Characterization of copy number variation in European cattle

M.R. Upadhyay (Presenter), Megens, H. J. W. C. (Contributor), Vinicius Da Silva (Contributor), M.H.P.W. Visker (Contributor), Groenen, M. (Contributor), Crooijmans, R. P. M. A. (Contributor)

Activity: Other

Description

Poster presentation: Copy number variation (CNV) is characterised by large-scale losses and gains of sequences and contributes significantly to genetic and phenotypic variation. Assessing CNVs across different European cattle breeds might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as result of natural and artificial selection. To explore the pattern of CNVs across various European cattle breeds, we genotyped 149 individuals, which represents five European regions, using Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. On average, animals originating from breeds of the Iberian, Balkan
and Italian, and British region displayed higher abundance of CNVs compared to animals of Dutch or Alpine breeds. A total of 923 CNV regions (CNVRs) were identified by aggregating overlapping CNVs with overlap identified in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high frequent CNVRs between different European cattle
populations. The CNVRs identified in the present study overlapped with more than 900 genes involved in many traits. In addition, we also detected and validated a CNV overlapping the Kit gene in English Longhorn cattle which has been identified previously in Belgian blue, white park and Galloway cattle and is associated with colour-sidedness. We provide a comprehensive overview of the
distribution of CNVs in the genomes of various European cattle breeds. Our results also hint at the important role of purifying selection and genomic drift in the distribution of CNVs in genome of various European cattle breeds.
Period17 Jul 2017
Event title36th conference of the International Society of Animal Genetics (ISAG)
Event typeConference
LocationDublin, Ireland
Degree of RecognitionInternational