Genetic Diversity and Population Structure of Advanced Lima Bean Breeding Lines Revealed by SNP Markers

Abstract The lima bean ( Phaseolus lunatus L.) is a legume of high agronomic and nutritional importance, particularly for smallholder farming in northeastern Brazil. The breeding program at the Federal University of Piauí (UFPI, Brazil) developed lines from biparental crosses, selecting traits of agronomic relevance for crop improvement, such as determinate growth habit, earliness, and yield. This study evaluated the genetic diversity and population structure of 34 ninth-generation lines using 3002 single-nucleotide polymorphism markers generated using genotyping-by-sequencing. Observed heterozygosity (H O ) was lower than the expected heterozygosity (H E ), with mean values of 0.01 and 0.19, respectively. Line H25-66 exhibited the highest number of private alleles and marked genetic divergence, whereas the lines from population H46 were highly homogeneous, with intermediate differentiation observed in the remaining populations. Multivariate analyses, including principal component analysis, Neighbor-joining clustering, heatmaps, and sparse non-negative matrix factorization ancestry plots, consistently revealed well-defined genetic groups. The consistent identification of highly homogeneous groups, such as population H46, together with strongly divergent materials, particularly line H25-66, demonstrates that the program harbored both stabilized genetic backgrounds suitable for cultivar development and contrasting sources of variation that can be strategically exploited in parental selection, enabling crosses between divergent genotypes to generate novel allele combinations. These findings provide valuable insights for guiding strategic breeding decisions and accelerating the development of improved lima bean cultivars adapted to Brazilian production systems.