Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA.
Virginia Institute of Marine Science, Aquaculture Genetics and Breeding Technology Center, Gloucester Point, VA 23062, USA.
G3 (Bethesda). 2022 Jan 4;12(1). doi: 10.1093/g3journal/jkab368.
As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still poorly understood. In this study, we used ddRAD sequencing to generate genome-wide single-nucleotide polymorphism (SNP) data for four F2 families to investigate the genomic regions associated with survival in extreme low salinity (<3). SNP data were also used to assess the feasibility of genomic selection (GS) for improving this trait. Quantitative trait locus (QTL) mapping and combined linkage disequilibrium analysis revealed significant QTL on eastern oyster chromosomes 1 and 7 underlying both survival and day to death in a 36-day experimental challenge. Significant QTL were located in genes related to DNA/RNA function and repair, ion binding and membrane transport, and general response to stress. GS was investigated using Bayesian linear regression models and prediction accuracies ranged from 0.48 to 0.57. Genomic prediction accuracies were largest using the BayesB prior and prediction accuracies did not substantially decrease when SNPs located within the QTL region on Chr1 were removed, suggesting that this trait is controlled by many genes of small effect. Our results suggest that GS will likely be a viable option for improvement of survival in extreme low salinity.
随着全球对海鲜的需求不断增加，研究能够提高水产养殖产量的性状的遗传基础至关重要。东方牡蛎（Crassostrea virginica）是美国大西洋和墨西哥湾沿岸重要的水产养殖物种，但强降雨事件的增加使牡蛎暴露在急性低盐度环境中，这对产量产生了负面影响。已知低盐度生存能力是一个中等可遗传的性状，但该性状的遗传结构仍知之甚少。在这项研究中，我们使用 ddRAD 测序为四个 F2 家系生成了全基因组单核苷酸多态性 (SNP) 数据，以研究与极端低盐度 (<3) 下生存相关的基因组区域。SNP 数据还用于评估基因组选择 (GS) 改善该性状的可行性。数量性状位点 (QTL) 作图和联合连锁不平衡分析揭示了东方牡蛎染色体 1 和 7 上与生存和 36 天实验挑战中死亡天数相关的显著 QTL。显著的 QTL 位于与 DNA/RNA 功能和修复、离子结合和膜转运以及一般应激反应相关的基因中。使用贝叶斯线性回归模型进行 GS 研究，预测准确率范围为 0.48 至 0.57。使用 BayesB 先验时，基因组预测准确率最大，当去除 Chr1 上 QTL 区域内的 SNPs 时，预测准确率没有大幅下降，这表明该性状受许多小效应基因控制。我们的研究结果表明，GS 很可能是提高极端低盐度生存能力的可行选择。
