Barría Agustín, Christensen Kris A, Yoshida Grazyella M, Correa Katharina, Jedlicki Ana, Lhorente Jean P, Davidson William S, Yáñez José M
Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile.
Doctorado en Acuicultura, Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, 8820808 Chile.
G3 (Bethesda). 2018 Mar 28;8(4):1183-1194. doi: 10.1534/g3.118.200053.
is one of the main infectious diseases affecting coho salmon () farming, and current treatments have been ineffective for the control of this disease. Genetic improvement for resistance has been proposed as a feasible alternative for the control of this infectious disease in farmed fish. Genotyping by sequencing (GBS) strategies allow genotyping of hundreds of individuals with thousands of single nucleotide polymorphisms (SNPs), which can be used to perform genome wide association studies (GWAS) and predict genetic values using genome-wide information. We used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic architecture of resistance against in a farmed coho salmon population and to identify molecular markers associated with the trait. We also evaluated genomic selection (GS) models in order to determine the potential to accelerate the genetic improvement of this trait by means of using genome-wide molecular information. A total of 764 individuals from 33 full-sib families (17 highly resistant and 16 highly susceptible) were experimentally challenged against and their genotypes were assayed using ddRAD sequencing. A total of 9,389 SNPs markers were identified in the population. These markers were used to test genomic selection models and compare different GWAS methodologies for resistance measured as day of death (DD) and binary survival (BIN). Genomic selection models showed higher accuracies than the traditional pedigree-based best linear unbiased prediction (PBLUP) method, for both DD and BIN. The models showed an improvement of up to 95% and 155% respectively over PBLUP. One SNP related with B-cell development was identified as a potential functional candidate associated with resistance to defined as DD.
是影响银大麻哈鱼（）养殖的主要传染病之一，目前的治疗方法对控制这种疾病无效。已提出通过遗传改良提高抗病性，作为控制养殖鱼类这种传染病的一种可行选择。测序基因分型（GBS）策略可对数百个个体进行数千个单核苷酸多态性（SNP）的基因分型，可用于进行全基因组关联研究（GWAS）并利用全基因组信息预测遗传值。我们使用双酶切限制性位点相关DNA（ddRAD）测序来剖析养殖银大麻哈鱼群体对的抗病遗传结构，并鉴定与该性状相关的分子标记。我们还评估了基因组选择（GS）模型，以确定利用全基因组分子信息加速该性状遗传改良的潜力。对来自33个全同胞家系（17个高抗性和16个高易感性）的764个个体进行了针对的实验性攻毒，并使用ddRAD测序分析了它们的基因型。在该群体中总共鉴定出9389个SNP标记。这些标记用于测试基因组选择模型，并比较以死亡天数（DD）和二元存活（BIN）衡量的抗病性的不同GWAS方法。对于DD和BIN，基因组选择模型均显示出比传统的基于系谱的最佳线性无偏预测（PBLUP）方法更高的准确性。与PBLUP相比，这些模型分别提高了95%和155%。一个与B细胞发育相关的SNP被鉴定为与以DD定义的对的抗性相关的潜在功能候选基因。
