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Aegilops umbellulata Zhuk., a wild diploid wheat-related species, has been used as a genetic resource for several important agronomic traits. However, its genetic variations have not been comprehensively studied. We sequenced RNA from 114 accessions of Ae. umbellulata to evaluate DNA polymorphisms and phenotypic variations. Bayesian clustering and phylogenetic analysis based on SNPs detected by RNA sequencing revealed two divergent lineages, UmbL1 and UmbL2. The main differences between them were in the sizes of spikes and spikelets, and culm diameter. UmbL1 is divided into two sublineages, UmbL1e and UmbL1w. These genetic differences corresponded to geographic distributions. UmbL1e, UmbL1w, and UmbL2 are found in Turkey, Iran/Iraq, and Greece, respectively. Although UmbL1e and UmbL1w were genetically similar, flowering time and other morphological traits were more distinct between these sublineages than those between the lineages. This discrepancy can be explained by the latitudinal and longitudinal differences in habitats. Specifically, latitudinal clines of flowering time were clearly observed in Ae. umbellulata, strongly correlated with solar radiation in the winter season. This observation implies that latitudinal differences are a factor in differences in the flowering times of Ae. umbellulata. Differences in flowering time could influence other morphological differences and promote genetic divergence between sublineages. [ABSTRACT FROM AUTHOR]