Background Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. Results By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. Conclusion We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding. Electronic supplementary material The online version of this article (10.1186/s13059-019-1744-x) contains supplementary material, which is available to authorized users.

Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. However, the molecular basis and regulatory network of barley grain development is not well understood at present. Here, we investigated the transcriptional dynamics of barley grain development through RNA sequencing at four developmental phases, including early prestorage phase (3 days post anthesis (DPA)), late prestorage or transition phase (8 DPA), early storage phase (13 DPA), and levels off stages (18 DPA). Transcriptome profiling found that pronounced shifts occurred in the abundance of transcripts involved in both primary and secondary metabolism during grain development. The transcripts’ activity was decreased during maturation while the largest divergence was observed between the transitions from prestorage phase to storage phase, which coincided with the physiological changes. Furthermore, the transcription factors, hormone signal transduction-related as well as sugar-metabolism-related genes, were found to play a crucial role in barley grain development. Finally, 4771 RNA editing events were identified in these four development stages, and most of the RNA editing genes were preferentially expressed at the prestore stage rather than in the store stage, which was significantly enriched in “essential” genes and plant hormone signal transduction pathway. These results suggested that RNA editing might act as a ‘regulator’ to control grain development. This study systematically dissected the gene expression atlas of barley grain development through transcriptome analysis, which not only provided the potential targets for further functional studies, but also provided insights into the dynamics of gene regulation underlying grain development in barley and beyond.

β-Glucan is an important chemical found in cereals, tremendously beneficial to human health. In this study, β-glucan contents in wild and cultivated barley from representative regions worldwide were investigated. Results exhibited that coefficient of variation of β-glucan content of wild and cultivated barley was 24.18% and 13.99%, respectively. The β-glucan contents of studied wild barley accessions were ranged from 3.26% to 7.67% while cultivated barley varieties were ranged from 2.68% to 4.74%. A significant difference of β-glucan content (p ≤ 0.001) was found between wild and cultivated barely. Wild barley showed a higher β-glucan content and variation than cultivated barley. This study gives an idea about elite germplasms for genetic improvement and shed light to trace barley domestication in relation to grain metabolite view.

Microgeographic adaptation is a fundamental driving force of evolution, but the underlying causes remain undetermined. Here, the phenotypic, genomic and transcriptomic variations of two wild barley populations collected from sharply divergent and adjacent micro-geographic sites to identify candidate genes associated with edaphic local adaptation are investigated. Common garden and reciprocal transplant studies show that large phenotypic differentiation and local adaptation to soils occur between these populations. Genetic, phylogenetic and admixture analyses based on population resequencing show that significant genetic divergences occur between basalt and chalk populations. These divergences are consistent with the phenotypic variations observed in the field. Genome sweep analyses reveal 162.7 Mb of selected regions driven by edaphic local adaptation, in which 445 genes identified, including genes associated with root architecture, metal transport/detoxification, and ABA signaling. When the phenotypic, genomic and transcriptomic data are combined, HvMOR, encoding an LBD transcription factor, is determined to be the vital candidate for regulating the root architecture to adapt to edaphic conditions at the microgeographic scale. This study provides new insights into the genetic basis of edaphic adaptation and demonstrates that edaphic factors may contribute to the evolution and speciation of barley.

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