Abstract
BackgroundThe carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process.ResultsA total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit.ConclusionsThe present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.
Highlights
The carcass value of cattle is a function of carcass weight and quality
The single copy number variant (CNV) and single nucleotide polymorphism (SNP) Log R ratio (LRR) association analyses were used to identify individual CNVs and SNP LRRs associated with carcass traits while both the CNV proportion and mean LRR per chromosome analyses were used to determine if overall CNV burden, or mean LRR as a metric possibly reflective of CNV burden, associated with carcass merit
Given that an association was detected for only two of these tests, it suggests that these results may not Shared quantitative trait loci A single CNV located on chromosome 25 at 15.58 Megabase pair (Mb) was associated with all three carcass traits but just in Holstein-Friesians (Table 2)
Summary
The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. The objectives of the present study were two-fold: firstly, to perform genomewide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). Many studies in cattle have attempted to locate quantitative trait loci (QTLs) associated with this genetic variation These studies have generally limited their investigation to biallelic single nucleotide polymorphism (SNP) allele count data [6,7,8]. Genome-wide association analyses in cattle using CNV data are limited in number, but those that exist have identified CNVs associated with meat tenderness in a population of 723 Nelore cattle [17], carcass and growth traits in a population of 2,230 Nelore cattle [18], milk performance in a population of 1,116 Brown Swiss cattle [19], and somatic cell count in 242 Holstein cows [20]
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