Landscape of copy number variations in Bos taurus: individual - and inter-breed variability

BMC Genomics
M MielczarekJ Szyda

Abstract

The number of studies of Copy Number Variation in cattle has increased in recent years. This has been prompted by the increased availability of data on polymorphisms and their relationship with phenotypes. In addition, livestock species are good models for some human phenotypes. In the present study, we described the landscape of CNV driven genetic variation in a large population of 146 individuals representing 13 cattle breeds, using whole genome DNA sequence. A highly significant variation among all individuals and within each breed was observed in the number of duplications (P < 10-15) and in the number of deletions (P < 10-15). We also observed significant differences between breeds for duplication (P = 0.01932) and deletion (P = 0.01006) counts. The same variation CNV length - inter-individual and inter-breed differences were significant for duplications (P < 10-15) and deletions (P < 10-15). Moreover, breed-specific variants were identified, with the largest proportion of breed-specific duplications (9.57%) found for Fleckvieh and breed-specific deletions found for Brown Swiss (5.00%). Such breed-specific CNVs were predominantly located in intragenic regions, however in Simmental, one deletion present in five individuals ...Continue Reading

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Software Mentioned

Variant Effect Predictor
Simmental
SAMtools
BWA
CNVnator
Pindel
Kobas
MEM
Gene2Farm
NGS

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