Abstract

The Mapuche fowl is one of the most representative animal genetic resources in Chile, traditionally maintained in small-scale backyard production systems. Despite its cultural and productive relevance, genomic studies evaluating its genetic diversity and population structure remain limited. The objective of this study was to characterize the genetic diversity and population structure of the Mapuche fowl using genome-wide SNP markers obtained through DArTseq technology. A total of 91 chickens representing seven populations-including three Mapuche fowl subtypes, Gallina de la Pasion, two commercial breeds, and one commercial hybrid line, were analyzed using 43,017 high-quality SNP markers generated through DArTseq. Genetic diversity parameters, population differentiation (FST), multivariate analyses (PCA and DAPC), phylogenetic relationships, population structure based on sNMF, and analysis of molecular variance (AMOVA) were evaluated. The results revealed intermediate levels of genetic diversity across populations, with expected heterozygosity ranging from 0.166 to 0.236. The Mapuche fowl varieties showed the highest levels of genetic diversity and formed a closely related genetic group with low levels of differentiation (FST = 0.026-0.032). In contrast, commercial breeds exhibited greater genetic divergence. Population structure analyses consistently showed clear differentiation between commercial and local populations, while the Mapuche fowl varieties shared ancestry components and clustered closely together. AMOVA indicated that most genetic variation occurred within populations (72.93%), whereas 13.25% was attributed to differences among populations. These findings highlight the genetic uniqueness of the Mapuche fowl and provide a genomic basis for its conservation and sustainable management as a valuable poultry genetic resource in Chile.