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

Journal of Dairy Science
Magda MielczarekJoanna Szyda

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 duplicatio...Continue Reading

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Citations

Mar 6, 2019·Animal : an International Journal of Animal Bioscience·J SzydaK Wojdak-Maksymiec
Jun 19, 2019·Proceedings of the National Academy of Sciences of the United States of America·David C RinkerJohn G Gibbons
Oct 14, 2019·Journal of Dairy Science·Md Mesbah-UddinGoutam Sahana

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