Rafter, Pierce and Purfield, Deirdre C. and Berry, Donagh P. and Parnell, Andrew and Gormley, I. Claire and Kearney, J. Francis and Coffey, Mike P. and Carthy, Tara R. (2018) Characterization of copy number variants in a large multibreed population of beef and dairy cattle using high-density single nucleotide polymorphism genotype data. Journal of Animal Science, 96 (10). pp. 4112-4124. ISSN 0021-8812

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Abstract

Copy number variants (CNVs) are a form of genomic variation that changes the structure of the genome through deletion or duplication of stretches of DNA. The objective of the present study was to characterize CNVs in a large multibreed population of beef and dairy bulls. The CNVs were called on the autosomes of 5,551 cattle from 22 different beef and dairy breeds, using 2 freely available software suites, QuantiSNP and PennCNV. All CNVs were classified into either deletions or duplications. The median concordance between PennCNV and QuantiSNP, per animal, was 18.5% for deletions and 0% for duplications. The low concordance rate between PennCNV and QuantiSNP indicated that neither algorithm, by itself, could identify all CNVs in the population. In total, PennCNV and QuantiSNP collectively identified 747,129 deletions and 432,523 duplications; 80.2% of all duplications and 69.1% of all deletions were present only once in the population. Only 0.154% of all CNVs identified were present in more than 50 animals in the population. The distribution of the percentage of the autosomes that were composed of deletions, per animal, was positively skewed, as was the distribution for the percentage of the autosomes that were composed of duplications, per animal. The first quartile, median, and third quartile of the distribution of the percentage of the autosomes that were composed of deletions were 0.019%, 0.037%, and 0.201%, respectively. The first quartile, median, and third quartile of the distribution of the percentage of the autosomes that were composed of duplications were 0.013%, 0.028%, and 0.076%, respectively. The distributions of the number of deletions and duplications per animal were both positively skewed. The interquartile range for the number of deletions per animal in the population was between 16 and 117, whereas for duplications it was between 8 and 23. Per animal, there tended to be twice as many deletions as duplications. The distribution of the length of deletions was positively skewed, as was the distribution of the length of duplications. The interquartile range for the length of deletions in the population was between 25 and 101 kb, and for duplications the interquartile range was between 46 and 235 kb. Per animal, duplications tended to be twice as long as deletions. This study provides a description of the characteristics and distribution of CNVs in a large multibreed population of beef and dairy cattle.

Item Type:	Article
Additional Information:	This work was supported by Science Foundation Ireland (SFI) principal investigator award grant number 14/IA/2576.
Keywords:	bovine; BovineHD; copy number variant; PennCNV; QuantiSNP; structural variant;
Academic Unit:	Faculty of Science and Engineering > Mathematics and Statistics Faculty of Science and Engineering > Research Institutes > Hamilton Institute
Item ID:	13273
Identification Number:	https://doi.org/10.1093/jas/sky302
Depositing User:	Andrew Parnell
Date Deposited:	24 Sep 2020 14:32
Journal or Publication Title:	Journal of Animal Science
Publisher:	American Society of Animal Science
Refereed:	Yes
Funders:	Science Foundation Ireland (SFI)
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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