Abstract

BackgroundFour traits related to carcass performance have been identified as economically important in beef production: carcass weight, carcass fat, carcass conformation of progeny and cull cow carcass weight. Although Holstein-Friesian cattle are primarily utilized for milk production, they are also an important source of meat for beef production and export. Because of this, there is great interest in understanding the underlying genomic structure influencing these traits. Several genome-wide association studies have identified regions of the bovine genome associated with growth or carcass traits, however, little is known about the mechanisms or underlying biological pathways involved. This study aims to detect regions of the bovine genome associated with carcass performance traits (employing a panel of 54,001 SNPs) using measures of genetic merit (as predicted transmitting abilities) for 5,705 Irish Holstein-Friesian animals. Candidate genes and biological pathways were then identified for each trait under investigation.ResultsFollowing adjustment for false discovery (q-value < 0.05), 479 quantitative trait loci (QTL) were associated with at least one of the four carcass traits using a single SNP regression approach. Using a Bayesian approach, 46 QTL were associated (posterior probability > 0.5) with at least one of the four traits. In total, 557 unique bovine genes, which mapped to 426 human orthologs, were within 500kbs of QTL found associated with a trait using the Bayesian approach. Using this information, 24 significantly over-represented pathways were identified across all traits. The most significantly over-represented biological pathway was the peroxisome proliferator-activated receptor (PPAR) signaling pathway.ConclusionsA large number of genomic regions putatively associated with bovine carcass traits were detected using two different statistical approaches. Notably, several significant associations were detected in close proximity to genes with a known role in animal growth such as glucagon and leptin. Several biological pathways, including PPAR signaling, were shown to be involved in various aspects of bovine carcass performance. These core genes and biological processes may form the foundation for further investigation to identify causative mutations involved in each trait. Results reported here support previous findings suggesting conservation of key biological processes involved in growth and metabolism.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-837) contains supplementary material, which is available to authorized users.

Highlights

  • Four traits related to carcass performance have been identified as economically important in beef production: carcass weight, carcass fat, carcass conformation of progeny and cull cow carcass weight

  • There have been no studies to date that have investigated the association of single nucleotide polymorphism (SNP) genotypes with carcass performance utilizing measures of genetic merit estimated in dairy breeds

  • Many studies have reported carcass Quantitative trait loci (QTL) in regions containing genes with a known role in animal growth, little is known about the mechanisms or underlying biological pathways involved in growth or carcass traits

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Summary

Introduction

Four traits related to carcass performance have been identified as economically important in beef production: carcass weight, carcass fat, carcass conformation of progeny and cull cow carcass weight. Carcass traits, related to animal growth, are critical to the biological and economical efficiency of cattle production and, as such, there is great interest in understanding the underlying genomic architecture influencing these traits. Quantitative trait loci (QTL) associated with a particular trait can be used to predict disease risk or genetic merit of an animal [1,2] This information may be used to investigate the molecular mechanisms and biological pathways involved in phenotypic variation between animals. Many studies have reported carcass QTL in regions containing genes with a known role in animal growth (such as the myostatin gene on bovine chromosome 2 [8,9]), little is known about the mechanisms or underlying biological pathways involved in growth or carcass traits. By using estimates of individual animal genetic merit, generated from the accumulation of phenotypic information on relatives, the accuracy of the phenotype can be considerably greater and the statistical power of the association study is greater for the same number of genotyped individuals

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