Comprehensive analysis of PLATZ family genes and their responses to abiotic stresses in Barley.

BACKGROUND: Plant A/T-rich protein and zinc-binding protein (PLATZ) transcription factors are pivotal regulators in various aspects of plant biology, including growth, development, and responses to environmental stresses. While PLATZ genes have been extensively studied and functionally characterized in various plants, limited information is available for these genes in barley. RESULTS: Here, we discovered a total of 11 PLATZ genes distributed across seven chromosomes in barley. Based on phylogenetic and conserved motif analysis, we classified PLATZ into five subfamilies, comprising 3, 1, 2, 1 and 4 genes, respectively. Analysis of gene structure demonstrated that these 11 HvPLATZ genes typically possessed two to four exons. Most HvPLATZ genes were found to possess at least one ABRE cis-element in their promoter regions, and a few of them also contained LTR, CAT-box, MRE, and DRE cis-elements. Then, we conducted an exploration of the expression patterns of HvPLATZs, which displayed notable differences across various tissues and in response to abiotic stresses. Functional analysis of HvPLATZ6 and HvPLATZ8 in yeast cells showed that they may be involved in drought tolerance. Additionally, we constructed a regulatory network including miRNA-targeted gene predictions and identified two miRNAs targeting two HvPLATZs, such as hvu-miR5053 and hvu-miR6184 targeting HvPLATZ2, hvu-miR6184 targeting HvPLATZ10. CONCLUSION: In summary, these findings provide valuable insights for future functional verification of HvPLATZs and contribute to a deeper understanding of the role of HvPLATZs in response to stress conditions in barley.

Characterization of metabolic features and potential anti-osteoporosis mechanism of pinoresinol diglucoside using metabolite profiling and network pharmacology.

RATIONALE: Eucommia cortex is the core herb in traditional Chinese medicine preparations for the treatment of osteoporosis. Pinoresinol diglucoside (PDG), the quality control marker and the key pharmacodynamic component in Eucommia cortex, has attracted global attention because of its definite effects on osteoporosis. However, the in vivo metabolic characteristics of PDG and its anti-osteoporotic mechanism are still unclear, restricting its development and application. METHODS: Ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry was used to analyze the metabolic characteristics of PDG in rats, and its anti-osteoporosis targets and mechanism were predicted using network pharmacology. RESULTS: A total of 51 metabolites were identified or tentatively characterized in rats after oral administration of PDG (10 mg/kg/day), including 9 in plasma, 28 in urine, 13 in feces, 10 in liver, 4 in heart, 3 in spleen, 11 in kidneys, and 5 in lungs. Furan-ring opening, dimethoxylation, glucuronidation, and sulfation were the main metabolic characteristics of PDG in vivo. The potential mechanism of PDG against osteoporosis was predicted using network pharmacology. PDG and its metabolites could regulate BCL2, MARK3, ALB, and IL6, involving PI3K-Akt signaling pathway, estrogen signaling pathway, and so on. CONCLUSIONS: This study was the first to demonstrate the metabolic characteristics of PDG in vivo and its potential anti-osteoporosis mechanism, providing the data for further pharmacological validation of PDG in the treatment of osteoporosis.

Osthole Activates the Cholinergic Anti-Inflammatory Pathway via α7nAChR Upregulation to Alleviate Inflammatory Responses.

Osthole (also known as Osthol) is the main anti-inflammatory coumarin found in Cnidium monnieri and severs as the exclusive quality-controlled component according the Chinese Pharmacopoeia. However, its underlying anti-inflammatory mechanism remains unknown. In this study, we demonstrated that Osthole treatment significantly inhibited the generation of TNF-α, but not IL-6 in the classical LPS-stimulated RAW264.7 macrophage model. In addition, LPS induced the activation of both MAPK and NF-κB signalling pathways, of which the former was dose-dependently restrained by Osthole via suppressing the phosphorylation of JNK and P38 proteins, while the phosphorylation of IκB and P65 proteins remained unaffected. Interestingly, Osthole dose-dependently up-regulated the expression of the key cholinergic anti-inflammatory pathway regulator α7nAChR, and the TNF-α inhibition effect of Osthole was also significantly alleviated by the treatment of α7nAChR antagonist methylbetaine. These results demonstrate that Osthole may regulate TNF-α by promoting the expression of α7nAChR, thereby activate the vagus nerve-dependent cholinergic anti-inflammatory pathway.

Comparative Long Non-Coding Transcriptome Analysis of Three Contrasting Barley Varieties in Response to Aluminum Stress.

Aluminum toxicity is a major abiotic stress on acidic soils, leading to restricted root growth and reduced plant yield. Long non-coding RNAs are crucial signaling molecules regulating the expression of downstream genes, particularly under abiotic stress conditions. However, the extent to which lncRNAs participate in the response to aluminum (Al) stress in barley remains largely unknown. Here, we conducted RNA sequencing of root samples under aluminum stress and compared the lncRNA transcriptomes of two Tibetan wild barley genotypes, XZ16 (Al-tolerant) and XZ61 (Al-sensitive), as well as the aluminum-tolerant cultivar Dayton. In total, 268 lncRNAs were identified as aluminum-responsive genes on the basis of their differential expression profiles under aluminum treatment. Through target gene prediction analysis, we identified 938 candidate lncRNA-messenger RNA (mRNA) pairs that function in a cis-acting manner. Subsequently, enrichment analysis showed that the genes targeted by aluminum-responsive lncRNAs were involved in diterpenoid biosynthesis, peroxisome function, and starch/sucrose metabolism. Further analysis of genotype differences in the transcriptome led to the identification of 15 aluminum-responsive lncRNAs specifically altered by aluminum stress in XZ16. The RNA sequencing data were further validated by RT-qPCR. The functional roles of lncRNA-mRNA interactions demonstrated that these lncRNAs are involved in the signal transduction of secondary messengers, and a disease resistance protein, such as RPP13-like protein 4, is probably involved in aluminum tolerance in XZ16. The current findings significantly contribute to our understanding of the regulatory roles of lncRNAs in aluminum tolerance and extend our knowledge of their importance in plant responses to aluminum stress.

Comparative Transcriptome Analysis Reveals the Genes and Pathways Related to Wheat Root Hair Length.

Tube-like outgrowths from root epidermal cells, known as root hairs, enhance water and nutrient absorption, facilitate microbial interactions, and contribute to plant anchorage by expanding the root surface area. Genetically regulated and strongly influenced by environmental conditions, longer root hairs generally enhance water and nutrient absorption, correlating with increased stress resistance. Wheat, a globally predominant crop pivotal for human nutrition, necessitates the identification of long root hair genotypes and their regulatory genes to enhance nutrient capture and yield potential. This study focused on 261 wheat samples of diverse genotypes during germination, revealing noticeable disparities in the length of the root hair among the genotypes. Notably, two long root hair genotypes (W106 and W136) and two short root hair genotypes (W90 and W100) were identified. Transcriptome sequencing resulted in the development of 12 root cDNA libraries, unveiling 1180 shared differentially expressed genes (DEGs). Further analyses, including GO function annotation, KEGG enrichment, MapMan metabolic pathway analysis, and protein-protein interaction (PPI) network prediction, underscored the upregulation of root hair length regulatory genes in the long root hair genotypes. These included genes are associated with GA and BA hormone signaling pathways, FRS/FRF and bHLH transcription factors, phenylpropanoid, lignin, lignan secondary metabolic pathways, the peroxidase gene for maintaining ROS steady state, and the ankyrin gene with diverse biological functions. This study contributes valuable insights into modulating the length of wheat root hair and identifies candidate genes for the genetic improvement of wheat root traits.

Genome-Wide Identification and Expression Profiling of the ABF Transcription Factor Family in Wheat (Triticum aestivum L.).

Members of the abscisic acid (ABA)-responsive element (ABRE) binding factor (ABF) and ABA-responsive element binding protein (AREB) families play essential roles in the regulation of ABA signaling pathway activity and shape the ability of plants to adapt to a range of stressful environmental conditions. To date, however, systematic genome-wide analyses focused on the ABF/AREB gene family in wheat are lacking. Here, we identified 35 ABF/AREB genes in the wheat genome, designated TaABF1-TaABF35 according to their chromosomal distribution. These genes were further classified, based on their phylogenetic relationships, into three groups (A-C), with the TaABF genes in a given group exhibiting similar motifs and similar numbers of introns/exons. Cis-element analyses of the promoter regions upstream of these TaABFs revealed large numbers of ABREs, with the other predominant elements that were identified differing across these three groups. Patterns of TaABF gene expansion were primarily characterized by allopolyploidization and fragment duplication, with purifying selection having played a significant role in the evolution of this gene family. Further expression profiling indicated that the majority of the TaABF genes from groups A and B were highly expressed in various tissues and upregulated following abiotic stress exposure such as drought, low temperature, low nitrogen, etc., while some of the TaABF genes in group C were specifically expressed in grain tissues. Regulatory network analyses revealed that four of the group A TaABFs (TaABF2, TaABF7, TaABF13, and TaABF19) were centrally located in protein-protein interaction networks, with 13 of these TaABF genes being regulated by 11 known miRNAs, which play important roles in abiotic stress resistance such as drought and salt stress. The two primary upstream transcription factor types found to regulate TaABF gene expression were BBR/BPC and ERF, which have previously been reported to be important in the context of plant abiotic stress responses. Together, these results offer insight into the role that the ABF/AREB genes play in the responses of wheat to abiotic stressors, providing a robust foundation for future functional studies of these genes.

Comprehensive Analysis of the INDETERMINATE DOMAIN (IDD) Gene Family and Their Response to Abiotic Stress in Zea mays.

Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize.

Genome-wide identification and characterization of GATA family genes in wheat.

BACKGROUND: Transcription factors GATAs were a member of zinc finger protein, which could bind DNA regulatory regions to control expression of target genes, thus influencing plant growth and development either in normal condition or environmental stresses. Recently, GATA genes have been found and functionally characterized in a number of plant species. However, little information of GATA genes were annotated in wheat. RESULTS: In the current study, 79 GATA genes were identified in wheat, which were unevenly located on 21 chromosomes. According to the analysis of phylogenetic tree and functional domain structures, TaGATAs were classified into four subfamilies (I, II, III, and IV), consist of 35, 21, 12, and 11 genes, respectively. Meanwhile, the amino acids of 79 TaGATAs exhibited apparent difference in four subfamilies according to GATA domains comparison, gene structures and conserved motif analysis. We then analyze the gene duplication and synteny between the genomes of wheat and Arabidopsis, rice and barley, which provided insights into evolutionary characteristics. In addition, expression patterns of TaGATAs were analyzed, and they showed obvious difference in diverse tissues and abiotic stresses. CONCLUSION: In general, these results provide useful information for future TaGATA gene function analysis, and it helps to better understand molecular breeding and stress response in wheat.

Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley.

BACKGROUND: Development of crop cultivars with high low nitrogen (LN) tolerance or nitrogen use efficiency (NUE) is imperative for sustainable agriculture development. Tibetan wild barley is rich in genetic diversity and may provide elite genes for LN tolerance improvement. Little has been known about transcriptional responses of the wild barley to chronic LN stress. RESULTS: In this study, transcriptomic profiling of two Tibetan wild barley genotypes, LN- tolerant XZ149 and LN-sensitive XZ56 has been conducted using RNA-Seq to reveal the genotypic difference in response to chronic LN stress. A total of 520 differentially expressed genes (DEGs) were identified in the two genotypes at 12 d after LN stress, and these DEGs could be mainly mapped to 49 metabolism pathways. Chronic LN stress lead to genotype-dependent responses, and the responsive pattern in favor of root growth and stress tolerance may be the possible mechanisms of the higher chronic LN tolerance in XZ149. CONCLUSION: There was a distinct difference in transcriptional profiling between the two wild barley genotypes in response to chronic LN stress. The identified new candidate genes related to LN tolerance may cast a light on the development of cultivars with LN tolerance.

Root plasticity and Pi recycling within plants contribute to low-P tolerance in Tibetan wild barley.

BACKGROUND: Barley is a low phosphorus (P) demand cereal crop. Tibetan wild barley, as a progenitor of cultivated barley, has revealed outstanding ability of tolerance to low-P stress. However, the underlying mechanisms of low-P adaption and the relevant genetic controlling are still unclear. RESULTS: We identified low-P tolerant barley lines in a doubled-haploid (DH) population derived from an elite Tibetan wild barley accession and a high-yield cultivar. The tolerant lines revealed greater root plasticity in the terms of lateral root length, compared to low-P sensitive lines, in response to low-P stress. By integrating the QTLs associated with root length and root transcriptomic profiling, candidate genes encoding isoflavone reductase, nitrate reductase, nitrate transporter and transcriptional factor MYB were identified. The differentially expressed genes (DEGs) involved the growth of lateral root, Pi transport within cells as well as from roots to shoots contributed to the differences between low-P tolerant line L138 and low-P sensitive lines L73 in their ability of P acquisition and utilization. CONCLUSIONS: The plasticity of root system is an important trait for barley to tolerate low-P stress. The low-P tolerance in the elite DH line derived from a cross of Tibetan wild barley and cultivated barley is characterized by enhanced growth of lateral root and Pi recycling within plants under low-P stress.

A Sodium Transporter HvHKT1;1 Confers Salt Tolerance in Barley via Regulating Tissue and Cell Ion Homeostasis.

Our previous studies showed that high salt tolerance in Tibetan wild barley accessions was associated with HvHKT1;1, a member of the high-affinity potassium transporter family. However, molecular mechanisms of HvHKT1;1 for salt tolerance and its roles in K+/Na+ homeostasis remain to be elucidated. Functional characterization of HvHKT1;1 was conducted in the present study. NaCl-induced transcripts of HvHKT1;1 were significantly higher in the roots of Tibetan wild barley XZ16 relative to other genotypes, being closely associated with its higher biomass and lower tissue Na+ content under salt stress. Heterologous expression of HvHKT1;1 in Saccharomyces cerevisiae (yeast) and Xenopus laevis oocytes showed that HvHKT1;1 had higher selectivity for Na+ over K+ and other monovalent cations. HvHKT1;1 was found to be localized at the cell plasma membrane of root stele and epidermis. Knock-down of HvHKT1;1 in barley led to higher Na+ accumulation in both roots and leaves, while overexpression of HvHKT1;1 in salt-sensitive Arabidopsis hkt1-4 and sos1-12 loss-of-function lines resulted in significantly less shoot and root Na+ accumulation. Additionally, microelectrode ion flux measurements and root elongation assay revealed that the transgenic Arabidopsis plants exhibited a remarkable capacity for regulation of Na+, K+, Ca2+ and H+ homeostasis under salt stress. These results indicate that HvHKT1;1 is critical in radial root Na+ transport, which eventually reduces shoot Na+ accumulation. Additionally, HvHKT1;1 may be indirectly involved in retention of K+ and Ca2+ in root cells, which also improves plant salt tolerance.

Root and leaf metabolite profiles analysis reveals the adaptive strategies to low potassium stress in barley.

BACKGROUND: Potassium (K) deficiency in arable land is one of the most important factors affecting crop productivity. Development of low K (LK) tolerant crop cultivars is regarded as a best economic and effective approach for solving the issue of LK. In previous studies, we found a wider variation of LK tolerance in the Tibetan wild barley accessions than cultivated barley. However, the mechanism of LK tolerance in wild barley is still elusive. RESULTS: In this study, two wild barley genotypes (XZ153, LK tolerant and XZ141, LK sensitive) and one cultivar (LuDaoMai, LK tolerant) was used to investigate metabolome changes in response to LK stress. Totally 57 kinds of metabolites were identified in roots and leaves of three genotypes at 16 d after LK treatment. In general, accumulation of amino acids and sugars was enhanced in both roots and leaves, while organic acids were reduced under LK stress compared to the control. Meanwhile, the concentrations of the negatively charged amino acids (Asp and Glu) and most organic acids was reduced in both roots and leaves, but more positively charged amino acids (Lys and Gln) were increased in three genotypes under LK. XZ153 had less reduction than other two genotypes in biomass and chlorophyll content under LK stress and showed greater antioxidant capacity as reflected by more synthesis of active oxygen scavengers. Higher LK tolerance of XZ153 may also be attributed to its less carbohydrate consumption and more storage of glucose and other sugars, thus providing more energy for plant growth under LK stress. Moreover, phenylpropanoid metabolic pathway mediated by PAL differed among three genotypes, which is closely associated with the genotypic difference in LK tolerance. CONCLUSIONS: LK tolerance in the wild barley is attributed to more active phenylpropanoid metabolic pathway mediated by PAL, energy use economy by reducing carbohydrate consumption and storage of glucose and other sugars, and higher antioxidant defense ability under LK stress.

Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen.

BACKGROUND: Nitrogen (N) is the most common limiting factor for crop productivity worldwide. An effective approach to solve N deficiency is to develop low N (LN) tolerant crop cultivars. Tibetan annual wild barley is well-known for its wide genetic diversity and high tolerance to poor soil fertility. Up to date, no study has been done to illustrate the mechanism of LN tolerance underlying the wild barley at transcriptional level. RESULTS: In this study, we employed Illumina RNA-Sequencing to determine the genotypic difference in transcriptome profile using two Tibetan wild barley genotypes differing in LN tolerance (XZ149, tolerant and XZ56, sensitive). A total of 1469 differentially expressed genes (DEGs) were identified in the two genotypes at 6 h and 48 h after LN treatment. Genetic difference existed in DEGs between XZ149 and XZ56, including transporters, transcription factors (TFs), kinases, antioxidant stress and hormone signaling related genes. Meanwhile, 695 LN tolerance-associated DEGs were mainly mapped to amino acid metabolism, starch and sucrose metabolism and secondary metabolism, and involved in transporter activity, antioxidant activities, and other gene ontology (GO). XZ149 had a higher capability of N absorption and use efficiency under LN stress than XZ56. The higher expression of nitrate transporters and energy-saving assimilation pattern could be attributed to its more N uptake and higher LN tolerance. In addition, auxin (IAA) and ethylene (ETH) response pathways may be also related to the genotypic difference in LN tolerance. CONCLUSION: The responses of XZ149 and XZ56 to LN stress differed dramatically at transcriptional level. The identified candidate genes related to LN tolerance may provide new insights into comprehensive understanding of the genotypic difference in N utilization and LN tolerance.

HvEXPB7, a novel ß-expansin gene revealed by the root hair transcriptome of Tibetan wild barley, improves root hair growth under drought stress.

Tibetan wild barley is a treasure trove of useful genes for crop improvement including abiotic stress tolerance, like drought. Root hair of single-celled structures plays an important role in water and nutrition uptake. Polyethylene-glycol-induced drought stress hydroponic/petri-dish experiments were performed, where root hair morphology and transcriptional characteristics of two contrasting Tibetan wild barley genotypes (drought-tolerant XZ5 and drought-sensitive XZ54) and drought-tolerant cv. Tadmor were compared. Drought-induced root hair growth was only observed in XZ5. Thirty-six drought tolerance-associated genes were identified in XZ5, including 16 genes specifically highly expressed in XZ5 but not Tadmor under drought. The full length cDNA of a novel ß-expansin gene (HvEXPB7), being the unique root hair development related gene in the identified genes, was cloned. The sequence comparison indicated that HvEXPB7 carried both DPBB_1 and Pollon_allerg_1 domains. HvEXPB7 is predominantly expressed in roots. Subcellular localization verified that HvEXPB7 is located in the plasma membrane. Barley stripe mosaic virus induced gene silencing (BSMV-VIGS) of HvEXPB7 led to severely suppressed root hairs both under control and drought conditions, and significantly reduced K uptake. These findings highlight and confer the significance of HvEXPB7 in root hair growth under drought stress in XZ5, and provide a novel insight into the genetic basis for drought tolerance in Tibetan wild barley.

Unpaired Dual-Modal Image Complementation Learning for Single-Modal Medical Image Segmentation.

OBJECTIVE: Multi-modal MR/CT image segmentation is an important task in disease diagnosis and treatment, but it is usually difficult to acquire aligned multi-modal images of a patient in clinical practice due to the high cost and specific allergic reactions to contrast agents. To address these issues, a task complementation framework is proposed to enable unpaired multi-modal image complementation learning in the training stage and single-modal image segmentation in the inference stage. METHOD: To fuse unpaired dual-modal images in the training stage and allow single-modal image segmentation in the inference stage, a synthesis-segmentation task complementation network is constructed to mutually facilitate cross-modal image synthesis and segmentation since the same content feature can be used to perform the image segmentation task and image synthesis task. To maintain the consistency of the target organ with varied shapes, a curvature consistency loss is proposed to align the segmentation predictions of the original image and the cross-modal synthesized image. To segment the small lesions or substructures, a regression-segmentation task complementation network is constructed to utilize the auxiliary feature of the target organ. RESULTS: Comprehensive experiments have been performed with an in-house dataset and a publicly available dataset. The experimental results have demonstrated the superiority of our framework over state-of-the-art methods. CONCLUSION: The proposed method can fuse dual-modal CT/MR images in the training stage and only needs single-modal CT/MR images in the inference stage. SIGNIFICANCE: The proposed method can be used in routine clinical occasions when only single-modal CT/MR image is available for a patient.

Style Consistency Unsupervised Domain Adaptation Medical Image Segmentation.

Unsupervised domain adaptation medical image segmentation is aimed to segment unlabeled target domain images with labeled source domain images. However, different medical imaging modalities lead to large domain shift between their images, in which well-trained models from one imaging modality often fail to segment images from anothor imaging modality. In this paper, to mitigate domain shift between source domain and target domain, a style consistency unsupervised domain adaptation image segmentation method is proposed. First, a local phase-enhanced style fusion method is designed to mitigate domain shift and produce locally enhanced organs of interest. Second, a phase consistency discriminator is constructed to distinguish the phase consistency of domain-invariant features between source domain and target domain, so as to enhance the disentanglement of the domain-invariant and style encoders and removal of domain-specific features from the domain-invariant encoder. Third, a style consistency estimation method is proposed to obtain inconsistency maps from intermediate synthesized target domain images with different styles to measure the difficult regions, mitigate domain shift between synthesized target domain images and real target domain images, and improve the integrity of interested organs. Fourth, style consistency entropy is defined for target domain images to further improve the integrity of the interested organ by the concentration on the inconsistent regions. Comprehensive experiments have been performed with an in-house dataset and a publicly available dataset. The experimental results have demonstrated the superiority of our framework over state-of-the-art methods.

Genome-wide analysis of FRF gene family and functional identification of HvFRF9 under drought stress in barley.

FHY3 and its homologous protein FAR1 are the founding members of FRS family. They exhibited diverse and powerful physiological functions during evolution, and participated in the response to multiple abiotic stresses. FRF genes are considered to be truncated FRS family proteins. They competed with FRS for DNA binding sites to regulate gene expression. However, only few studies are available on FRF genes in plants participating in the regulation of abiotic stress. With wide adaptability and high stress-resistance, barley is an excellent candidate for the identification of stress-resistance-related genes. In this study, 22 HvFRFs were detected in barley using bioinformatic analysis from whole genome. According to evolution and conserved motif analysis, the 22 HvFRFs could be divided into subfamilies I and II. Most promoters of subfamily I members contained abscisic acid and methyl jasmonate response elements; however, a large number promoters of subfamily II contained gibberellin and salicylic acid response elements. HvFRF9, one of the members of subfamily II, exhibited a expression advantage in different tissues, and it was most significantly upregulated under drought stress. In-situ PCR revealed that HvFRF9 is mainly expressed in the root epidermal cells, as well as xylem and phloem of roots and leaves, indicating that HvFRF9 may be related to absorption and transportation of water and nutrients. The results of subcellular localization indicated that HvFRF9 was mainly expressed in the nuclei of tobacco epidermal cells and protoplast of arabidopsis. Further, transgenic arabidopsis plants with HvFRF9 overexpression were generated to verify the role of HvFRF9 in drought resistance. Under drought stress, leaf chlorosis and wilting, MDA and O2 - contents were significantly lower, meanwhile, fresh weight, root length, PRO content, and SOD, CAT and POD activities were significantly higher in HvFRF9-overexpressing arabidopsis plants than in wild-type plants. Therefore, overexpression of HvFRF9 could significantly enhance the drought resistance in arabidopsis. These results suggested that HvFRF9 may play a key role in drought resistance in barley by increasing the absorption and transportation of water and the activity of antioxidant enzymes. This study provided a theoretical basis for drought resistance in barley and provided new genes for drought resistance breeding.

Impact of "Green Revolution" gene Rht-B1b on coleoptile length of wheat.

Wheat coleoptile is a sheath-like structure that helps to deliver the first leaf from embryo to the soil surface. Here, a RIL population consisting of 245 lines derived from Zhou 8425B × Chinese Spring cross was genotyped by the high-density Illumina iSelect 90K assay for coleoptile length (CL) QTL mapping. Three QTL for CL were mapped on chromosomes 2BL, 4BS and 4DS. Of them, two major QTL QCL.qau-4BS and QCL.qau-4DS were detected, which could explain 9.1%-22.2% of the phenotypic variances across environments on Rht-B1 and Rht-D1 loci, respectively. Several studies have reported that Rht-B1b may reduce the length of wheat CL but no study has been carried out at molecular level. In order to verify that the Rht-B1 gene is the functional gene for the 4B QTL, an overexpression line Rht-B1b-OE and a CRISPR/SpCas9 line Rht-B1b-KO were studied. The results showed that Rht-B1b overexpression could reduce the CL, while loss-of-function of Rht-B1b would increase the CL relative to that of the null transgenic plants (TNL). To dissect the underlying regulatory mechanism of Rht-B1b on CL, comparative RNA-Seq was conducted between Rht-B1b-OE and TNL. Transcriptome profiles revealed a few key pathways involving the function of Rht-B1b in coleoptile development, including phytohormones, circadian rhythm and starch and sucrose metabolism. Our findings may facilitate wheat breeding for longer coleoptiles to improve seedling early vigor for better penetration through the soil crust in arid regions.

Wheat Quality Formation and Its Regulatory Mechanism.

Elucidation of the composition, functional characteristics, and formation mechanism of wheat quality is critical for the sustainable development of wheat industry. It is well documented that wheat processing quality is largely determined by its seed storage proteins including glutenins and gliadins, which confer wheat dough with unique rheological properties, making it possible to produce a series of foods for human consumption. The proportion of different gluten components has become an important target for wheat quality improvement. In many cases, the processing quality of wheat is closely associated with the nutritional value and healthy effect of the end-products. The components of wheat seed storage proteins can greatly influence wheat quality and some can even cause intestinal inflammatory diseases or allergy in humans. Genetic and environmental factors have great impacts on seed storage protein synthesis and accumulation, and fertilization and irrigation strategies also greatly affect the seed storage protein content and composition, which together determine the final end-use quality of wheat. This review summarizes the recent progress in research on the composition, function, biosynthesis, and regulatory mechanism of wheat storage proteins and their impacts on wheat end-product quality.

Genome-wide identification of sucrose non-fermenting-1-related protein kinase genes in maize and their responses to abiotic stresses.

Introduction: Protein kinases play an important role in plants in response to environmental changes through signal transduction. As a large family of protein kinases, sucrose non-fermenting-1 (SNF1)-related kinases (SnRKs) were found and functionally verified in many plants. Nevertheless, little is known about the SnRK family of Zea mays. Methods: Evolutionary relationships, chromosome locations, gene structures, conserved motifs, and cis-elements in promoter regions were systematically analyzed. Besides, tissue-specific and stress-induced expression patterns of ZmSnRKs were determined. Finally, functional regulatory networks between ZmSnRKs and other proteins or miRNAs were constructed. Results and Discussion: In total, 60 SnRK genes located on 10 chromosomes were discovered in maize. ZmSnRKs were classified into three subfamilies (ZmSnRK1, ZmSnRK2, and ZmSnRK3), consisting of 4, 14, and 42 genes, respectively. Gene structure analysis showed that 33 of the 42 ZmSnRK3 genes contained only one exon. Most ZmSnRK genes contained at least one ABRE, MBS, and LTR cis-element and a few ZmSnRK genes had AuxRR-core, P-box, MBSI, and SARE ciselements in their promoter regions. The Ka:Ks ratio of 22 paralogous ZmSnRK gene pairs revealed that the ZmSnRK gene family had experienced a purifying selection. Meanwhile, we analyzed the expression profiles of ZmSnRKs, and they exhibited significant differences in various tissues and abiotic stresses. In addition, A total of eight ZmPP2Cs, which can interact with ZmSnRK proteins, and 46 miRNAs, which can target 24 ZmSnRKs, were identified. Generally, these results provide valuable information for further function verification of ZmSnRKs, and improve our understanding of the role of ZmSnRKs in the climate resilience of maize.