Conservation & local programs

Genetic Diversity and Population Structure of Gir Cattle in Mexico Based on SNP Molecular Markers.

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Abstract

Mexican Gir cattle are an important genetic resource for tropical livestock production. Genomic characterization of their diversity and population structure using high-density markers is essential to guide breeding programs for productivity and tropical adaptation while preserving genetic diversity. This study aimed to characterize the genomic diversity and population structure of Mexican Gir cattle using SNP markers, evaluating both within-breed diversity and their position within a global context of bovine breeds. For intra-breed analysis, 226 hair samples were collected from Gir cattle across three tropical herds in Mexico, randomly sampled from Mexican Zebu Breeders Association records. Hair follicles were genotyped using the GGP Indicus 50K chip, with quality control performed in PLINK v1.90 (call rate ≥0.90, MAF ≥0.01, autosomal SNPs, LD pruning), retaining 212 animals and 28,394 SNPs. Additionally, these Gir cattle were integrated with 1,543 animals from 134 bovine breeds genotyped with BovineSNP50 (UMD3.0) from a public repository. After published quality control procedures (call rate ≥0.90, exclusion of monomorphic loci), 43,043 SNPs were available. Combining both datasets yielded 9,095 common markers used for inter-breed analyses. Subsequently, observed (HO) and expected (HE) heterozygosity, three genomic inbreeding coefficients, and runs of homozygosity (ROH; criteria: ≥1 Mb, ≥20 consecutive SNPs) were evaluated. Between-breed diversity was analyzed through multidimensional scaling (MDS), pairwise FST, identity by state (IBS), and ADMIXTURE (K=2-30). Intra-breed genetic diversity was high (HO=0.40; HE=0.38), while genomic inbreeding was low according to three independent estimators: F_IS=-0.04, F_GRM=-0.02, and F_ROH=0.012 calculated using ROH ≥ 1 Mb, suggesting lineage admixture or recent gene flow. ROH analysis revealed predominance of short segments (1-2 Mb), containing 5,353 ROH with average length of 1.18 Mb, consistent with historical rather than recent inbreeding. Correlations between estimators were significant, particularly between F_ROH and F_ROH 1-2Mb (r=0.82), confirming most homozygosity derives from ancestral matings. MDS clustered Mexican Gir with Asian zebu, particularly Gir from India and Pakistan. FST values were lowest with Gir, Red Sindhi, Lohani, Rojhan, and Tharparkar. The IBS similarity matrix showed greater similarity with other Gir populations and Asian breeds than with unrelated zebu breeds. ADMIXTURE confirmed ancestry components concordant with documented introduction history from India through Brazil and the United States. Mexican Gir cattle exhibited broad genomic variability, low recent inbreeding, and a population structure shaped by multiple Asian indicine introgressions. The predominance of short ROH segments suggested historical inbreeding, favorable for breeding programs. Close relationships with Asian Gir populations confirmed preservation of original genetic heritage. Based on these results, the population structure and genetic diversity of Mexican Gir cattle provide a solid foundation for intensifying selection toward productivity and tropical adaptation while protecting genetic diversity. Results support implementing genomic monitoring, balanced use of breeding sires to prevent bottlenecks, and strategic introduction of external germplasm.

Keywords: 2026

How to Cite:

Domà­nguez Viveros, J., Hidalgo, J., Martà­nez Rocha, R., Núà±ez Domà­nguez, R., Ordeà±ez Baquera, P., Ramà­rez Valverde, R. & VALERIO HERNàNDEZ, J., (2026) “Genetic Diversity and Population Structure of Gir Cattle in Mexico Based on SNP Molecular Markers.”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2295915. doi: https://doi.org/10.31274/wcgalp.24383

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