Intraspecific lineage divergence in Aegilops umbellulata Zhuk.: its association with variation in morphological and reproductive traits

Abstract Aegilops umbellulata Zhuk. is a wild diploid wheat species (UU genome) native to the Eastern Mediterranean and Middle East. To characterize the natural variation, 202 accessions were analyzed across their distribution ranges at the molecular and phenotypic levels. Population structure analysis revealed two major genetic lineages, UmbL1 and UmbL2. UmbL1 was further divided into western (UmbL1w) and eastern (UmbL1e) sublineages, whereas UmbL2 was restricted to the far west. Two additional groups, Intermediate-w and Intermediate-e, were genetically and geographically intermediate between UmbL1w and UmbL2 and between UmbL1w and UmbL1e, respectively. Among the 24 morphological and phenological traits, flowering time, awn length, trichome level, and seed-related traits showed clear lineage-associated variations. The UmbL1w accessions tended to flower later and had longer awns, higher trichome levels, and smaller seeds, with more spikelets per spike, whereas the UmbL1e accessions tended to flower earlier and produced larger seeds with fewer spikelets. The UmbL2 accessions showed intermediate flowering times and broad seeds with few spikelets. Genome-wide association analysis identified loci potentially associated with the trichome level, and comparative analysis highlighted a candidate gene on chromosome 3U. These findings provide insights into the diversity of Ae. umbellulata and its potential use in bread wheat breeding.