Rafter, Pierce and Gormley, Isobel Claire and Parnell, Andrew C. and Naderi, Saeid and Berry, Donagh P. (2021) The Contribution of Copy Number Variants and Single Nucleotide Polymorphisms to the Additive Genetic Variance of Carcass Traits in Cattle. Frontiers in Genetics, 12. ISSN 1664-8021

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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.

Item Type:	Article
Additional Information:	Cite as:Rafter, P., Gormley, I.C., Parnell, A.C., Naderi, S. & Berry, D.P. 2021, "The Contribution of Copy Number Variants and Single Nucleotide Polymorphisms to the Additive Genetic Variance of Carcass Traits in Cattle", Frontiers in genetics, vol. 12, pp. 761503-761503.
Keywords:	CNV; Charolais; Holstein-Friesian; Limousin; SNP; LASSO;
Academic Unit:	Faculty of Science and Engineering > Mathematics and Statistics Faculty of Science and Engineering > Research Institutes > Hamilton Institute Faculty of Social Sciences > Research Institutes > Irish Climate Analysis and Research Units, ICARUS
Item ID:	17989
Identification Number:	https://doi.org/10.3389/fgene.2021.761503
Depositing User:	Andrew Parnell
Date Deposited:	04 Jan 2024 14:33
Journal or Publication Title:	Frontiers in Genetics
Publisher:	Frontiers Media SA
Refereed:	Yes
URI:	Publisher
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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