Doctorado en Acuicultura, Programa Cooperativo: Universidad de Chile. Universidad Católica del Norte. Pontificia Universidad Católica de Valparaíso, Chile.
Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile.
Genes (Basel). 2022 Dec 30;14(1):114. doi: 10.3390/genes14010114.
Genome-wide association studies (GWAS) allow the identification of associations between genetic variants and important phenotypes in domestic animals, including disease-resistance traits. Whole Genome Sequencing (WGS) data can help increase the resolution and statistical power of association mapping. Here, we conduced GWAS to asses he facultative intracellular bacterium , which affects farmed rainbow trout, , in Chile using imputed genotypes at the sequence level and searched for candidate genes located in genomic regions associated with the trait. A total of 2130 rainbow trout were intraperitoneally challenged with under controlled conditions and genotyped using a 57K single nucleotide polymorphism (SNP) panel. Genotype imputation was performed in all the genotyped animals using WGS data from 102 individuals. A total of 488,979 imputed WGS variants were available in the 2130 individuals after quality control. GWAS revealed genome-wide significant quantitative trait loci (QTL) in Omy02, Omy03, Omy25, Omy26 and Omy27 for time to death and in Omy26 for binary survival. Twenty-four (24) candidate genes associated with resistance were identified, which were mainly related to phagocytosis, innate immune response, inflammation, oxidative response, lipid metabolism and apoptotic process. Our results provide further knowledge on the genetic variants and genes associated with resistance to intracellular bacterial infection in rainbow trout.
全基因组关联研究（GWAS）允许鉴定遗传变异与家畜重要表型之间的关联，包括抗病性性状。全基因组测序（WGS）数据可以帮助提高关联作图的分辨率和统计能力。在这里，我们使用序列水平的推断基因型进行了 GWAS 分析，以评估影响智利养殖虹鳟鱼的兼性细胞内细菌 ，并搜索与该性状相关的基因组区域中位于候选基因。总共 2130 条虹鳟鱼在受控条件下用 进行了腹膜内挑战，并使用 57K 单核苷酸多态性（SNP）面板进行了基因型分型。在所有基因分型的动物中，使用来自 102 个个体的 WGS 数据进行了基因型推断。在经过质量控制后，2130 个个体中有 488,979 个推断的 WGS 变体可用。GWAS 揭示了 Omy02、Omy03、Omy25、Omy26 和 Omy27 中与死亡时间相关的全基因组显著数量性状位点（QTL），以及 Omy26 中与二元生存相关的 QTL。鉴定出 24 个与 抗性相关的候选基因，主要与吞噬作用、先天免疫反应、炎症、氧化反应、脂质代谢和凋亡过程有关。我们的研究结果为虹鳟鱼抵抗细胞内细菌感染的遗传变异和相关基因提供了进一步的知识。
