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Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India |
S. Vani1,2 
, D. Balasubramanyam1
, K. G. Tirumurugaan3
, A. Gopinathan1
, S. M. K. Karthickeyan1,*
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1Department of Animal Genetics and Breeding, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600 051, India
2Current address: Department of Animal Genetics and Breeding, College of Veterinary Science, Proddatur, Sri Venkateswara Veterinary University, Andhra Pradesh 516360, India
3Department of Animal Biotechnology, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600 051, India |
Correspondence:
S. M. K. Karthickeyan, Tel: +91-9791103976, Fax: +91-9080232154, Email: kannikarthi@yahoo.co.in
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Received: 13 December 2023 • Revised: 4 February 2024 • Accepted: 4 July 2024 |
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| Abstract |
Objective
Identification of large scale structural polymorphisms (copy number variations [CNVs]) of more than 50 bp between the individuals of a species would help in knowing genetic diversity, phenotypic variability, adaptability to tropical environment and disease resistance.
Methods
Read depth-based method implemented in CNVnator was used for calling copy number variant regions on sequenced data obtained from whole-genome sequencing from 15 pooled samples belonging to five draught cattle breeds of Tamil Nadu.
Results
A total of 11,605 CNV regions (CNVRs) were observed covering a genome size of 18.63 percent. Among these, 11,459 were restricted to autosomes, consisting of 11,013 deletions, 353 duplications and 93 complex events. These CNVRs were annotated to 4,989 candidate genes. A total of 8,291 numbers of CNVRs were shared among the five cattle breeds as also supported by principal component analysis and STRUCTURE analyses and 1,172 CNVRs were breed-specific. Four out of five selected breed-specific CNVRs were validated using real-time polymerase chain reaction. Genes with CNVRs are related to milk production (BTN1A1, ABCA1, and LAP3), disease resistance (TLR4 and DNAH8), adaptability (SOD1, CAST, and SMARCAL1), growth (EGFR, NKAIN3), reproduction (BRWD1 and PDE6D), meat and carcass traits (MAP3K5 and NCAM1) and exterior (ATRN and MITF) traits. Gene enrichment analysis based on the gene list retrieved from the CNVRs disclosed over-represented terms (p<0.01) associated with milk fat production. NETWORK analysis had identified 13 putative candidate genes involved in milk fat percentage, milk fat yield, lactation persistency, milk yield, heat tolerance, calving ease, growth and conformation traits.
Conclusion
The genome-wide CNVRs identified in the present study produced genomewide partial CNV map in indigenous cattle breeds of Tamil Nadu. |
| Keywords:
Bos indicus Cattle; Copy Number Variations; Tamil Nadu; Whole Genome Sequencing |
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