Table2_Use of whole-genome sequence data for fine mapping and genomic prediction of sea louse resistance in Atlantic salmon.pdf

Sea louse (Lepeophtheirus salmonis) infestation of Atlantic salmon (Salmo salar) is a significant challenge in aquaculture. Over the years, this parasite has developed immunity to medicinal control compounds, and non-medicinal control methods have been proven to be stressful, hence the need to study the genomic architecture of salmon resistance to sea lice. Thus, this research used whole-genome sequence (WGS) data to study the genetic basis of the trait since most research using fewer SNPs did not identify significant quantitative trait loci. Mowi Genetics AS provided the genotype (50 k SNPs) and phenotype data for this research after conducting a sea lice challenge test on 3,185 salmon smolts belonging to 191 full-sib families. The 50 k SNP genotype was imputed to WGS using the information from 197 closely related individuals with sequence data. The WGS and 50 k SNPs of the challenged population were then used to estimate genetic parameters, perform a genome-wide association study (GWAS), predict genomic breeding values, and estimate its accuracy for host resistance to sea lice. The heritability of host resistance to sea lice was estimated to be 0.21 and 0.22, while the accuracy of genomic prediction was estimated to be 0.65 and 0.64 for array and WGS data, respectively. In addition, the association test using both array and WGS data did not identify any marker associated with sea lice resistance at the genome-wide level. We conclude that sea lice resistance is a polygenic trait that is moderately heritable. The genomic predictions using medium-density SNP genotyping array were equally good or better than those based on WGS data.

大西洋鲑（Salmo salar）海虱（Lepeophtheirus salmonis）感染是水产养殖领域的一大挑战。多年来，该寄生虫已对治疗性控制化合物产生了免疫力，而非治疗性控制方法已被证实具有压力性，因此有必要研究鲑鱼对海虱的基因组架构。因此，本研究利用全基因组序列（WGS）数据来研究该性状的遗传基础，因为大多数使用较少单核苷酸多态性（SNPs）的研究并未识别出显著的定量性状位点。在完成对191个全同胞家族的3,185条鲑鱼幼鱼的海洋寄生虫挑战测试后，Mowi Genetics AS 提供了该研究的基因型（50 k SNPs）和表型数据。利用与序列数据相关的197个密切相关的个体的信息，对50 k SNP基因型进行了全基因组序列（WGS）的推断。随后，使用挑战群体的WGS和50 k SNPs数据来估计遗传参数、执行全基因组关联研究（GWAS）、预测基因组育种值以及估计其准确度，以评估宿主对海虱的抵抗力。宿主对海虱抵抗力的遗传力估计为0.21和0.22，而基于阵列和WGS数据的基因组预测的准确度估计分别为0.65和0.64。此外，使用阵列和WGS数据进行关联测试并未在基因组水平上识别出与海虱抵抗力相关的任何标记。我们得出结论，海虱抵抗力是一种多基因性状，其遗传力中等。使用中等密度SNP基因分型阵列进行的基因组预测与基于WGS数据的预测效果相当或更优。