Genomic insights into wheatgrass: unravelling genetic diversity, population structure, and evolutionary dynamics in Pseudoroegneria species

Pseudoroegneria species are outcrossing perennial grasses with significant ecological and agricultural value due to its resilience in challenging environmental conditions in the temperate regions. Understanding the extent and pattern of genetic diversity and population structure is essential for the breeding improvement and conservation of these species. In the current research, we analyzed genomic variations of 145 genotypes representing seven species (P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata) from major global lineages, using genotyping-by-sequencing. Different metrics including nucleotide diversity, observed heterozygosity, and Tajima's D were used to evaluate genetic diversity among populations revealing significant variation among species, with P. stipifolia exhibiting the highest diversity and P. spicata the lowest. Population structure analyses, including principal component analysis, admixture inference, and phylogenetic reconstruction, identified six distinct genetic clusters, with P. spicata (a North American species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutionary history of Eurasian Pseudoroegneria species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, and f-branch statistics confirmed close relationships among P. spicata, P. libanotica, and P. tauri, with evidence of unidirectional gene flow between P. stipifolia, P. geniculata, and P. strigosa. These findings highlight the importance of high genetic variation in the P. stipifolia population, suggesting its potential to be a reservoir of valuable alleles for resilient genotypes.