Type

Journal Article

Authors

Tara R. Carthy
Mike P Coffey
J. Francis Kearney
I. Claire Gormley
Andrew Parnell
Donagh P. Berry
Deirdre C Purfield
Pierce Rafter

Subjects

Veterinary

Topics
variants population density dairy cattle beef cattle beef breeds animals genotype population number

Characterization of copy number variants in a large multibreed population of beef and dairy cattle using high-density single nucleotide polymorphism genotype data (2018)

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.
Collections Ireland -> Maynooth University -> Type = Article
Ireland -> Maynooth University -> Academic Unit = Faculty of Science and Engineering: Research Institutes: Hamilton Institute
Ireland -> Maynooth University -> Status = Published
Ireland -> Maynooth University -> Academic Unit = Faculty of Science and Engineering: Mathematics and Statistics

Full list of authors on original publication

Tara R. Carthy, Mike P Coffey, J. Francis Kearney, I. Claire Gormley, Andrew Parnell, Donagh P. Berry, Deirdre C Purfield, Pierce Rafter

Experts in our system

1
Tara R. Carthy
Teagasc
Total Publications: 3
 
2
M. P. Coffey
Teagasc
Total Publications: 10
 
3
Andrew Parnell
Maynooth University
Total Publications: 45
 
4
D P Berry
Teagasc
Total Publications: 243
 
5
Deirdre C Purfield
Teagasc
Total Publications: 23