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J Dairy Sci. 2017 Jul;100(7):5515-5525. doi: 10.3168/jds.2016-11987. Epub 2017 May 10.

Analysis of copy number variations in Holstein-Friesian cow genomes based on whole-genome sequence data.

Author information

1
Biostatistics group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631 Wroclaw, Poland.
2
The Group of Molecular Epidemiology, Fondazione Parco Tecnologico Padano, Via Einstein Albert, Lodi, Lo 26900, Italy.
3
The Group of Molecular Epidemiology, Fondazione Parco Tecnologico Padano, Via Einstein Albert, Lodi, Lo 26900, Italy; Department of Veterinary Medicine, Università di Milano, Via Celoria 10, 20133 Milano, Italy.
4
The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy SA 5371, South Australia.
5
Department of Genetics, Plant Breeding and Biotechnology, West Pomeranian University of Technology, Piastów 17, 70-310 Szczecin, Poland.
6
Biostatistics group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631 Wroclaw, Poland. Electronic address: joanna.szyda@upwr.edu.pl.

Abstract

Thirty-two whole genome DNA sequences of cows were analyzed to evaluate inter-individual variability in the distribution and length of copy number variations (CNV) and to functionally annotate CNV breakpoints. The total number of deletions per individual varied between 9,731 and 15,051, whereas the number of duplications was between 1,694 and 5,187. Most of the deletions (81%) and duplications (86%) were unique to a single cow. No relation between the pattern of variant sharing and a family relationship or disease status was found. The animal-averaged length of deletions was from 5,234 to 9,145 bp and the average length of duplications was between 7,254 and 8,843 bp. Highly significant inter-individual variation in length and number of CNV was detected for both deletions and duplications. The majority of deletion and duplication breakpoints were located in intergenic regions and introns, whereas fewer were identified in noncoding transcripts and splice regions. Only 1.35 and 0.79% of the deletion and duplication breakpoints were observed within coding regions. A gene with the highest number of deletion breakpoints codes for protein kinase cGMP-dependent type I, whereas the T-cell receptor α constant gene had the most duplication breakpoints. The functional annotation of genes with the largest incidence of deletion/duplication breakpoints identified 87/112 Kyoto Encyclopedia of Genes and Genomes pathways, but none of the pathways were significantly enriched or depleted with breakpoints. The analysis of Gene Ontology (GO) terms revealed that a cluster with the highest enrichment score among genes with many deletion breakpoints was represented by GO terms related to ion transport, whereas the GO term cluster mostly enriched among the genes with many duplication breakpoints was related to binding of macromolecules. Furthermore, when considering the number of deletion breakpoints per gene functional category, no significant differences were observed between the "housekeeping" and "strong selection" categories, but genes representing the "low selection pressure" group showed a significantly higher number of breakpoints.

KEYWORDS:

Gene Ontology term; Kyoto Encyclopedia of Genes and Genomes pathway; copy number variation; next-generation sequencing

PMID:
28501396
DOI:
10.3168/jds.2016-11987
[Indexed for MEDLINE]

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