Development history, genomic diversity, population structure, and selection signatures in worldwide Boer goat populations

The Boer goat, a key global meat breed originating from South Africa, has been exported for breeding in over 70 countries, leading to diverse selection pressures and environmental adaptations. In this context, the main objectives of this study were to quantify genome-wide diversity, breed structure, and selection signatures in Boer goats from nine countries to identify shared and population-specific adaptation and production-related signals. Genomic information of 321 Boer goats from nine populations worldwide was analysed: Australia (AUS), Canada (CAN), New Zealand (NZL), South Africa (ZAF), Switzerland (CHE), Tanzania (TZA), Uganda (UGA), United States (USA), and Zimbabwe (ZWE). Genetic diversity varied markedly among populations. The ZAF population exhibited the lowest observed heterozygosity (0.360) and the highest fraction of the genome in runs of homozygosity, suggesting recent inbreeding or strong selection. Population structure analyses, including principal component analysis and ADMIXTURE (optimal K = 8), revealed clear genetic differentiation. AUS Boer goats were the most divergent, while others formed clusters indicating shared ancestry. Four complementary selection signature methods, Fixation index, Divergence index, integrated haplotype score, and cross-population extended haplotype homozygosity, identified 4 706 unique genes under putative selection. No identified genes were common to all populations, indicating strong local adaptation, but 35 candidate genes were identified across five to six populations, highlighting shared selection for core production traits like growth, metabolism, and reproduction. Key shared genes regulating metabolism, including PPP2R2B, SCP2, and PRELID2, were detected in six populations. Regulatory hub genes such as MAPK3, HIF1A, PRKACA, and CREB1 were also detected, playing crucial roles in coordinating important biological processes. Population-specific adaptations included heat tolerance genes in AUS, cold adaptation and reproductive performance genes in CAN, and disease resistance genes in ZAF. These results underscore the need to monitor local genetic diversity while improving production traits in Boer goat breeding worldwide.