Genomic diversity reveals breeding pools in Brazilian tetraploid potato germplasm

Abstract

Potato germplasm developed under tropical conditions may contain diversity for breeding, but the Brazilian materials remain poorly characterized. We evaluated 449 tetraploid potato clones, most from Brazilian breeding programs, with 12,595 SNPs. Dosage-aware analyses and STRUCTURE supported four breeding-related clusters. Genetic differentiation between Brazilian and foreign populations was low (Φ ST  = 0.04), indicating extensive use of external germplasm in Brazilian breeding. In contrast, differentiation among the genetic clusters was moderate (Φ ST  = 0.22), suggesting preferable restricted parental use in their pipelines. Heterozygosity and inbreeding estimates depended strongly on genotype encoding. Tajima’s D was positive (4.46), and suggested selection favoring increased heterozygosity. Three genome scans identified 92 shared candidate outlier SNPs within broad LD-based windows. The functional annotations generated hypotheses related to stress responses for further studies to be functionally validated. The results provide insights at a panel-level baseline for germplasm management and candidate prioritization in Brazilian potato breeding.