Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent

Abstract

Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1–13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.

Keywords:

• CNV/CNVRs
• hot and cold adaptation
• functional annotation
• Bos taurus/Bos indicus
• Kankrej/Hallikar/Ladhaki/Siri

Acknowledgments

The authors are grateful to the Director, ICAR-NBAGR, Karnal, as well as the Incharges of various livestock farms and Veterinary Officers of State Animal Husbandry Departments, for providing the required facilities and assistance in collecting blood samples for this study.

Disclosure statement

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

Data availability statement

We have uploaded the data on ICAR-Krishi portal and is in public domain with the URL http://krishi.icar.gov.in/jspui/handle/123456789/69832.

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

The authors acknowledge the funding support received from the ICAR-National Bureau of Animal Genetic Resources, Karnal from the institute project (project code 7.70).