Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland.
Natural Resources Institute Finland (LUKE), FI-70210 Kuopio, Finland.
G3 (Bethesda). 2022 Jul 29;12(8). doi: 10.1093/g3journal/jkac137.
We present a comparative genetic analysis of the quantitative trait loci underlying resistance to warm water columnaris disease in 2 farmed rainbow trout (Oncorhynchus mykiss) populations. We provide evidence for the conservation of a major quantitative trait loci on Omy03, and the putative role played by a chromosomal rearrangement on Omy05. A total of 3,962 individuals from the 2 populations experienced a natural Flavobacterium columnare outbreak. Data for 25,823 genome-wide SNPs were generated for both cases (fatalities) and controls (survivors). FST and pairwise additive genetic relationships suggest that, despite being currently kept as separate broodstocks, the 2 populations are closely related. Association analyses identified a major quantitative trait loci on chromosome Omy03 and a second smaller quantitative trait loci on Omy05. Quantitative trait loci on Omy03 consistently explained 3-11% of genetic variation in both populations, whereas quantitative trait loci on Omy05 showed different degree of association across populations and sexes. The quantitative trait loci on Omy05 was found within a naturally occurring, 54.84 cM long inversion which is easy to tag due to a strong linkage disequilibrium between the 375 tagging SNPs. The ancestral haplotype on Omy05 was associated with decreased mortality. Genetic correlation between mortality in the 2 populations was estimated at 0.64, implying that the genetic basis of resistance is partly similar in the 2 populations. Our quantitative trait loci validation identifies markers that can be potentially used to complement breeding value evaluations to increase resistance against columnaris disease, and help to mitigate effects of climate change on aquaculture.
我们对 2 个养殖虹鳟（Oncorhynchus mykiss）群体中抗温水柱状病的数量性状位点进行了比较遗传分析。我们为 Omy03 上主要数量性状位点的保守性提供了证据，并为 Omy05 上染色体重排的可能作用提供了证据。来自这两个群体的 3962 只个体经历了一次自然的柱状屈挠杆菌爆发。为两个案例（死亡）和对照组（幸存者）生成了 25823 个全基因组 SNPs 的数据。FST 和成对的加性遗传关系表明，尽管目前被保持为单独的亲鱼，但这两个群体是密切相关的。关联分析确定了 Omy03 染色体上的一个主要数量性状位点和 Omy05 上的第二个较小的数量性状位点。Omy03 上的数量性状位点在两个群体中始终解释了 3-11%的遗传变异，而 Omy05 上的数量性状位点在不同的群体和性别中表现出不同程度的关联。在 Omy05 上的数量性状位点被发现在一个自然发生的 54.84 cM 长的倒位之内，由于 375 个标记 SNP 之间存在强烈的连锁不平衡，因此很容易标记。Omy05 上的祖先单倍型与死亡率降低有关。这两个群体之间的死亡率遗传相关性估计为 0.64，这意味着这两个群体的抗性遗传基础在一定程度上是相似的。我们的数量性状位点验证确定了可以潜在地用于补充繁殖值评估的标记，以提高对柱状病的抗性，并有助于减轻气候变化对水产养殖的影响。
