Genome-wide genetic differentiation between Guaymí and Guabalá Creole cattle from Panama

Abstract

Background: Panamanian Creole cattle are valuable animal genetic resources, but the genomic differentiation between the Guaymí and Guabalá populations remains incompletely characterized. Aim: To quantify population structure and genome-wide differentiation between Guaymí and Guabalá cattle and to prioritize an empirical set of highly differentiated single-nucleotide polymorphisms (SNPs) for future validation. Methods: The initial dataset comprised 69 animals (37 Guaymí and 32 Guabalá) genotyped with the Axiom BovMDv3 medium-density array. After individual and marker call-rate filtering (≥0.98), restriction to autosomes 1–29, and minor allele frequency filtering (≥0.05), 63 animals (35 Guaymí and 28 Guabalá) and 30,289 SNPs remained. Linkage disequilibrium (LD) pruning retained 4,237 SNPs for principal component analysis (PCA). Genetic differentiation was estimated using Weir and Cockerham\'s fixation index (FST). Empirical differentiation outliers were defined as the upper 1% of the observed per-SNP FST distribution. Annotation was restricted to direct gene overlaps in UMD3.1.1 Results: PCA separated the two populations along PC1, which explained 9.53% of the variance; PC2 explained 5.05%. The weighted genome-wide FST was 0.1206 (unweighted mean, 0.1039). The empirical 99th percentile was FST = 0.5128, and the 303 SNPs above this value comprised the outlier set. Of the 303 complete-dataset outliers, 162 (53.5%) were recovered in both relationship-controlled subsets. A total of 136 outliers directly overlapped 123 annotated genes. FHOD3, KIAA1211, NCKAP5, and NRXN3 each contained three empirical outlier SNPs. Outlier counts and densities varied across autosomes after normalization by the number of quality-controlled SNPs. Conclusion: Guaymí and Guabalá cattle show clear genome-wide structure and moderate overall differentiation. The empirical outliers are priorities for replication and functional evaluation rather than definitive evidence of selection. The results support managing the two populations as distinct genetic resources while preserving within-population diversity.