The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.Tibetan hulless barley | Triticeae evolution | genetic diversity | adaptation | selective sweep

Whether the caryopsis of barley is naked or covered is controlled by the Nud gene encoding an ethylene response factor (ERF) family transcription factor (TF) of the AP2/ERF TF superfamily that is involved in the lipid biosynthesis pathway. In covered barley, lipids on the surface of caryopses act as a glue for their tight adhesion with hulls. Separation of hulls in naked barley is due to the absence of surface lipids on caryopses. A natural deletion event of Nud was found to be the determinant of naked caryopsis and had been proposed as the monophyletic origin of domesticated naked barley. In the present study, we re-sequenced the nud locus in 162 barleys, comprising 79 covered and 83 naked barleys varieties. Besides the normal deletion mutation of Nud contributing to naked caryopsis, we found a novel allele of Nud, designated as nud1.g, distinctly in three naked barleys collected from Tibet. nud1.g contains a non-synonymous SNP T643A when compared with the functional Nud gene. Genetic analysis indicated that the SNP T643A of nud1.g co-segregates with the naked phenotype. The nud1.g gene was expressed normally in the three naked barleys. Furthermore, in silico prediction of functionally conserved sites and 3D structures showed that the amino acid substitution (valine to aspartate) caused by SNP T643A may lead to a dramatic structural alteration of NUD that may result in loss of function. This study provides evidence of a new origin of the naked phenotype of domesticated barley in Tibet.