and evolutionary consequences as well as economical and conservation significance. Rapid changes in growth rate associated with anthropogenic stressors have been reported for several marine fishes, but little is known about the genetic basis of growth traits in teleosts. We used reduced genome representation data and genome-wide association approaches to identify growth-related genetic variation in the commercially, recreationally, and culturally important Australian snapper (Chrysophrys auratus, Sparidae). Based on 17,490 high-quality single-nucleotide polymorphisms and 363 individuals representing extreme growth phenotypes from 15,000 fish of the same age and reared under identical conditions in a sea pen, we identified 100 unique candidates that were annotated to 51 proteins. We documented a complex polygenic nature of growth in the species that included several loci with small effects and a few loci with larger effects. Overall heritability was high (75.7%), reflected in the high accuracy of the genomic prediction for the phenotype (small vs large). Although the single-nucleotide polymorphisms were distributed across the genome, most candidates (60%) clustered on chromosome 16, which also explains the largest proportion of heritability (16.4%). This study demonstrates that reduced genome representation single-nucleotide polymorphisms and the right bioinformatic tools provide a cost-efficient approach to identify growth-related loci and to describe genomic architectures of complex quantitative traits. Our results help to inform captive aquaculture breeding programs and are of relevance to monitor growth-related evolutionary shifts in wild populations in response to anthropogenic pressures.
生长是生物体最重要的特征之一。对于受开发物种而言，该特征具有生态和进化意义，以及经济和保护意义。已报道了几种海洋鱼类的生长率与人为压力源相关的快速变化，但人们对硬骨鱼类生长特征的遗传基础知之甚少。我们使用了简化的基因组代表数据和全基因组关联方法，鉴定了商业上、娱乐上和文化上重要的澳大利亚鲷鱼（Chrysophrys auratus， Sparidae）的与生长相关的遗传变异。基于 17490 个高质量的单核苷酸多态性和 363 个个体，这些个体代表了在海笔中相同年龄和相同条件下饲养的 15000 条鱼中具有极端生长表型的个体，我们鉴定出了 100 个独特的候选基因，这些候选基因注释到 51 种蛋白质上。我们记录了该物种生长的复杂多基因性质，包括几个具有小效应的基因座和少数具有较大效应的基因座。总体遗传力很高（75.7%），这反映了表型的基因组预测准确性很高（小 vs 大）。尽管单核苷酸多态性分布在整个基因组中，但大多数候选基因（60%）聚集在第 16 号染色体上，这也解释了最大比例的遗传力（16.4%）。这项研究表明，简化的基因组代表单核苷酸多态性和正确的生物信息学工具提供了一种具有成本效益的方法，可以鉴定与生长相关的基因座，并描述复杂数量性状的基因组结构。我们的研究结果有助于指导圈养水产养殖的育种计划，并有助于监测野生种群中与生长相关的进化变化，以应对人为压力。
