Animal Production Science Animal Production Science Society
Food, fibre and pharmaceuticals from animals
RESEARCH ARTICLE

Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set

K. Karimi A B F , A. Esmailizadeh A , D. D. Wu C D and C. Gondro E
+ Author Affiliations
- Author Affiliations

A Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.

B Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.

C State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.

D Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.

E School of Environmental and Rural Science, University of New England, Armidale, NSW Australia.

F Corresponding author. Email: karim.karimi81@gmail.com

Animal Production Science - https://doi.org/10.1071/AN16384
Submitted: 14 June 2016  Accepted: 15 November 2016   Published online: 30 January 2017

Abstract

The objective of this study was to present the first map of the copy number variations (CNVs) in Iranian indigenous cattle based on a high-density single nucleotide polymorphism (SNP) dataset. A total of 90 individuals were genotyped using the Illumina BovineHD BeadChip containing 777 962 SNPs. The QuantiSNP algorithm was used to perform a genome-wide CNV detection across autosomal genome. After merging the overlapping CNV, a total of 221 CNV regions were identified encompassing 36.4 Mb or 1.44% of the bovine autosomal genome. The length of the CNV regions ranged from 3.5 to 2252.8 Kb with an average of 163.8 Kb. These regions included 147 loss (66.52%) and 74 gain (33.48%) events containing a total of 637 annotated Ensembl genes. Gene ontology analysis revealed that most of genes in the CNV regions were involved in environmental responses, disease susceptibility and immune system functions. Furthermore, 543 of these genes corresponded to the human orthologous genes, which involved in a wide range of biological functions. Altogether, 73% of the 221 CNV regions overlapped either completely or partially with those previously reported in other cattle studies. Moreover, novel CNV regions involved several quantitative trait loci (QTL)-related to adaptative traits of Iranian indigenous cattle. These results provided a basis to conduct future studies on association between CNV regions and phenotypic variations in the Iranian indigenous cattle.

Additional keywords: bovine genome, CNV annotation, structural variations.


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