Genetic Diversity and Phylogenetic Relationships of Cultivated and Wild Urochloa Species Conserved in the ILRI Forage Genebank

Abstract

Understanding the genetic diversity and evolutionary relationships within the genus Urochloa is essential for effective germplasm conservation and the development of improved forage cultivars. In this study, we assessed the genetic diversity, population structure, and phylogenetic relationships of 545 accessions representing 17 Urochloa species conserved in the ILRI Forage Genebank for the last four decades at its Zway field site in Ethiopia. Large numbers of genome-wide SNP and SilicoDArT markers were generated by the GBS based Diversity Arrays Technology (DArT)seq platform, providing valuable resources for genetic analysis in Urochloa spp. From these, we filtered a subset of high-quality SNP and SilicoDArT markers suitable for cross-species analysis, which was then used to characterize species differentiation and to detect admixture patterns across wild and cultivated species. Hierarchical clustering grouped all 545 accessions into two major groups, clearly separating the brizantha complex (U. brizantha, U. decumbens, and U. ruziziensis) from the rest of the species, which were primarily wild and less domesticated relatives. The analysis further identified four well-defined phylogenetic clades, largely consistent with previously reported evolutionary relationships within the genus. The three clades, primarily composed of wild species, exhibited clear genetic separation, high diversity, and strong geographic structuring with limited admixture, reflecting reproductive isolation (their apomictic nature) and differing ploidy levels that have driven local adaptation. In contrast, the brizantha complex exhibited extensive admixture and comparatively lower genetic variation, consistent with their historical polyploidization events, shared ancestry, and domestication (particularly in the key forage species U. brizantha and U. decumbens). Population structure analysis using the admixture model revealed multiple genetically distinct clusters and populations across clades, including species-specific clusters, mixed-species groups, and within-species populations, highlighting substantial genetic variation within and among species shaped by historical gene flow (particularly among diploid and sexual types), differences in ploidy levels, and adaptive divergence. The identification of genetically differentiated populations in wild species underscores their potential as reservoirs of unique adaptive traits such as drought tolerance, waterlogging and disease resistances, and nutrient-use efficiency. Meanwhile, the genetically diverse cultivated gene pool provides valuable resources for improving biomass productivity, nutritional quality, and resilience to environmental stress. Our findings provide a comprehensive genetic overview of one of the most important tropical forage genera and offer strategic insights for the conservation and utilization of Urochloa genetic resources.