GWAS & Selection signatures

Genomic Footprints of Selection and Adaptation in 40 breeds of Indian Zebu Cattle

---

Abstract

India's diverse zebu cattle serve as a testament to adaptation and breed differentiation. To investigate the genomic footprints of selection, adaptation, and differentiation across 40 Zebu breeds, we developed the 788K high-density IndiGau SNP chip from whole-genome sequencing data of 176 animals of 43 breeds with an average coverage of 30X, addressing the limitations of existing commercial arrays that inadequately represent Indian Zebu genomes. Genotyping 2,169 animals from 40 breeds with IndiGau yielded a higher mean MAF (0.27) than the BovineHD 770K array (0.17), demonstrating IndiGau's superior informativeness for indigenous Zebu cattle. From the genotype data, we comprehensively mapped genetic diversity (Fst, ROH, FROH), population structure (phylogeny, admixture, Ne), phenotypic associations (GWAS for milk, dual, and draft groups; height; and adaptive traits such as coat colour and climatic-zone contrasts), conserved regions of low diversity (CRsLD), and breed-specific selection signatures. A strong north - south ancestry split with a recent decline in effective population size was observed in Indian Zebu.A strong selective sweep (~680 kb) on chromosome 6 in dairy breeds harbors LEF1, OSTC, COL25A1, and ETNPPL, genes central to mammary development, milk protein glycosylation, and metabolic pathways underlying efficient lactation.The positive selection of this region was confirmed through haplotype homogeneity, iHS, and Tajima's D analyses. Similarly, a selective region on chromosome 19 containing ALOX12 and MINK1 was identified in dwarf breeds (Vechur and Malnad Gidda), indicating the role of these genes in reduced body size. Further, a region on chromosome 13 harboring several coat color genes - ASIP, AHCY, ACSS2, GGT7, PIGU, DYNLR1, ITCH and RALY was found positively selected in white cattle (Gaoloa, Ongole, Nagori and Tharparkar) on comparison with Red - Brown cattle (Red Khandari, Red Sindhi and Gir).On chromosome 18, positive selection around MC1R was detected in cold-adapted Ladakhi cattle, contrasting with hot-climate breeds (Gir, Rathi, Tharparkar, Nagori, Mewati, and Kankrej), suggesting dark pigmentation - mediated adaptation to high-altitude, cold environments. The climate-zone comparison revealed shared genomic signals across all breeds on chromosomes 22 and 6, encompassing genes such as GPX1, TREX1, MITF, and CORIN, which play critical roles in cellular stress response, oxidative balance, immune regulation, and pigmentation pathways. By integrating PCA-assisted XGBoost machine learning, we achieved highly accurate breed assignment in an independent validation cohort. Here, We demonstrated the utility of the IndiGau 788K high-density SNP array in uncovering the genomic diversity, breed differentiation, and adaptive signatures among breeds of Zebu cattle. Key regions associated with milk production, stature, coat color, thermoregulation, immunity, and stress tolerance were identified, reflecting strong influence of environment and historical breeding practices on Zebu evolution. This study offers genomic insights that will guide conservation efforts, breed improvement programs, and the sustainable utilization of these uniquely adapted livestock resources.

Keywords: 2026

How to Cite:

Gandham, R., Azam, S., Topno, N., Praharaj, M., Periasamy, K., Das, S., Patil, H., Suthar, D., Hosamani, N., Arya, S., Vohra, V., BMK, R., Bhatia, A., Mukesh, M., Kumar, A., Dige, M. & Majumdar, S., (2026) “Genomic Footprints of Selection and Adaptation in 40 breeds of Indian Zebu Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2295254. doi: https://doi.org/10.31274/wcgalp.24334

Rights: 1