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Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

•Understanding the mechanisms of cold stress response at the molecular level is crucial for improving crops against the stresses without yield penalty.•The ICE-CBF/DREB1 pathway is the most crucial plant cold acclimation response pathway.•There are limited research works on cold tolerance improvement in forage species which is most likely due to the complex genomic compositions of these non-model species.•High-throughput phenomics and genomics-based plant improvement methods and the latest genome-editing techniques are promising approaches to improve cold tolerance of forages.