ArticleAnimal bioscience2025
Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India.
Article in Animal bioscience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Genetic Diversification and Population Admixture Signatures in Yunnan Native Cattle.Animals : an open access journal from MDPI · 2026Article
- Genome-wide characterization of copy number variants and their functional relevance in indigenous draught cattle of South Asia.PloS one · 2026Article
- Mapping copy number variable regions correlated with reproduction and production traits in Karan Fries cattle mammalian genomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
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5 authors.
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Abstract
objectiveIdentification 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.
methodsRead 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.
resultsA 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.
conclusionThe genome-wide CNVRs identified in the present study produced genomewide partial CNV map in indigenous cattle breeds of Tamil Nadu.
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