Genome‐wide association studies for epistatic genetic effects on fertility and reproduction traits in Holstein cattle

作者：Kristen Alves, Luiz F. Brito, Mehdi Sargolzaei, Flávio S. Schenkel · 发表于：Journal of Animal Breeding and Genetics · 年份：2023 · DOI：10.1111/jbg.12813 · 被引用次数：10 · 研究领域：Genetic and phenotypic traits in livestock、Genetic Mapping and Diversity in Plants and Animals、Reproductive Physiology in Livestock

Abstract Non‐additive genetic effects are well known to play an important role in the phenotypic expression of complex traits, such as fertility and reproduction. In this study, a genome scan was performed using 41,640 single nucleotide polymorphism (SNP) markers to identify genomic regions associated with epistatic (additive‐by‐additive) effects in fertility and reproduction traits in Holstein cattle. Nine fertility and reproduction traits were analysed on 5825 and 6090 Holstein heifers and cows with phenotypes and genotypes, respectively. The Marginal Epistasis Test (MAPIT) was used to identify SNPs with significant marginal epistatic effects at a chromosome‐wise 5% and 10% false discovery rate (FDR) level. The −log 10 ( p ) values were adjusted by the genomic inflation factor (λ) to correct for the potential bias on the p ‐values and minimize the possible effects of population stratification. After adjustments, MAPIT enabled the identification of genomic regions with significant marginal epistatic effects for heifers on BTA5 for age at first insemination, BTA3 and BTA24 for non‐return rate (NRR); BTA16 and BTA28 for gestation length (GL); BTA1, BTA4 and BTA17 for stillbirth (SB). For the cow traits, MAPIT enabled the identification of regions on BTA11 for GL, BTA11 and BTA16 for SB and BTA19 for calf size (CZ). An additional approach for mapping epistasis in a genome‐wide association study was also proposed, in which the genome scan was performed using estimates of epistat...