Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
Department of Animal and Poultry Production, Damanhour University, Damanhour, Egypt.
Genet Sel Evol. 2018 Oct 5;50(1):48. doi: 10.1186/s12711-018-0405-y.
Heterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide polymorphisms (SNPs) with significant dominance effects associated with variation in growth and carcass traits and to understand the mode of action of these associations.
Illumina BovineSNP50 genotypes and phenotypes for 11 growth and carcass traits were available for 6796 multi-breed and crossbred beef cattle. After performing quality control, 42,610 SNPs and 6794 animals were used for further analyses. A single-SNP GWAS for the joint association of additive and dominance effects was conducted in purebred, crossbred, and combined datasets using the ASReml software. Genomic breed composition predicted from admixture analyses was included in the mixed effect model to account for possible population stratification and breed effects. A threshold of 10% genome-wide false discovery rate was applied to declare associations as significant. The significant SNPs with dominance association were mapped to their corresponding genes at 100 kb.
Seven SNPs with significant dominance associations were detected for birth weight, weaning weight, pre-weaning daily gain, yearling weight and marbling score across the three datasets at a false discovery rate of 10%. These SNPs were located on bovine chromosomes 1, 3, 4, 6 and 21 and mapped to six putative candidate genes: U6atac, AGBL4, bta-mir-2888-1, REPIN1, ICA1 and NXPH1. These genes have interesting biological functions related to the regulation of gene expression, glucose and lipid metabolism and body fat mass. For most of the identified loci, we observed over-dominance association with the studied traits, such that the heterozygous individuals at any of these loci had greater genotypic values for the trait than either of the homozygous individuals.
Our results revealed very few regions with significant dominance genetic effects across all the traits studied in the three datasets used. Regarding the SNPs that were detected with dominance associations, further investigation is needed to determine their relevance in crossbreeding programs assuming that dominance effects are the main cause of (or contribute usefully to) heterosis.
杂种优势被认为是由显性效应引起的。我们使用多品种和杂交肉牛的数据进行了全基因组关联分析（GWAS），以鉴定与生长和胴体性状变异相关的具有显著显性效应的单核苷酸多态性（SNP），并了解这些关联的作用模式。
6796 头多品种和杂交肉牛的 Illumina BovineSNP50 基因型和 11 个生长和胴体性状的表型数据可用于质量控制后，42610 个 SNP 和 6794 个个体用于进一步分析。使用 ASReml 软件在纯系、杂交和组合数据集中进行了单 SNP GWAS，以联合分析加性和显性效应。从混合分析中预测的基因组品种组成被包含在混合效应模型中，以解释可能的群体分层和品种效应。应用 10%全基因组假发现率阈值宣布关联显著。具有显性关联的显著 SNP 被映射到它们在 100kb 处对应的基因上。
在三个数据集的出生体重、断奶体重、断奶前日增重、1 岁体重和大理石花纹评分中，检测到 7 个具有显著显性关联的 SNP，假发现率为 10%。这些 SNP 位于牛染色体 1、3、4、6 和 21 上，映射到六个假定的候选基因：U6atac、AGBL4、bta-mir-2888-1、REPIN1、ICA1 和 NXPH1。这些基因具有有趣的生物学功能，与基因表达、葡萄糖和脂质代谢以及体脂肪量的调节有关。对于大多数鉴定出的基因座，我们观察到与研究性状的过显性关联，即这些基因座中的任何杂合个体的性状基因型值都大于任何纯合个体。
我们的结果显示，在所研究的三个数据集的所有性状中，具有显著显性遗传效应的区域非常少。关于检测到具有显性关联的 SNP，需要进一步研究它们在杂交计划中的相关性，假设显性效应是（或有助于）杂种优势的主要原因。
