Genetic diversity and population structure of regional rice genotypes from Colombia’s Caribbean and pacific regions: differentiation and ancestry in relation to the 3000 Rice genomes project

Abstract Regional rice genotypes cultivated in Colombia's Caribbean and Pacific regions play a crucial role in food security. However, unfavorable environmental conditions have led to the gradual disappearance of these traditional cultivars. Therefore, analyzing the genetic diversity of these regional genotypes is essential for their conservation and potential use in breeding programs. In this study, we evaluated the genetic diversity, population structure, and ancestry of 72 rice genotypes cultivated in Colombia using single nucleotide polymorphism (SNP) variants. Among these, 68 were regional genotypes, and four were commercial cultivars used as genetic controls. We also compared the ancestry and genetic differentiation of these materials with genotypes from the 3000 Rice Genomes Project (3 K RGP). A total of 77931 SNPs were identified in the Colombian materials, while 64892 SNPs were detected when integrating this information with the 3 K RGP genomes. Genetic population analyses revealed three subpopulations: COL_Pop_1, COL_Pop_2, and COL_Pop_3, with significant genetic differentiation (Phi = 0.718). The highest genetic diversity was observed in COL_Pop_2 (Ho = 0.11, F = 0.61), which primarily included genotypes from the La Mojana region (Caribbean) and Chocó (Pacific). In contrast, COL_Pop_1 and COL_Pop_3 exhibited low heterozygosity (Ho < 0.06) and high inbreeding (F > 0.81), predominantly consisting of materials collected from the La Mojana region, with a few from Chocó. Phylogenetic analysis, supported by the analysis of molecular variance (AMOVA; Phi = 0.349) and pairwise F ST values (> 0.113), revealed significant genetic differences between the Colombian materials and the 3 K RGP reference genomes. Ancestry analysis showed that COL_Pop_1 predominantly belonged to the tropical japonica A group, with admixture from temperate japonica and tropical japonica B, including cultivars such as Colombia 1, Blue Bonnet, and Oryzica Turipana. On the other hand, COL_Pop_2 exhibited ancestry combinations from indica subgroups and temperate japonica , including the Fedearroz 2000 cultivar. These findings highlight the genetic diversity of regional rice cultivated in Colombia’s Caribbean and Pacific regions and underscore their differentiation from the 3 K RGP populations. This provides crucial information for the conservation of these genotypes and their potential use in future rice breeding programs.