Abstract
The relative contributions of both copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) to the additive genetic variance of carcass traits in cattle is not well understood. A detailed understanding of the relative importance of CNVs in cattle may have implications for study design of both genomic predictions and genome-wide association studies. The first objective of the present study was to quantify the relative contributions of CNV data and SNP genotype data to the additive genetic variance of carcass weight, fat, and conformation for 945 Charolais, 923 Holstein-Friesian, and 974 Limousin sires. The second objective was to jointly consider SNP and CNV data in a least absolute selection and shrinkage operator (LASSO) regression model to identify genomic regions associated with carcass weight, fat, and conformation within each of the three breeds separately. A genomic relationship matrix (GRM) based on just CNV data did not capture any variance in the three carcass traits when jointly evaluated with a SNP-derived GRM. In the LASSO regression analysis, a total of 987 SNPs and 18 CNVs were associated with at least one of the three carcass traits in at least one of the three breeds. The quantitative trait loci (QTLs) corresponding to the associated SNPs and CNVs overlapped with several candidate genes including previously reported candidate genes such as MSTN and RSAD2, and several potential novel candidate genes such as ACTN2 and THOC1. The results of the LASSO regression analysis demonstrated that CNVs can be used to detect associations with carcass traits which were not detected using the set of SNPs available in the present study. Therefore, the CNVs and SNPs available in the present study were not redundant forms of genomic data.
Highlights
Carcass value is an important component of both beef-on-beef (Connolly et al, 2016) and beef-on dairy (Berry et al, 2019) breeding objectives
This was more than three times greater than the percentage variance explained by the top principal component of the single nucleotide polymorphism (SNP)-derived genomic relationship matrix (GRM) for either the Charolais or the Limousin populations
The proportion of the variance accounted for by the SNP-derived GRM when considered in a linear mixed model was between 0.032 and 0.291 for the three carcass traits analysed in the three breeds (Supplementary Table S1)
Summary
Carcass value is an important component of both beef-on-beef (Connolly et al, 2016) and beef-on dairy (Berry et al, 2019) breeding objectives. Several CNV association analyses in cattle have identified CNVs associated with important traits, including meat quality traits (da Silva et al, 2016), carcass merit (Zhou et al, 2016), and milk yield (Xu et al, 2014; Prinsen et al, 2017) While these CNV association analyses have identified genomic regions associated with important traits in cattle using only CNV data, it is not always clear whether those same genomic regions could have been detected using another type of genetic marker such as SNPs. A fundamental principle of genome-wide association studies is that linkage disequilibrium exists between the genetic markers and the causal mutation(s) affecting the trait of interest (Balding et al, 2006). While this study by Hay et al (2018) did not directly calculate the additive genetic variance accounted for by CNVs, it suggests that CNVs do account for some of the additive genetic variance of carcass traits which cannot be accounted for by SNP data
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