Genomic Predictions and Genome-Wide Association Study of Resistance Against Piscirickettsia salmonis in Coho Salmon (Oncorhynchus kisutch) Using ddRAD Sequencing.
Genomic Predictions and Genome-Wide Association Study of Resistance Against Piscirickettsia salmonis in Coho Salmon (Oncorhynchus kisutch) Using ddRAD Sequencing.
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DOI：
10.1534/g3.118.200053
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发表时间：
2018-03-28
期刊：
影响因子：
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通讯作者：
Yáñez JM
中科院分区：
文献类型：
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作者：
Barría A;Christensen KA;Yoshida GM;Correa K;Jedlicki A;Lhorente JP;Davidson WS;Yáñez JM
鲑鱼立克次体病是影响银鲑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。遗传改良抗鲑性鲍氏体病已被认为是控制养殖鱼类这种传染病的一种可行的选择。测序基因分型（GBS）策略允许对具有数千个单核苷酸多态性（SNP）的数百个个体进行基因分型，这可用于进行全基因组关联研究（GWAS）并使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）测序来剖析养殖的银鲑种群中对鲑鱼疫霉的抗性的遗传结构，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，以确定通过使用全基因组分子信息加速该性状遗传改良的潜力。来自33个全同胞家系（17个高抗性和16个高敏感）的共764个个体被实验性地攻击鲑鱼疫霉，并且使用ddRAD测序来测定其基因型。在人群中共鉴定了9，389个SNP标记。这些标记物用于测试基因组选择模型，并比较不同的GWAS方法用于以死亡日（DD）和二元存活（BIN）测量的抗性。对于DD和BIN，基因组选择模型显示出比传统的基于谱系的最佳线性无偏预测（PBLUP）方法更高的准确性。该模型显示了高达95%和155%的改善分别超过PBLUP。一个与B细胞发育相关的SNP被鉴定为与对鲑鱼P. salmonis的抗性相关的潜在功能候选者，定义为DD。
Piscirickettsia salmonis is one of the main infectious diseases affecting coho salmon (Oncorhynchus kisutch) farming, and current treatments have been ineffective for the control of this disease. Genetic improvement for P. salmonis 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 P. salmonis 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 P. salmonis 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 P. salmonis defined as DD.