Sequencing & Pangenomes

Identification and Characterization of Copy Number Variations Regions in African and South Asian zebu cattle

---

Abstract

Zebu cattle are well-known for their ability to adapt to challenging environments, particularly their heat tolerance and drought resistance, which enable them to thrive in tropical and subtropical regions. These adaptive traits are inherited but complex as they are influenced by both genetic factors and environmental conditions. One genetic factor of interest is copy number variations (CNVs), which are structural changes in the genome caused by the gain or loss of DNA segments. CNVs can impact gene structure, expression and dosage making them potentially significant for understanding adaptive traits. However, the connection between CNVs and zebu cattle adaptability traits has not been extensively explored. In this study, we identified and characterized CNV regions (CNVRs) in 40 cattle from eight distinct breeds, including African zebu breeds (Goudali, Zebu Peuhl, Angoni and Malagasy Zebu) and South Asian zebu breeds (Deoni, Kangayam, White Cattle and Shwe Ni). Five samples were taken from each breed, and whole genome sequenced at 20à— coverage. Using two read depths calling programs CNVnator and CNVcaller we identified 11,305 CNVRs covering 6.84% of the genome. Of these, 9,506 CNVRs were shared across all breeds, while 1,411 were specific to African zebu and 388 were specific to South Asian zebu. The CNVR sizes ranged from 1 kb to 930.8 kb with an average length of 16.4 kb. Among the identified CNVRs, 6,585 were deletions, 3,095 were duplications and 1,645 were mixed/complex. Gene annotation revealed that 10,917 CNVRs in African zebu were associated with 3,414 genes, while 9,893 CNVRs in South Asian zebu were linked to 2,216 genes. African zebu genes were enriched in 24 Gene Ontology biological processes (GOBPs) and 15 KEGG pathways, while South Asian zebu genes showed enrichment in 18 GOBP and 10 KEGG pathways. Key pathways included glucagon and cAMP signalling, which regulate glycogen metabolism a crucial factor for efficient energy storage and growth traits. Renal development pathways were also enriched, highlighting the importance of efficient kidney function in zebu cattle, for maintaining water balance, and conserving resources in hot, arid environments. The study also mapped CNVRs to quantitative trait loci (QTLs). In African zebu, 63 QTLs were identified, including 32 linked to carcass, 14 to reproduction, 2 to growth, 6 to disease resistance, 3 to milk composition, and 6 to other traits. Similarly, 53 QTLs were mapped in South Asian zebu, with 29 linked to carcass, 11 to reproduction, 5 to disease resistance, and 2 to growth traits. The abundance of QTLs related to carcass traits, fertility, and disease resistance underscores the zebu's resilience in tropical environments. Our findings reveal the genetic basis of zebu cattle's adaptability and highlight CNVRs as key to resilience, providing a foundation for improving their traits in diverse environments.

Keywords: 2026

How to Cite:

Mavunga, T., Sölkner, J., Mészáros, G., Pichler, R., Zoroboguai, L., Chileshe, B., Ralambomanana, N., Ramasamy, S., LGS, L., Thandar, E., Phem, M., Muchadeyi, F., Ressaissi, Y. & Periasamy, K., (2026) “Identification and Characterization of Copy Number Variations Regions in African and South Asian zebu cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2271921. doi: https://doi.org/10.31274/wcgalp.23408

Rights: 1