College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Beijing Zhongyu Pig Breeding Co., Ltd, Beijing, 100194, China.
Anim Genet. 2021 Oct;52(5):749-753. doi: 10.1111/age.13131. Epub 2021 Aug 17.
The dominance effect is a kind of non-additive effect due to the interaction between alleles at the same locus. Quantitative traits such as growth traits in farm animals have been found to be influenced by dominance effects. However, dominance effects are usually ignored in the genome-wide association study (GWAS) of complex traits for farm animals. In this study, we performed GWAS and genetic parameters estimation for the two traits age at 100 kg (AGE) and backfat thickness at 100 kg (BF) of 3572 Large White pigs. The pigs were from three breeding farms of China and were genotyped by an in-house designed 50k SNP chip. Our results showed significant non-zero variance for the dominance effect of AGE, while the dominance effect of BF was not significant. Using a GWAS model accounting for both additive and dominance effects, we identified three additive and two dominance significant SNPs for the trait AGE. For the trait BF, three genome-wide significant additive SNPs were detected, but no significant SNP was found for the dominance effect. In total, six important functional genes (NPAS3, USP16, PARN, ARL15, GPC3, ABHD4) near significant SNPs were identified as candidate genes associated with AGE or BF. Notably, ARL15 and PARN were associated with AGE near the dominance association signals. Overall, the newly detected SNPs and newly identified candidate genes in our study added new information about the genetic architectures of growth and fatness traits in pigs, and have the potential to be applied to the pig breeding program in the future.
显性效应是一种由于同一基因座上等位基因相互作用而产生的非加性效应。已发现农场动物的生长等数量性状受显性效应的影响。然而，在对农场动物的复杂性状进行全基因组关联研究（GWAS）时，通常会忽略显性效应。在这项研究中，我们对 3572 头大白猪的 100kg 年龄（AGE）和 100kg 背膘厚（BF）这两个性状进行了 GWAS 和遗传参数估计。这些猪来自中国的三个养殖场，采用内部设计的 50k SNP 芯片进行了基因分型。我们的结果表明，AGE 的显性效应存在显著的非零方差，而 BF 的显性效应不显著。使用同时考虑加性和显性效应的 GWAS 模型，我们鉴定出了与 AGE 性状相关的三个加性和两个显性显著 SNP。对于 BF 性状，检测到三个全基因组显著的加性 SNP，但未发现显性效应的显著 SNP。总共鉴定到六个重要的功能基因（NPAS3、USP16、PARN、ARL15、GPC3、ABHD4）位于显著 SNP 附近，这些基因可能与 AGE 或 BF 相关。值得注意的是，ARL15 和 PARN 与 AGE 附近的显性关联信号有关。总体而言，本研究新检测到的 SNP 和新鉴定的候选基因增加了猪生长和脂肪性状遗传结构的新信息，未来有潜力应用于猪的选育计划。
