Multi-omics analysis reveals the mechanism underlying the edaphic adaptation in wild barley at Evolution Slope (Tabigha)

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

Interim position emission tomography-computed tomography during multimodality treatment of locally advanced esophageal cancer: a scoping review.

BACKGROUND Among cancers, esophageal cancer (EC) has one of the highest incidences and mortality in Asia. As recognized in many national guidelines, functional imaging performed with position emission tomography is recommended for patients with locally advanced disease. This review evaluated evidence for the use of fluorodeoxyglucose (FDG) interim positron emission tomography (PETint) in bimodality (chemoradiation) and trimodality (chemoradiation followed by surgery) management of locally advanced esophageal cancer (LAEC), with a focus on its prognostic and predictive value. METHODS The MEDLINE database was searched from January 1, 2001, to January 1, 2022, as part of a scoping review. References of selected articles were manually checked to identify other articles meeting the inclusion criteria; only original articles were included, and reviews, guidelines, letters, editorials, and case reports were excluded. RESULTS A total of 63 articles were included in this review. PET-computed tomography (PET-CT) is recognized as having a significant role in the assessment of treatment response. Studies on the predictive PETint suggest that it has a certain value, particularly for early response. Identification of poor responders or nonresponders soon after commencement of multimodality treatment allows for treatment modification. CONCLUSIONS The scoping review indicated variable utility for the prognostic value of PETint. There is a need to improve its accuracy, which can likely be achieved through greater standardization of measurements and reporting and testing as well as combination with other promising measures of response to residual disease

The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies

The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na+ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops

Identification of microRNAs Responding to Aluminium, Cadmium and Salt Stresses in Barley Roots

Plants are frequently exposed to various abiotic stresses, including aluminum, cadmium and salinity stress. Barley (Hordeum vulgare) displays wide genetic diversity in its tolerance to various abiotic stresses. In this study, small RNA and degradome libraries from the roots of a barley cultivar, Golden Promise, treated with aluminum, cadmium and salt or controls were constructed to understand the molecular mechanisms of microRNAs in regulating tolerance to these stresses. A total of 525 microRNAs including 198 known and 327 novel members were identified through high-throughput sequencing. Among these, 31 microRNAs in 17 families were responsive to these stresses, and Gene Ontology (GO) analysis revealed that their targeting genes were mostly highlighted as transcription factors. Furthermore, five (miR166a, miR166a-3p, miR167b-5p, miR172b-3p and miR390), four (MIR159a, miR160a, miR172b-5p and miR393) and three (miR156a, miR156d and miR171a-3p) microRNAs were specifically responsive to aluminum, cadmium and salt stress, respectively. Six miRNAs, i.e., miR156b, miR166a-5p, miR169a, miR171a-5p, miR394 and miR396e, were involved in the responses to the three stresses, with different expression patterns. A model of microRNAs responding to aluminum, cadmium and salt stresses was proposed, which may be helpful in comprehensively understanding the mechanisms of microRNAs in regulating stress tolerance in barley

Transcriptome Analysis Reveals Genetic Factors Related to Callus Induction in Barley

Barley is an important cereal crop worldwide. Its genetic transformation is now limited to very few cultivars because of the high genotype dependence of embryogenic callus. To reveal the key genes or factors controlling the callus induction and plantlet regeneration in barley, we compared the transcriptomic profiles of immature embryos of Golden Promise and ZU9, which differed dramatically in the efficiency of the genetic transformation. The samples were taken at 0, 5, 10 and 20 days of the culture, respectively. In total, 5386 up-regulated and 6257 down-regulated genes were identified in Golden Promise. Several genes, identified exclusively in GP callus, were selected for further investigation. These genes were mainly involved in protein metabolism, energy metabolism, stress response, detoxification and ubiquitin–proteasome. Four YUCCA flavin monooxygenases, one PIN-FORMED, one tryptophan aminotransferase related, three small auxin up RNA, three indole-3-acetic acid and one adenylate isopentenyl transferase, seven cytokinin oxidase/dehydrogenase, three Arabidopsis histidine kinase, three Arabidopsis histidine phosphotransfer protein, and one Arabidopsis response regulator were differentially expressed in the calli of the two barley genotypes, suggesting that biosynthesis, response and transport of auxin and cytokinin might be associated with cell reprogramming during callus induction. The current results provide insights into molecular mechanisms of callus induction at an early developmental stage and are helpful for optimizing the tissue culture system in barley

Genome-Wide Identification, Expression Pattern and Sequence Variation Analysis of <i>SnRK</i> Family Genes in Barley

Sucrose non-fermenting 1 (SNF1)-related protein kinase (SnRK) is a large family of protein kinases that play a significant role in plant stress responses. Although intensive studies have been conducted on SnRK members in some crops, little is known about the SnRK in barley. Using phylogenetic and conserved motif analyses, we discovered 46 SnRK members scattered across barley’s 7 chromosomes and classified them into 3 sub-families. The gene structures of HvSnRKs showed the divergence among three subfamilies. Gene duplication and synteny analyses on the genomes of barley and rice revealed the evolutionary features of HvSnRKs. The promoter regions of HvSnRK family genes contained many ABRE, MBS and LTR elements responding to abiotic stresses, and their expression patterns varied with different plant tissues and abiotic stresses. HvSnRKs could interact with the components of ABA signaling pathway to respond to abiotic stress. Moreover, the haplotypes of HvSnRK2.5 closely associated with drought tolerance were detected in a barley core collection. The current results could be helpful for further exploration of the HvSnRK genes responding to abiotic stress tolerance in barley

Ionomic responses and correlations between elements and metabolites under salt stress in wild and cultivated 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

Biochar-Dual Oxidant Composite Particles Alleviate the Oxidative Stress of Phenolic Acid on Tomato Seed Germination

Phenolic acid is a well-known allelochemical, but also a pollutant in soil and water impeding crop production. Biochar is a multifunctional material widely used to mitigate the phenolic acids allelopathic effect. However, phenolic acid absorbed by biochar can still be released. In order to improve the removal efficiency of phenolic acids by biochar, the biochar-dual oxidant (BDO) composite particles were synthesized in this study, and the underlying mechanism of the BDO particles in ameliorating p-coumaric acid (p-CA) oxidative damage to tomato seed germination was revealed. Upon p-CA treatment, the BDO composite particles application increased the radical length, radical surface area, and germination index by 95.0%, 52.8%, and 114.6%, respectively. Compared to using biochar or oxidants alone, the BDO particles addition resulted in a higher removal rate of p-CA and produced more O2•−, HO•, SO4•− and 1O2 radicals via autocatalytic action, suggesting that BDO particles removed phenolic acid by both adsorption and free radical oxidation. The addition of BDO particles maintained the levels of the antioxidant enzyme activity close to the control, and reduced the malondialdehyde and H2O2 by 49.7% and 49.5%, compared to the p-CA treatment. Integrative metabolomic and transcriptomic analyses revealed that 14 key metabolites and 62 genes were involved in phenylalanine and linoleic acid metabolism, which increased dramatically under p-CA stress but down-regulated with the addition of BDO particles. This study proved that the use of BDO composite particles could alleviate the oxidative stress of phenolic acid on tomato seeds. The findings will provide unprecedented insights into the application and mechanism of such composite particles as continuous cropping soil conditioners

Calmodulin HvCaM1 negatively regulates salt tolerance via modulation of HvHKT1s and HvCAMTA4

Calcium (Ca2+) signaling modulates sodium (Na+) transport in plants; however, the role of the Ca2+ 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

Additional file 3: Table S1. of Multi-omics analysis reveals molecular mechanisms of shoot adaption to salt stress in Tibetan wild barley

The fold changes of metabolites in the shoots of XZ26 and XZ169 under control (CK), 200 (S200) and 400 (S400) mM salinity conditions. (XLSX 45 kb