Genome-wide detection of copy number variations in Tharparkar cattle

Abstract

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome.

Keywords:

• Copy number variation
• indigenous cattle
• QTLs
• SNP array

Acknowledgment

This study was supported by the ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar. The authors would wish to acknowledge the Director, IVRI, Bareilly, India, for their support to carry out this work.

Ethical approval

All the procedures performed in this study involving animals were following the ethical standards of the Institutional Animal Ethics Committee (IAEC) of ICAR- IVRI, Izatnagar, Bareilly, India {NO.F.1-53/2018-19/J. D(R)}.

Disclosure statement

No potential conflict of interest was reported by the author(s).