Table1_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）的海洋寄生物（Lepeophtheirus salmonis）感染是水产养殖领域的一大挑战。历经岁月，此寄生虫已对治疗性控制化合物产生了免疫力，且非治疗性控制方法已被证实具有压力性，因此研究鲑鱼对海洋寄生物抵抗力的基因组结构显得尤为必要。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数量性状位点。在完成对191个全同胞家族、共计3,185尾鲑鱼幼苗的海洋寄生物挑战测试后，Mowi Genetics AS为本研究提供了基因型（50 k SNPs）和表型数据。利用与序列数据紧密相关的197个个体的信息，将50 k SNP基因型推断为WGS。随后，利用挑战人群的WGS和50 k SNPs数据来估算遗传参数，执行全基因组关联分析（GWAS），预测基因组育种值，并估计其对宿主抵抗海洋寄生物的准确性。宿主对海洋寄生物的遗传力估计为0.21和0.22，而基因组预测的准确性估计为0.65和0.64，分别对应于阵列和WGS数据。此外，使用阵列和WGS数据进行关联测试，在基因组水平上未识别出与海洋寄生物抵抗性相关的任何标记。我们得出结论，海洋寄生物抵抗性是一种多基因性状，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。