Epistatic interactions associated with fatty acid concentrations of beef from angus sired beef cattle

Abstract

BackgroundConsumers are becoming increasingly conscientious about the nutritional value of their food. Consumption of some fatty acids has been associated with human health traits such as blood pressure and cardiovascular disease. Therefore, it is important to investigate genetic variation in content of fatty acids present in meat. Previously publications reported regions of the cattle genome that are additively associated with variation in fatty acid content. This study evaluated epistatic interactions, which could account for additional genetic variation in fatty acid content.ResultsEpistatic interactions for 44 fatty acid traits in a population of Angus beef cattle were evaluated with EpiSNPmpi. False discovery rate (FDR) was controlled at 5 % and was limited to well-represented genotypic combinations. Epistatic interactions were detected for 37 triacylglyceride (TAG), 36 phospholipid (PL) fatty acid traits, and three weight traits. A total of 6,181, 7,168, and 0 significant epistatic interactions (FDR < 0.05, 50-animals per genotype combination) were associated with Triacylglyceride fatty acids, Phospholipid fatty acids, and weight traits respectively and most were additive-by-additive interactions. A large number of interactions occurred in potential regions of regulatory control along the chromosomes where genes related to fatty acid metabolism reside.ConclusionsMany fatty acids were associated with epistatic interactions. Despite a large number of significant interactions, there are a limited number of genomic locations that harbored these interactions. While larger population sizes are needed to accurately validate and quantify these epistatic interactions, the current findings point towards additional genetic variance that can be accounted for within these fatty acid traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3235-8) contains supplementary material, which is available to authorized users.

An assessment of genomic connectedness measures in Nellore cattle

“… Li et al (2012) detected significant additive and dominant effects for 19 individual FA in commercial beef steers. Kramer et al (2016) identified epistatic interactions associated with FA concentrations in Angus cattle. Thus, the use of connectedness metrics including additive and non-additive gene effects may help to improve the quality of genetic value comparisons in breeding programs.…”

Identification of genome-wide SNP-SNP interactions associated with important traits in chicken

“…In other words, it is not possible to separate true interaction effects from haplotype effects if the two SNPs are located on the same chromosome. Therefore, in order to increase the power to detect the true interaction effects for the growth and carcass traits, we deleted interactions that occurred on the same chromosome [ 12 ]. Third, the smaller the number of birds in any given genotype class, the less likely it is to get a good estimate of the genotype effect.…”

“…Third, the smaller the number of birds in any given genotype class, the less likely it is to get a good estimate of the genotype effect. Thus, in order to increase the power to detect the true interactions, only those interactions that contained at least 10 animals in every genotype combination were considered [ 12 ]. We carried out the filter of the interactions according to these criteria in order to reduce the chances of obtaining false-positive results (type I errors).…”

“…The P -values of the epistatic effects were Bonferroni corrected for multiple testing (5.96 × 10 9 independent tests, with a significance threshold of P < 0.05), which resulted in P < 8.39 × 10 −12 as a significance threshold. Significant interactions, including additive by additive (AA), additive by dominance (AD) or dominance by additive (DA) and dominance by dominance (DD), between two SNPs on the same chromosome were deleted because these interactions may potentially be markers for a haplotype effect that contains a single QTL [ 12 ]. The remaining significant SNP interactions were further filtered with the criterion that only those interaction with at least 10 animals in every genotype combination were considered [ 12 ], which is roughly equivalent to a 15% minor allele frequency for each variant in an additive by additive epistatic interaction.…”

“…Recently, genome wide SNP-SNP interaction analysis have been conducted in humans [ 4 , 9 ] and domestic livestock species [ 10 – 12 ]. In chicken ( Gallus gallus ), it has been suggested that epistatic interactions between genes (or QTLs) are important for variation in quantitative traits [ 8 , 13 , 14 ].…”