Tropical potato breeding: population structure, genetic diversity and putative regions under selection in a Brazilian tetraploid potato germplasm

Potato germplasm developed under tropical conditions harbors valuable genetic diversity. In Brazil, where potato is cultivated under diverse and complex tropical cropping systems, the population structure of locally adapted germplasm remains poorly understood. In this study, we evaluated the genetic structure and diversity of a panel of 450 potato clones, primarily derived from Brazilian national breeding initiatives. Genotyping yielded 18,481 high-quality SNPs for analyses. The panel exhibited a clear population structure with four genetic clusters, largely reflecting their breeding program’s genetic background. The genetic differentiation among the clusters was low (mean F _ST = 0.05), whereas the heterozygosity was high (mean H _O ≈ 0.50; range: 0.38–0.60). Negative inbreeding coefficients (mean F = -0.46) and elevated Tajima’s D values (4.32) suggest selection for increased heterozygosity. Additionally, the footprint analysis revealed regions linked to traits such as tuber quality, plant maturity, and disease resistance when Brazilian vs. foreign clones were compared. Furthermore, genomic regions under selection across the genetic clusters revealed unique gene ontology terms across categories enriched within selected regions. These findings provide insights into the genetic basis of adaptation and differentiation in tropical potato germplasms and offer valuable guidance for parental selection, trait introgression, and strategic management of genetic diversity.