Genomic Characterization of Peruvian Creole Goats from Southern Peru and their relationship with Iberian, Brazilian, and Argentine Populations

Abstract This study presents the first genome-wide characterization of Southern Peruvian Creole goats, defining their genetic structure and relationship to Iberian and other South American breeds. Using SNP data, we analyzed goats from Ayacucho (PE_AYA) and Ica (PE_ICA) and compared them with Iberian, Brazilian, and Argentine goats to explore their genetic relationships. Principal Component Analysis (PCA) revealed clear differentiation among populations, with Iberian breeds forming a compact cluster and Peruvian Creole goats occupying an intermediate position, partially overlapping with Argentine Creole (CRE) and Nubian (NBN) populations. Pairwise fixation index (FST) estimates confirmed the closest affinities of PE_AYA and PE_ICA with South American populations (FST = 0.02–0.04), while moderate differentiation was observed with Iberian breeds (FST = 0.08–0.09). Admixture analyses (K = 3–5) consistently grouped PE_AYA and PE_ICA, sharing common ancestry with CRE and partially with NBN. Phylogenetic analysis further supported these results, separating Iberian from South American clades, while clustering PE_AYA, PE_ICA, and CRE as a distinct subgroup. Collectively, our results demonstrate that while Peruvian Creole goats retain traces of Iberian ancestry, they have evolved into a unique genetic resource shaped by centuries of local adaptation and regional admixture. This study fills a major knowledge gap by integrating Peruvian Creole goats into global genomic frameworks, and provides an essential foundation for the design of conservation and sustainable breeding strategies tailored to local production systems.