Copy number variation of individual cattle genomes using next-generation sequencing
Author
Bickhart, D.M.
Hou, Y.
Schroeder, S.G.
Alkan C.
Cardone, M.F.
Matukumalli L.K.
Song J.
Schnabel, R.D.
Ventura M.
Taylor J.F.
Garcia J.F.
Van Tassell, C.P.
Sonstegard, T.S.
Eichler, E. E.
Liu G.E.
Date
2012Source Title
Genome Research
Print ISSN
10889051
Volume
22
Issue
4
Pages
778 - 790
Language
English
Type
ArticleItem Usage Stats
149
views
views
100
downloads
downloads
Abstract
Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome - wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ∼55.6-Mbp sequence-476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (∼52%, χ 2 test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome. © 2012 by Cold Spring Harbor Laboratory Press.
Keywords
apolipoproteinfatty acid binding protein 2
taurine
adaptation
article
beef cattle
breeding
cattle
chromosome map
comparative genomic hybridization
copy number variation
fluorescence in situ hybridization
gene duplication
gene sequence
genome analysis
lipid metabolism
lipid transport
molecular genetics
nonhuman
nucleotide sequence
pedigree analysis
polymerase chain reaction
priority journal
promoter region
quantitative analysis
quantitative trait locus
sequence analysis
Animals
Cattle
Chromosome Mapping
Chromosomes, Mammalian
Comparative Genomic Hybridization
DNA Copy Number Variations
Fatty Acid-Binding Proteins
Female
Gene Dosage
Gene Duplication
Genome
Genomics
In Situ Hybridization, Fluorescence
Male
Polymerase Chain Reaction
Sequence Analysis, DNA
Species Specificity
Bos
Permalink
http://hdl.handle.net/11693/21516Published Version (Please cite this version)
http://dx.doi.org/10.1101/gr.133967.111Collections
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