Barley remains dated to the dawn of agriculture have been found at several archaeological sites 1,2 . In addition to indications that barley was an important food crop, recent excavations have fuelled speculation that beverages from fermented grains may have motivated early Neolithic hunter-gatherers to erect some of humankind's oldest monuments 3,4 . Moreover, brewing beer may also have played a role in the eastward spread of the crop after its initial domestication in the Fertile Crescent 5,6 . Since 2012, both genetic research and crop improvement in barley have benefited from a partly ordered draft sequence assembly 7 . This community resource has underpinned gene isolation 8,9 and population genomic studies 10 . However, these and other efforts have also revealed limitations of the current draft assembly. The limitations are often direct consequences of two characteristic genomic features: the extreme abundance of repetitive elements, and the severely reduced frequency of meiotic recombination in pericentromeric regions 11 .These factors have limited the contiguity of whole-genome assemblies to kilobase-sized sequences originating from low-copy regions of the genome. Thus, a detailed investigation of the composition of the repetitive fraction of the genome-including expanded gene families-and of the distribution of targets of selection and crop improvement in (genetically defined) pericentromeric regions has been beyond reach.Here we present a map-based reference sequence of the barley genome including the first comprehensively ordered assembly of the pericentromeric regions of a Triticeae genome. The resource highlights a conspicuous distinction between distal and proximal regions of chromosomes that is reflected by the intranuclear chromatin organization. Moreover, chromosomal compartments are differentiated by an exponential gradient of gene density and recombination rate, striking contrasts in the distribution of retrotransposon families, and distinct patterns of genetic diversity.Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlightin...

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The Near East Fertile Crescent is well recognized as a primary center of barley origin, diversity, and domestication. A large number of wild barleys have been collected from the Tibetan Plateau, which is characterized by an extreme environment. We used genome-wide diversity array technology markers to analyze the genotypic division between wild barley from the Near East and Tibet. Our results confirmed the existence of Tibetan wild barley and suggested that the split between the wild barleys in the Near East and those in Tibet occurred around 2.76 million years ago (Mya). To test the concept of polyphyletic domestication of barley, we characterized a set of worldwide cultivated barley. Some Chinese hulless and six-rowed barleys showed a close relationship with Tibetan wild barley but showed no common ancestor with other cultivated barley. Our data support the concept of polyphyletic domestication of cultivated barley and indicate that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. The current results may be highly significant in exploring the elite germplasm for barley breeding, especially against cold and drought stresses.adaptation | evolution | harsh environment

Abscisic acid (ABA)-driven stomatal regulation reportedly evolved after the divergence of ferns, during the early evolution of seed plants approximately 360 million years ago. This hypothesis is based on the observation that the stomata of certain fern species are unresponsive to ABA, but exhibit passive hydraulic control. However, ABA-induced stomatal closure was detected in some mosses and lycophytes. Here, we observed that a number of ABA signaling and membrane transporter protein families diversified over the evolutionary history of land plants. The aquatic ferns Azolla filiculoides and Salvinia cucullata have representatives of 23 families of proteins orthologous to those of Arabidopsis (Arabidopsis thaliana) and all other land plant species studied. Phylogenetic analysis of the key ABA signaling proteins indicates an evolutionarily conserved stomatal response to ABA. Moreover, comparative transcriptomic analysis has identified a suite of ABAresponsive genes that differentially expressed in a terrestrial fern species, Polystichum proliferum. These genes encode proteins associated with ABA biosynthesis, transport, reception, transcription, signaling, and ion and sugar transport, which fit the general ABA signaling pathway constructed from Arabidopsis and Hordeum vulgare. The retention of these key ABA-responsive genes could have had a profound effect on the adaptation of ferns to dry conditions. Furthermore, stomatal assays have shown the primary evidence for ABA-induced closure of stomata in two terrestrial fern species P. proliferum and Nephrolepis exaltata. In summary, we report, to our knowledge, new molecular and physiological evidence for the presence of active stomatal control in ferns.

Sub-micrometer hybrid spheres with a poly-dopamine core and loaded with silver nanoparticles (NPs) were fabricated by a facile method. The new hybrid spheres show a strong antibacterial activity due to their special structure, effectively preventing silver NP aggregation.

A thorough understanding of the mechanisms underlying barley salt tolerance and exploitation of elite genetic resource are essential for utilizing wild barley germplasm in developing barley varieties with salt tolerance. In order to reveal the physiological and molecular difference in salt tolerance between Tibetan wild barley (Hordeum spontaneum) and cultivated barley (Hordeum vulgare), profiles of 82 key metabolites were studies in wild and cultivated barley in response to salinity. According to shoot dry biomass under salt stress, XZ16 is a fast growing and salt tolerant wild barley. The results of metabolite profiling analysis suggested osmotic adjustment was a basic mechanism, and polyols played important roles in developing salt tolerance only in roots, and high level of sugars and energy in roots and active photosynthesis in leaves were important for barley to develop salt tolerance. The metabolites involved in tolerance enhancement differed between roots and shoots, and also between genotypes. Tibetan wild barley, XZ16 had higher chlorophyll content and higher contents of compatible solutes than CM72, while the cultivated barley, CM72 probably enhanced its salt tolerance mainly through increasing glycolysis and energy consumption, when the plants were exposed to high salinity. The current research extends our understanding of the mechanisms involved in barley salt tolerance and provides possible utilization of Tibetan wild barley in developing barley cultivars with salt tolerance.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Chloroplast retrograde signaling networks are vital for chloroplast biogenesis, operation, and signaling, including excess light and drought stress signaling. To date, retrograde signaling has been considered in the context of land plant adaptation, but not regarding the origin and evolution of signaling cascades linking chloroplast function to stomatal regulation. We show that key elements of the chloroplast retrograde signaling process, the nucleotide phosphatase (SAL1) and 3′-phosphoadenosine-5′-phosphate (PAP) metabolism, evolved in streptophyte algae—the algal ancestors of land plants. We discover an early evolution of SAL1-PAP chloroplast retrograde signaling in stomatal regulation based on conserved gene and protein structure, function, and enzyme activity and transit peptides of SAL1s in species including flowering plants, the fern Ceratopteris richardii, and the moss Physcomitrella patens. Moreover, we demonstrate that PAP regulates stomatal closure via secondary messengers and ion transport in guard cells of these diverse lineages. The origin of stomata facilitated gas exchange in the earliest land plants. Our findings suggest that the conquest of land by plants was enabled by rapid response to drought stress through the deployment of an ancestral SAL1-PAP signaling pathway, intersecting with the core abscisic acid signaling in stomatal guard cells.