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Gene editing using clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) has revolutionized biotechnology and provides genetic tools for medicine and life sciences. However, the application of this technology to miRNAs, with the function as negative gene regulators, has not been extensively reviewed in plants. Here, we summarize the evolution, biogenesis, and structure of miRNAs, as well as their interactions with mRNAs and computational models for predicting target genes. In addition, we review current advances in CRISPR/Cas for functional analysis and for modulating miRNA genes in plants. Extending our knowledge of miRNAs and their manipulation with CRISPR will provide fundamental understanding of the functions of plant miRNAs and facilitate more sustainable and publicly acceptable genetic engineering of crops.

Pre-treatment with low concentration of CuO NPs alleviated Cd toxicity in rice and barley, attributing to inhibition of Cd uptake and enhancement of antioxidative capacity, which might be an alternative approach for crops to fight against Cd pollution.

Vacuolar H+-pumping pyrophosphatases (VPs) provide a proton gradient for Na+ sequestration in the tonoplast; however, the regulatory mechanisms of VPs in developing salt tolerance have not been fully elucidated. Here, we cloned a barley (Hordeum vulgare) VP gene (HVP10) that was identified previously as the HvNax3 gene. Homology analysis showed VP10 in plants had conserved structure and sequence and likely originated from the ancestors of the Ceramiales order of Rhodophyta (Cyanidioschyzon merolae). HVP10 was mainly expressed in roots and upregulated in response to salt stress. After salt treatment for 3 weeks, HVP10 knockdown (RNA interference) and knockout (CRISPR/Cas9 gene editing) barley plants showed greatly inhibited growth and higher shoot Na+ concentration, Na+ transportation rate and xylem Na+ loading relative to wild-type (WT) plants. Reverse transcription quantitative polymerase chain reaction and microelectronic Ion Flux Estimation results indicated that HVP10 likely modulates Na+ sequestration into the root vacuole by acting synergistically with Na+/H+ antiporters (HvNHX1 and HvNHX4) to enhance H+ efflux and K+ maintenance in roots. Moreover, transgenic rice (Oryza sativa) lines overexpressing HVP10 also showed higher salt tolerance than the WT at both seedling and adult stages with less Na+ translocation to shoots and higher grain yields under salt stress. This study reveals the molecular mechanism of HVP10 underlying salt tolerance and highlights its potential in improving crop salt tolerance.

Salt stress is one of the major environmental restricts for crop production and food safety. Barley (Hordeum vulgare L.) is the most salt-tolerant cereal crop, which could be the pioneer for shifting agricultural crop production to marginal saline lands. However, probably due to high genetic complexity of salinity tolerance trait, the progress in the identification of salt-tolerant locus or genes of barley roots moves slowly. Here, we determined physiological and ionic changes in mini-core barley accessions under salt conditions. Na+ content was lower in whole-plant but higher in roots of the salt tolerant genotypes than sensitive ones under salt stress. Genome-wide association study (GWAS) analysis identified 43 significant SNPs out of 12,564 SNPs and 215 candidate genes (P

At the microsite “Evolution Slope”, Tabigha, Israel, wild barley (Hordeum spontaneum) populations adapted to dry Terra Rossa soil, and its derivative abutting wild barley population adapted to moist and fungi‐rich Basalt soil. However, the mechanisms underlying the edaphic adaptation remain elusive. Accordingly, whole genome bisulfite sequencing, RNA‐sequencing, and metabolome analysis are performed on ten wild barley accessions inhabiting Terra Rossa and Basalt soil. A total of 121 433 differentially methylated regions (DMRs) and 10 478 DMR‐genes are identified between the two wild barley populations. DMR‐genes in CG context (CG‐DMR‐genes) are enriched in the pathways related with the fundamental processes, and DMR‐genes in CHH context (CHH‐DMR‐genes) are mainly associated with defense response. Transcriptome and metabolome analysis reveal that the primary and secondary metabolisms are more active in Terra Rossa and Basalt wild barley populations, respectively. Multi‐omics analysis indicate that sugar metabolism facilitates the adaptation of wild barley to dry Terra Rossa soil, whereas the enhancement of phenylpropanoid/phenolamide biosynthesis is beneficial for wild barley to inhabit moist and fungi pathogen‐rich Basalt soil. The current results make a deep insight into edaphic adaptation of wild barley and provide elite genetic and epigenetic resources for developing barley with high abiotic stress tolerance., Two wild barley populations adapt to hot‐dry Terra Rossa soil, and abutting moist fungi‐rich Basalt soil at the microsite “Evolution Slope”, Tabigha, Israel. Sugar metabolism facilitates edaphic adaptation of wild barley to dry Terra Rossa soil, and phenylpropanoid/phenolamide biosynthesis enables the edaphic adaptation of wild barley to moist and fungi‐rich Basalt soil at epigenomic, genomic, transcriptomic, and metabolomic levels.

Salt stress is one of the major environmental restricts for crop production and food safety. Barley (Hordeum vulgare L.) is the most salt-tolerant cereal crop, which could be the pioneer for shifting agricultural crop production to marginal saline lands. However, probably due to high genetic complexity of salinity tolerance trait, the progress in the identification of salt-tolerant locus or genes of barley roots moves slowly. Here, we determined physiological and ionic changes in mini-core barley accessions under salt conditions. Na

Little study was performed to know how microRNAs (miRNAs) are responsive to cadmium (Cd) stress in barley (Hordeum vulgare). In this study, 16 small RNA libraries of shoot and root tissues from a wild barley accession (WB-1) and cultivated barley (Golden Promise) with contrasting Cd tolerance were constructed and sequenced. Moreover, a degradome library was constructed and analyzed to identify target genes of the miRNAs. Based on high-throughput sequencing, 216 conserved miRNAs (in 59 miRNA families) and 87 novel miRNAs were identified. A total of 238 target genes for 149 miRNAs (113 conserved and 36 novel miRNAs) were detected by the degradome analysis. Among these miRNAs, 45 miRNAs (40 conserved and 5 novel miRNAs) and 43 miRNAs (40 conserved and 3 novel miRNAs) showed differential expression in roots and shoots of two genotypes under Cd conditions. Compared with cultivar Golden Promise, the wild genotype WB-1 had genotype-dependent responses of miR156, miR159, miR166, miR167, miR171 and miR393, which regulate target genes including SPL, MYB, HD-Zip, ARF, GRAS and TIR. Correspondingly, WB-1 had lower Cd concentration and stronger Cd tolerance than Golden Promise. It indicates that miRNAs may play critical roles underlying genotypic difference of Cd tolerance in barley.

Nitrogen (N) availability and form have a dramatic effect on N uptake and assimilation in plants, affecting growth and development. In the previous studies, we found great differences in low-N tolerance between Tibetan wild barley accessions and cultivated barley varieties. We hypothesized that there are different responses to N forms between the two kinds of barleys. Accordingly, this study was carried out to determine the response of four barley genotypes (two wild, XZ16 and XZ179, and two cultivated, ZD9 andHua30) under 4Nforms (NO3−, NH4+, urea and glycine). The results showed significant reduction in growth parameters such as root/shoot length and biomass, as well as photosynthesis parameters and total soluble protein content under glycine treatment relative to other N treatments, for both wild and cultivated barley, however, XZ179 was least affected. Similarly, ammonium adversely affected growth parameters in both wild and cultivated barleys, with XZ179 being severely affected. On the other hand, both wild and cultivated genotypes showed higher biomass, net photosynthetic rate, chlorophyll and protein in NO3− treatment relative to other three N treatments. It may be concluded that barley undisputedly grows well under inorganic nitrogen (NO3−), however in response to the organic N wild barley prefer glycine more than cultivated barely.

Cadmium (Cd) pollutants restrict crop yield and food security in long-term agricultural activities. Crops have evolved adaptive strategies under Cd condition, however, the transcriptional regulatory mechanism of Cd-tolerant genes remains to be largely illustrated. In this study, barley roots were exposed to 5 µM CdCl2 for physiological response and transcriptome-wide m6A methylation profile. Cd stress inhibited root growth after 7 d Cd treatment, which is mainly associated with inhibited absorption of Mn. After Cd treatment, 8151 significantly modified m6A sites and 3920 differentially expressed genes were identified. Transcriptome-wide m6A hypermethylation was widely induced by Cd stress and enriched near the stop codon and 3′ UTR regions. Among 435 m6A modified DEGs, 319 hypermethylated genes were up-regulated and 84 hypomethylated genes were down-regulated, respectively, indicating a positive correlation of m6A methylation and expression. But well-known Cd transporter genes (HvNramp5, HvIRT1, HvHMA3, etc.) were not modified by m6A methylation, except for ABC transporters. We further found key Cd-responding regulatory genes were positively modulated with m6A methylation, including MAPK, WRKY and MYB members. This study proposed a transcriptional regulatory network of Cd stress response in barley roots, which may provide new insight into gene manipulation of controlling low Cd accumulation for crops.

Calcium (Ca(2+)) signaling modulates sodium (Na(+)) transport in plants; however, the role of the Ca(2+) sensor calmodulin (CaM) in salt tolerance is elusive. We previously identified a salt-responsive calmodulin (HvCaM1) in a proteome study of barley (Hordeum vulgare) roots. Here, we employed bioinformatic, physiological, molecular, and biochemical approaches to determine the role of HvCaM1 in barley salt tolerance. CaM1s are highly conserved in green plants and probably originated from ancestors of green algae of the Chlamydomonadales order. HvCaM1 was mainly expressed in roots and was significantly up-regulated in response to long-term salt stress. Localization analyses revealed that HvCaM1 is an intracellular signaling protein that localizes to the root stele and vascular systems of barley. After treatment with 200 mm NaCl for 4 weeks, HvCaM1 knockdown (RNA interference) lines showed significantly larger biomass but lower Na(+) concentration, xylem Na(+) loading, and Na(+) transportation rates in shoots compared with overexpression lines and wild-type plants. Thus, we propose that HvCaM1 is involved in regulating Na(+) transport, probably via certain class I high-affinity potassium transporter (HvHKT1;5 and HvHKT1;1)-mediated Na(+) translocation in roots. Moreover, we demonstrated that HvCaM1 interacted with a CaM-binding transcription activator (HvCAMTA4), which may be a critical factor in the regulation of HKT1s in barley. We conclude that HvCaM1 negatively regulates salt tolerance, probably via interaction with HvCAMTA4 to modulate the down-regulation of HvHKT1;5 and/or the up-regulation of HvHKT1;1 to reduce shoot Na(+) accumulation under salt stress in barley.

Aluminum (Al) toxicity is a major abiotic stress that restricts crop production in acid soils. Plants have evolved internal and external mechanisms of tolerance, and among them it is well known that AtSTOP1 and OsART1 are key transcription factors involved in tolerance through regulation of multiple downstream genes. Here, we identified the closest homolog of these two proteins in barley, namely HvATF1, Al-tolerance Transcription Factor 1, and determined its potential function in Al stress. HvATF1 is expressed in the nucleus, and functions in transcriptional activation. The transcription of HvATF1 was found to be constitutive in different tissues, and was little affected by Al stress. Knockdown of HvATF1 by RNAi resulted in increased Al sensitivity. Transcriptomics analysis identified 64 differently expressed genes in the RNAi lines compared to the wild-type, and these were considered as candidate downstream genes regulated by HvATF1. This study provides insights into the different molecular mechanisms of Al tolerance in barley and other plants.

Barley (Hordeum vulgare) and rice (Oryza sativa) differ greatly in their salt tolerance, although both species belong to the Poaceae family. To understand the mechanisms in the difference of salt tolerance between the two species, the responses of ionome, metabolome and gene expression of Na and K transporters to the different salt treatments were analyzed using 4 barley and 4 rice genotypes differing in salt tolerance. In comparison with 4 rice genotypes, four barley genotypes showed better plant growth, lower shoot Na concentration and higher K concentration at the 9 day after salt treatments. There was a dramatic difference in absolute expression levels of SOS, HKT and NHX family genes between barley and rice, which might account for their difference in Na/K homeostasis and salt tolerance. Moreover, rice leaves accumulated excess Na under salt treatments, which caused serious damages to physiological metabolisms based on metabolomic analysis, but barley leaves had lower Na concentration and small changes in the most metabolites. These results provide useful insights into the molecular mechanism in the difference of salt tolerance between rice and barley.

Maintaining low intracellular Na(+) concentrations is an essential physiological strategy in salt stress tolerance in most cereal crops. Here, we characterized a member of the high-affinity K(+) transporter (HKT) family in barley (Hordeum vulgare), HvHKT1;5, which negatively regulates salt tolerance and has different functions from its homology in other cereal crops. HvHKT1;5 encodes a plasma membrane protein localized to root stele cells, particularly in xylem parenchyma cells adjacent to the xylem vessels. Its expression was highly induced by salt stress. Heterogenous expression of HvHKT1;5 in Xenopus laevis oocytes showed that HvHKT1;5 was permeable to Na(+), but not to K(+), although its Na(+) transport activity was inhibited by external K(+). HvHKT1;5 knockdown barley lines showed improved salt tolerance, a dramatic decrease in Na(+) translocation from roots to shoots, and increases in K(+)/Na(+) when compared with wild-type plants under salt stress. The negative regulation of HvHKT1;5 in salt tolerance distinguishes it from other HKT1;5 members, indicating that barley has a distinct Na(+) transport system. These findings provide a deeper understanding of the functions of HKT family members and the regulation of HvHKT1;5 in improving salt tolerance of barley.

Tillering or branching is an important agronomic trait in plants, especially cereal crops. Previously, in barley (Hordeum vulgare) ‘Vlamingh’, we identified the high number of tillers1 (hnt1) mutant from a γ-ray-treated segregating population. hnt1 exhibited more tillers per plant, narrower leaves, and reduced plant height compared with the wild-type parent. In this study, we show that the hnt1-increased tiller number per plant is caused by accelerated outgrowth of tiller buds and that hnt1 narrower leaves are caused by a reduction in vascular tissue and cell number. Genetic analysis revealed that a 2-bp deletion in the gene HORVU2Hr1G098820 (HvHNT1), encoding a trypsin family protein, was responsible for the hnt1 mutant phenotype. Gene function was further confirmed by transgenic complementation with HvHNT1 and RNA interference experiments. HvHNT1 was expressed in vascular tissue, leaf axils, and adventitious root primordia and shown to negatively regulate tiller development. Mutation of HvHNT1 led to the accumulation of a putative cyclophilin-type peptidyl-prolyl cis/trans-isomerase (HvPPIase), which physically interacts with the HvHNT1 protein in the nucleus of plant cells. Our data suggest that HvHNT1 controls tiller development and leaf width through HvPPIase, thus contributing to understanding of the molecular players that control tillering in barley.

Barley (Hordeum vulgare L.) is well known for its relatively high salt tolerance among cereal crops. However, the genetic variation of cultivated barley becomes narrower due to continuous artificial selection and breeding processes. Compared with cultivated barley, wild barley contains wider genetic variation and abundant sources for abiotic stress tolerance, considering as an elite resource for mechanism study on salt tolerance. In this study, Tibetan wild barley accession XZ113 identified with high salt tolerance, was used to investigate ionic responses and to identify proteins involved in salt tolerance in roots and shoots at early stage of salt stress, during 48 h. Exposed to salinity, shoot growth is more sensitive than root growth. Conversely, K/Na ratio in the shoots was larger than that in the roots, and both were above 1.0. Steady-state K+ flux experiment showed XZ113 had a strong K+-retaining ability under salt stress, maybe contributing to its good performance of the absolute growth rate. Proteomic results suggested that monodehydroascorbate reductase and peroxidases related to reactive oxygen species scavenging in the roots and phosphoglycerate kinase, triosephosphate isomerase and sedoheptulose-1,7-bisphosphatase associated with photosynthesis and metabolisms in the shoots, played important roles in salt tolerance at early stage of salinity in wild barley.

Background Barley is relatively sensitive to Aluminum (Al) toxicity among cereal crops, but shows a wide genotypic difference in Al tolerance. The well-known Al-tolerant mechanism in barley is related to Al exclusion mediated by a citrate transporter HvAACT1 (Al-activated citrate transporter 1). A 1-kb insertion in the promoter region of HvAACT1 gene results in a dramatic increase of its expression level, which only occurs in some Al-tolerant cultivars. However, Al-tolerant Tibetan wild barley accession XZ29 did not have the 1-kb insertion. Results We confirmed that the expression of HvAACT1 and secretion of citrate and other organic acids did not explain the difference in Al-tolerant wild barley XZ29 and Al-sensitive cultivated barley Golden Promise. To identify microRNAs (miRNAs) and their target genes responsive to Al stress in barley roots, eight small RNA libraries with two biological replicates from these two genotypes exposed to control and Al-treated conditions were constructed and submitted to deep sequencing. A total of 342 miRNAs were identified in Golden Promise and XZ29, with 296 miRNAs being commonly shared in the two genotypes. Target genes of these miRNAs were obtained through bioinformatics prediction or degradome identification. Comparative analysis detected 50 miRNAs responsive to Al stress, and some of them were found to be exclusively expressed in XZ29 and associated with Al tolerance. Conclusions miRNAs exclusively expressing in the wild barley were identified and found to be associated with Al stress tolerance. The current results provide a model of describing the roles of some special miRNAs associated with Al tolerance in the Tibetan wild barley. Electronic supplementary material The online version of this article (10.1186/s12864-018-4953-x) contains supplementary material, which is available to authorized users.

Both barley ( Hordeum vulgare ) and rice ( Oryza sativa ) belong to Poaceae family, but differ greatly in salt tolerance. In order to understand molecular mechanisms in the difference of salt tolerance between the two species, the responses of transcriptomic profiles to salt stress were compared between rice (cultivar Nipponbare) and barley (accession XZ26) to reveal how alternative splicing (AS) coordinates with transcriptional regulation in adaptation to salt stress. Physiological study showed that XZ26 had higher salt tolerance than Nipponbare, as reflected by less growth inhibition, lower shoot Na + concentration and higher K + /Na + ratio when exposed to salt stress. Transcriptomic analysis identified 606 and 186 DEGs in the roots and shoots for XZ26, and 4667 and 2817 DEGs for Nipponbare, respectively. While alternative splicing analysis identified 40 and 33 AS genes (salt-responsive DEGs) in the roots and shoots of XZ26. Moreover, AS genes related to ion transporters and transcription factors could enhance and amplify K + /Na + homeostasis in barley. The current results suggest that higher salt tolerance of barley accession XZ26 is attributed to its superior K + /Na + homeostasis, tissue detoxification and less energy consumption.

Figure S1. The difference in root elongation of three genotypes under Al stress. Three-day-old seedlings were exposed to Al for 9 days. The root elongation were measured. Data are means +SD of six biological replicates and means labeled with different letters are significantly different at p

In our previous study, Tibetan wild barley (Hordeum spontaneum L.) has been found to be rich in the elite accessions with strong abiotic stress tolerance, including salt stress tolerance. However, the molecular mechanism of salt tolerance underlying the wild barley remains to be elucidated. In this study, two Tibetan wild barley accessions, XZ26 (salt-tolerant) and XZ169 (salt-sensitive), were used to investigate ionomic, metabolomic and proteomic responses in roots when exposed to 0, 200 (moderate) and 400 mM (high) salinity. XZ26 showed stronger root growth and maintained higher K concentrations when compared with XZ169 under moderate salinity, while no significant difference was found between the two accessions under high salinity. A total of 574 salt-regulated proteins and 153 salt-regulated metabolites were identified in the roots of both accessions based on quantitative proteomic (iTRAQ methods) and metabolomic (GC-TOF/MS) analysis. XZ26 developed its root adaptive strategies mainly by accumulating more compatible solutes such as proline and inositol, acquiring greater antioxidant ability to cope with ROS, and consuming less energy under salt stress for producing biomass. These findings provide a better understanding of molecular responses of root adaptive strategies to salt stress in the wild barley.

A thorough understanding of ionic detoxification and homeostasis is imperative for improvement of salt tolerance in crops. However, the homeostasis of elements and their relationship to metabolites under salt stress have not been fully elucidated in plants. In this study, Tibetan wild barley accessions, XZ16 and XZ169, differing in salt tolerance, and a salt-tolerant cultivar CM72 were used to investigate ionomic profile changes in tissues in response to 150 and 300 mM NaCl at the germination and seedling stages. At the germination stage, the contents of Ca and Fe significantly decreased in roots, while K and S contents increased, and Ca and Mg contents decreased in shoots, after 10 d of treatment. At the seedling stage, the contents of K, Mg, P and Mn in roots and of K, Ca, Mg and S in shoots decreased significantly after 21 d of treatment. Moreover, Na had a significant negative correlation with metabolites involved in glycolysis, α-ketoglutaric acid, maleic acid and alanine in roots, and metabolites associated with the tricarboxylic acid (TCA) cycle, sucrose, polyols and aspartate in leaves. The salt-tolerant genotypes XZ16 and CM72 showed a lower Na content in tissues, and less reduction in Zn and Cu in roots, of Ca, Mg and S in leaves, and shoot DW than the sensitive genotype XZ169, when exposed to a higher salt level. The results indicated that restriction of Na accumulation and rearrangement of nutrient elements and metabolites in barley tissues are possibly attributable to development of salt tolerance.

Background Tibetan wild barley (Hordeum spontaneum L.) has been confirmed to contain elite accessions in tolerance to abiotic stresses, including salinity. However, molecular mechanisms underlying genotypic difference of salt tolerance in wild barley are unknown. Results In this study, two Tibetan wild barley accessions (XZ26 and XZ169), differing greatly in salt tolerance, were used to determine changes of ionomic, metabolomic and proteomic profiles in the shoots exposed to salt stress at seedling stage. Compared with XZ169, XZ26 showed better shoot growth and less Na accumulation after 7 days treatments. Salt stress caused significant reduction in concentrations of sucrose and metabolites involved in glycolysis pathway in XZ169, and elevated level of tricarboxylic acid (TCA) cycle, as reflected by up-accumulation of citric acid, aconitic acid and succinic acid, especially under high salinity, but not in XZ26. Correspondingly, proteomic analysis further proved the findings from the metabolomic study. Conclusion XZ26 maintained a lower Na concentration in the shoots and developed superior shoot adaptive strategies to salt stress. The current result provides possible utilization of Tibetan wild barley in developing barley cultivars for salt tolerance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3242-9) contains supplementary material, which is available to authorized users.

The concentration of Cu, Fe, Mn and Zn in the shoots of XZ26 and XZ169 under control (CK), moderate (200Â mM, S200) and high (400Â mM, S400) salinity conditions. (PDF 88 kb)

Gene Ontology (GO) classification of the differentially accumulated proteins in the shoots of XZ26 and XZ169 after moderate (200Â mM, S200) and high (400Â mM, S400) salt treatments. (PDF 96 kb)

Relative shoot length and relative shoot dry weight of XZ26 and XZ169 after moderate (200Â mM, S200) and high (400Â mM, S400) salinity. (PDF 9 kb)

Identification and characterization of proteins involved in salt tolerance are imperative for revealing its genetic mechanisms. In this study, ionic and proteomic responses of a Tibetan wild barley XZ16 and a well-known salt-tolerant barley cv. CM72 were analyzed using inductively coupled plasma-optical emission spectrometer, 2DE, and MALDI-TOF/TOF MS techniques to determine salt-induced differences in element and protein profiles between the two genotypes. In total, 41 differentially expressed proteins were identified in roots and leaves, and they were associated with ion homeostasis, cell redox homeostasis, metabolic process, and photosynthesis. Under salinity stress, calmodulin, Na/K transporters, and H(+) -ATPases were involved in establishment of ion homeostasis for barley plants. Moreover, ribulose-1,5-bisphosphate carboxylase/oxygenase activase and oxygen-evolving enhancer proteins were significantly upregulated under salinity stress, indicating the great impact of salinity on photosynthesis. In comparison with CM72, XZ16 had greater relative dry weight and lower Na accumulation in the shoots under salinity stress. A higher expression of HvNHX1 in the roots, and some specific proteins responsible for ion homeostasis and cell redox homeostasis, was also found in XZ16 exposed to salt stress. The current results showed that Tibetan wild barley XZ16 and cultivated barley cultivar CM72 differ in the mechanism of salt tolerance.