Abstract
Epistasis is widely considered important, but epistasis studies lag those of SNP effects. Genome-wide association study (GWAS) using 76,109 SNPs and 294,079 first-lactation Holstein cows was conducted for testing pairwise epistasis effects of five production traits and three fertility traits: milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FPC), protein percentage (PPC), and daughter pregnancy rate (DPR). Among the top 50,000 pairwise epistasis effects of each trait, the five production traits had large chromosome regions with intra-chromosome epistasis. The percentage of inter-chromosome epistasis effects was 1.9% for FPC, 1.6% for PPC, 10.6% for MY, 29.9% for FY, 39.3% for PY, and 84.2% for DPR. Of the 50,000 epistasis effects, the number of significant effects with log10(1/p) ≥ 12 was 50,000 for FPC and PPC, and 10,508, 4763, 4637 and 1 for MY, FY, PY and DPR, respectively, and A × A effects were the most frequent epistasis effects for all traits. Majority of the inter-chromosome epistasis effects of FPC across all chromosomes involved a Chr14 region containing DGAT1, indicating a potential regulatory role of this Chr14 region affecting all chromosomes for FPC. The epistasis results provided new understanding about the genetic mechanism underlying quantitative traits in Holstein cattle.
Highlights
Epistasis effects are widely considered important [1,2,3,4], but the number of reported epistasis effects is far behind the number of single-point effects [2,4,5]
The purpose of this study was to identify pairwise epistasis effects associated with five dairy production traits and one fertility trait using the same Holstein cattle population that we previously used for a large-scale Genome-wide association study (GWAS) to detect SNP additive and dominance effects [19]
Protein yield that had the highest frequency of inter-chromosome epistasis effects among the five production traits had 34.9% of inter-chromosome A × A effects (Table 2)
Summary
Epistasis effects are widely considered important [1,2,3,4], but the number of reported epistasis effects is far behind the number of single-point effects [2,4,5]. Genome-wide association study (GWAS) in several dairy cattle breeds have reported many single-SNP effects on dairy traits [6,7,8,9,10,11,12,13,14,15,16,17,18,19,20]. The U.S Holstein cattle have uniquely large sample sizes [25,26] and provide an opportunity to identify epistasis effects associated with dairy traits using GWAS. The purpose of this study was to identify pairwise epistasis effects associated with five dairy production traits and one fertility trait using the same Holstein cattle population that we previously used for a large-scale GWAS to detect SNP additive and dominance effects [19]. For each SNP pair, we tested four types of epistasis effects, additive × additive, additive × dominance, dominance × additive, and dominance × dominance, and investigated the intra- and inter-chromosome epistasis effects
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