Transcriptome analysis of drought-responsive genes regulated by hydrogen sulfide in wheat (Triticum aestivum L.) leaves

Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding

Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.

A novel TF molecular switch-mechanism found in two contrasting ecotypes of a psammophyte, Agriophyllum squarrosum, in regulating transcriptional drought memory

BACKGROUND

Prior drought stress may change plants response patterns and subsequently increase their tolerance to the same condition, which can be referred to as "drought memory" and proved essential for plants well-being. However, the mechanism of transcriptional drought memory in psammophytes remains unclear. Agriophyllum squarrosum, a pioneer species on mobile dunes, is widely spread in Northern China's vast desert areas with outstanding ability of water use efficiency. Here we conducted dehydration-rehydration treatment on A. squarrosum semi-arid land ecotype AEX and arid land ecotype WW to dissect the drought memory mechanism of A. squarrosum, and to determine the discrepancy in drought memory of two contrasting ecotypes that had long adapted to water heterogeneity.

RESULT

Physiological traits monitoring unveiled the stronger ability and longer duration in drought memory of WW than that of AEX. A total of 1,642 and 1,339 drought memory genes (DMGs) were identified in ecotype AEX and WW, respectively. Furthermore, shared DMGs among A. squarrosum and the previously studied species depicted that drought memory commonalities in higher plants embraced pathways like primary and secondary metabolisms; while drought memory characteristics in A. squarrosum were mainly related to response to heat, high light intensity, hydrogen peroxide, and dehydration, which might be due to local adaptation to desert circumstances. Heat shock proteins (HSPs) occupied the center of the protein-protein interaction (PPI) network in drought memory transcription factors (TF), thus playing a key regulatory role in A. squarrosum drought memory. Co-expression analysis of drought memory TFs and DMGs uncovered a novel regulating module, whereby pairs of TFs might function as molecular switches in regulating DMG transforming between high and low expression levels, thus promoting drought memory reset.

CONCLUSION

Based on the co-expression analysis, protein-protein interaction prediction, and drought memory metabolic network construction, a novel regulatory module of transcriptional drought memory in A. squarrosum was hypothesized here, whereby recurrent drought signal is activated by primary TF switches, then amplified by secondary amplifiers, and thus regulates downstream complicated metabolic networks. The present research provided valuable molecular resources on plants' stress-resistance basis and shed light on drought memory in A. squarrosum.

Recent advances and mechanistic interactions of hydrogen sulfide with plant growth regulators in relation to abiotic stress tolerance in plants

Adverse environmental constraints such as drought, heat, cold, salinity, and heavy metal toxicity are the primary concerns of the agricultural industry across the globe, as these stresses negatively affect yield and quality of crop production and therefore can be a major threat to world food security. Recently, it has been demonstrated that hydrogen sulfide (H₂S), which is well-known as a gasotransmitter in animals, also plays a potent role in various growth and developmental processes in plants. H₂S, as a potent signaling molecule, is involved in several plant processes such as in the regulation of stomatal pore movements, seed germination, photosynthesis and plant adaptation to environmental stress through gene regulation, post-translation modification of proteins and redox homeostasis. Moreover, a number of experimental studies have revealed that H₂S could improve the adaptation capabilities of plants against diverse environmental constraints by mitigating the toxic and damaging effects triggered by stressful environments. An attempt has been made to uncover recent development in the biosynthetic and metabolic pathways of H₂S and various physiological functions modulated in plants, H₂S donors, their functional mechanism, and application in plants. Specifically, our focus has been on how H₂S is involved in combating the destructive effects of abiotic stresses and its role in persulfidation. Furthermore, we have comprehensively elucidated the crosstalk of H₂S with plant growth regulators.

Brassinosteroids induced drought resistance of contrasting drought-responsive genotypes of maize at physiological and transcriptomic levels

The present study investigated the brassinosteroid-induced drought resistance of contrasting drought-responsive maize genotypes at physiological and transcriptomic levels. The brassinosteroid (BR) contents along with different morphology characteristics, viz., plant height (PH), shoot dry weight (SDW), root dry weight (RDW), number of leaves (NL), the specific mass of the fourth leaf, and antioxidant activities, were investigated in two maize lines that differed in their degree of drought tolerance. In response to either control, drought, or brassinosteroid treatments, the KEGG enrichment analysis showed that plant hormonal signal transduction and starch and sucrose metabolism were augmented in both lines. In contrast, the phenylpropanoid biosynthesis was augmented in lines H21L0R1 and 478. Our results demonstrate drought-responsive molecular mechanisms and provide valuable information regarding candidate gene resources for drought improvement in maize crop. The differences observed for BR content among the maize lines were correlated with their degree of drought tolerance, as the highly tolerant genotype showed higher BR content under drought stress.

The secret of H2 S to keep plants young and fresh and its products

Recently, accumulating evidence has shown that hydrogen sulphide (H₂ S), a newly determined gasotransmitter, plays important roles in senescence, which is an essential biological process for plant fitness and an important agricultural trait that is critical for the yield and quality of farm produce. Here, in this review, we summarize the roles of H₂ S in senescence, both before and after the harvesting of agricultural products, and the underlying mechanism is also discussed. During the plant growth process, the function of H₂ S in the leaf senescence process has been studied extensively, and H₂ S plays roles during the whole process, including the initiation, reorganization and terminal stages. While during the postharvest stage, H₂ S can prevents farm products from deterioration resulting from over-ripening, pathogen attack and incorrect storage. The underlying H₂ S-related mechanisms during different stages of the senescence process are summarized and compared. The most prominent interaction occurs between H₂ S and reactive oxygen species, and the molecular mechanism is explored. Additionally, the conserved action mode of H₂ S in different life processes and different species is also discussed. In the future, multi-omics analyses over time will be needed to investigate the detailed mechanisms of H₂ S, and a safety attribute analysis of H₂ S is also required before it can be used in agricultural production.

Hydrogen sulfide: an emerging component against abiotic stress in plants

As a result of climate change, abiotic stresses are the most common cause of crop losses worldwide. Abiotic stresses significantly impair plants' physiological, biochemical, molecular and cellular mechanisms, limiting crop productivity under adverse climate conditions. However, plants can implement essential mechanisms against abiotic stressors to maintain their growth and persistence under such stressful environments. In nature, plants have developed several adaptations and defence mechanisms to mitigate abiotic stress. Moreover, recent research has revealed that signalling molecules like hydrogen sulfide (H₂ S) play a crucial role in mitigating the adverse effects of environmental stresses in plants by implementing several physiological and biochemical mechanisms. Mainly, H₂ S helps to implement antioxidant defence systems, and interacts with other molecules like nitric oxide (NO), reactive oxygen species (ROS), phytohormones, etc. These molecules are well-known as the key players that moderate the adverse effects of abiotic stresses. Currently, little progress has been made in understanding the molecular basis of the protective role of H₂ S; however, it is imperative to understand the molecular basis using the state-of-the-art CRISPR-Cas gene-editing tool. Subsequently, genetic engineering could provide a promising approach to unravelling the molecular basis of stress tolerance mediated by exogenous/endogenous H₂ S. Here, we review recent advances in understanding the beneficial roles of H₂ S in conferring multiple abiotic stress tolerance in plants. Further, we also discuss the interaction and crosstalk between H₂ S and other signal molecules; as well as highlighting some genetic engineering-based current and future directions.

Changes in phenolic compounds production as a defensive mechanism against hydrogen sulfide pollution in Scrophularia striata

Increasing pollutants such as hydrogen sulfide (H₂S) from industrial activities is an ecological challenge for plants, which seriously affects their health and productivity. Scrophularia striata is a plant endemic to Iran growing in the province of Ilam, wherein a gas refinery releases toxic agents such as H₂S whose detrimental effects on the function and tolerability of medicinal plants in this region have yet to be elucidated. Thus, we initiated a hydroponic study into hormetic effect of sodium hydrogen sulfide (NaHS) concentrations (0, 3 and 7 mM) as H₂S-donor at different time points on oxidative status and phenolic compounds, focusing more on phenylethanoid glycosides (PhGs) in S. striata. Our results indicated that hydrogen peroxide (H₂O₂) increased significantly at 3 mM NaHS after 48 h, while its peak at 7 mM occurred after 24 h. Nitric oxide (NO) level peaked at 3 mM and 7 mM after 24 h. Treatment with NaHS also resulted in a dose-dependent induction of phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) enzyme activities, phenolic acids production (cinnamic acid, coumaric acid, ferulic acid, caffeic acid and salicylic acid) and acteoside accumulation, ultimately leading to an increase in antioxidant capacity. Modulation of soluble sugars contents including glucose, mannose and rhamnose/xylose, occurred after the treatment with NaHS, likely increasing plant tolerance due to their biological activity and structural effects. Overall, our results suggest that dose-dependent accumulation of phenolics, notably acteoside, leads to an augmentation in antioxidant system to deal with H₂S stress in S. striata.

Time-course transcriptome and WGCNA analysis revealed the drought response mechanism of two sunflower inbred lines

Drought is one of the most serious abiotic stress factors limiting crop yields. Although sunflower is considered a moderate drought-tolerant plant, drought stress still has a negative impact on sunflower yield as cultivation expands into arid regions. The extent of drought stress is varieties and time-dependent, however, the molecular response mechanisms of drought tolerance in sunflower with different varieties are still unclear. Here, we performed comparative physiological and transcriptome analyses on two sunflower inbred lines with different drought tolerance at the seedling stage. The analysis of nine physiological and biochemical indicators showed that the leaf surface area, leaf relative water content, and cell membrane integrity of drought tolerance inbred line were higher than those of drought-sensitive inbred line under drought stress, indicating that DT had stronger drought resistance. Transcriptome analyses identified 24,234 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed the up-regulated genes were mainly enriched in gibberellin metabolism and rRNA processing, while the down-regulated genes were mainly enriched in cell-wall, photosynthesis, and terpene metabolism. Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis showed genes related to GABAergic synapse, ribosome biogenesis were up-regulated, while genes related with amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, photosynthesis were down-regulated. Mapman analysis revealed differences in plant hormone-signaling genes over time and between samples. A total of 1,311 unique putative transcription factors (TFs) were identified from all DEGs by iTAK, among which the high abundance of transcription factor families include bHLH, AP2/ERF, MYB, C2H2, etc. Weighted gene co-expression network analysis (WGCNA) revealed a total of 2,251 genes belonging to two modules(blue 4, lightslateblue), respectively, which were significantly associated with six traits. GO and KEGG enrichment analysis of these genes was performed, followed by visualization with Cytoscape software, and the top 20 Hub genes were screened using the CytoHubba plugin.

The Impact of Treated Wastewater Irrigation on the Metabolism of Barley Grown in Arid and Semi-Arid Regions

The use of treated wastewater (TWW) for irrigation has gained global attention since it reduces pressure on groundwater (GW) and surface water. This study aimed to evaluate the effect of TWW on agronomic, photosynthetic, stomatal, and nutritional characteristics of barley plants. The experiment with barley was established on two bands: one band was irrigated with GW and the other with TWW. The evaluation was performed 25, 40, 60, 90, and 115 days after sowing (DAS). Results showed that irrigation with TWW increased (p < 0.01) grain yield by 54.3% and forage yield by 39.4% compared to GW irrigation. In addition, it increased plant height (PH) (p = 0.013), chlorophyll concentration index (CCI) (p = 0.006), and leaf area index (LAI) (p = 0.002). TWW also produced a positive effect (p < 0.05) in all the photosynthetic efficiency parameters evaluated. Barley plants irrigated with TWW had lower stomatal density (SD) and area (SA) (p < 0.001) than plants irrigated with GW. Plants irrigated with TWW had a higher P concentration (p < 0.05) in stems and roots and K concentration in leaves than plants irrigated with GW. We concluded that the use of TWW induced important biochemical, physiological, and agronomic changes in barley plants. Hence, the use of TWW may be a sustainable alternative for barley production in arid and semi-arid regions. This study was part of a government project, which aimed to develop a new metropolitan irrigation district with TWW. This study may contribute to the sustainability of water resources and agricultural practices in northern Mexico.

Metal tolerance in plants: Molecular and physicochemical interface determines the "not so heavy effect" of heavy metals

An increase in technological interventions and ruthless urbanization in the name of development has deteriorated our environment over time and caused the buildup of heavy metals (HMs) in the soil and water resources. These heavy metals are gaining increased access into our food chain through the plant and/or animal-based products, to adversely impact human health. The issue of how to restrict the entry of HMs or modulate their response in event of their ingress into the plant system is worrisome. The current knowledge on the interactive-regulatory role and contribution of different physical, biophysical, biochemical, physiological, and molecular factors that determine the heavy metal availability-uptake-partitioning dynamics in the soil-plant-environment needs to be updated. The present review critically analyses the interactive overlaps between different adaptation and tolerance strategies that may be causally related to their cellular localization, conjugation and homeostasis, a relative affinity for the transporters, rhizosphere modifications, activation of efflux pumps and vacuolar sequestration that singly or collectively determine a plant's response to HM stress. Recently postulated role of gaseous pollutants such as SO₂ and other secondary metabolites in heavy metal tolerance, which may be regulated at the whole plant and/or tissue/cell is discussed to delineate and work towards a "not so heavy" response of plants to heavy metals present in the contaminated soils.

Identification of HvLRX, a new dehydration and light responsive gene in Tibetan hulless barley (Hordeum vulgare var. nudum)

BACKGROUND

Tibetan hulless barley (Hordeum vulgare var. nudum), adjusting to the harsh environment on Qinghai-Tibet Plateau, is a good subject for analyzing drought tolerance mechanism. Several unannotated differentially expressed genes (DEGs) were identified through our previous RNA-Seq study using two hulless barley accessions with contrasting drought tolerance. One of these DEGs, HVU010048.2, showed up-regulated pattern under dehydration stress in both drought tolerant (DT) and drought susceptible (DS) accessions, while its function in drought resistance remains unknown. This new gene was named as HvLRX (light responsive X), because its expression was induced under high light intensity while suppressed under dark.

OBJECTIVE

To provide preliminary bioinformatics prediction, expression pattern, and drought resistance function of this new gene.

METHODS

Bioinformatics analysis of HvLRX were conducted by MEGA, PlantCARE, ProtParam, CELLO et al. The expression pattern of HvLRX under different light intensity, dehydration shock, gradual drought stress, NaCl stress, polyethylene glycol (PEG) 6000 stress and abscisic acid (ABA) treatment was investigated by quantitative reverse transcription-polymerase chain reaction (RT-qPCR). The function of HvLRX was analyzed by virus induced gene silencing (VIGS) in hulless barley and by transgenic method in tobacco.

RESULTS

Full cDNAs of HvLRX were cloned and compared in three hulless barley accessions. Homologues of HvLRX protein in other plants were excavated and their phylogenetic relationship was analyzed. Several light responsive elements (ATC-motif, Box 4, G-box, Sp1, and chs-CMA1a) were identified in its promoter region. Its expression can be promoted under high light intensity, dehydration shock, gradual drought stress, PEG 6000, and NaCl stress, but was almost unchanged in ABA treatment. HvLRX-silenced plants had a higher leaf water loss rate (WLR) and a lower survival rate (SR) compared with controls under dehydration stress. The infected leaves of HvLRX-silenced plants lost their water content quickly and became withered at 10 dpi. The SR of HvLRX overexpressed transgenic tobacco plants was significantly higher than that of wild-type plants. These results indicated HvLRX play a role in drought resistance. Besides, retarded vegetative growth was detected in HvLRX-silenced hulless barley plants, which suggested that this gene is important for plant development.

CONCLUSIONS

This study provided data of bioinformatics, expression pattern, and function of HvLRX. To our knowledge, this is the first report of this new dehydration and light responsive gene.

Hydrogen sulfide: An emerging signaling molecule regulating drought stress response in plants

Hydrogen sulfide (H₂ S) is a small, reactive signaling molecule that is produced within chloroplasts of plant cells as an intermediate in the assimilatory sulfate reduction pathway by the enzyme sulfite reductase. In addition, H₂ S is also produced in cytosol and mitochondria by desulfhydration of l-cysteine catalyzed by l-cysteine desulfhydrase (DES1) in the cytosol and from β-cyanoalanine in mitochondria, in a reaction catalyzed by β-cyano-Ala synthase C1 (CAS-C1). H₂ S exerts its numerous biological functions by post-translational modification involving oxidation of cysteine residues (RSH) to persulfides (RSSH). At lower concentrations (10-1000 μmol L^-1 ), H₂ S shows huge agricultural potential as it increases the germination rate, the size, fresh weight, and ultimately the crop yield. It is also involved in abiotic stress response against drought, salinity, high temperature, and heavy metals. H₂ S donor, for example, sodium hydrosulfide (NaHS), has been exogenously applied on plants by various researchers to provide drought stress tolerance. Exogenous application results in the accumulation of polyamines, sugars, glycine betaine, and enhancement of the antioxidant enzyme activities in response to drought-induced osmotic and oxidative stress, thus, providing stress adaptation to plants. At the biochemical level, administration of H₂ S donors reduces malondialdehyde content and lipoxygenase activity to maintain the cell integrity, causes abscisic acid-mediated stomatal closure to prevent water loss through transpiration, and accelerates the photosystem II repair cycle. Here, we review the crosstalk of H₂ S with secondary messengers and phytohormones towards the regulation of drought stress response and emphasize various approaches that can be addressed to strengthen research in this area.

Comparative Transcriptome Analysis of Sophora japonica (L.) Roots Reveals Key Pathways and Genes in Response to PEG-Induced Drought Stress under Different Nitrogen Conditions

Sophora japonica is a native leguminous tree species in China. The high stress tolerance contributes to its long lifespan of thousands of years. The lack of genomic resources greatly limits genetic studies on the stress responses of S. japonica. In this study, RNA-seq was conducted for S. japonica roots grown under short-term 20% polyethylene glycol (PEG) 6000-induced drought stress under normal N and N starvation conditions (1 and 0 mM NH4NO3, respectively). In each of the libraries, we generated more than 25 million clean reads, which were then de novo assembled to 46,852 unigenes with an average length of 1310.49 bp. In the differential expression analyses, more differentially expressed genes (DEGs) were found under drought with N starvation than under single stresses. The number of transcripts identified under N starvation and drought in S. japonica was nearly the same, but more upregulated genes were induced by drought, while more downregulated genes were induced by N starvation. Genes involved in “phenylpropanoid biosynthesis” and “biosynthesis of amino acids” pathways were upregulated according to KEGG enrichment analyses, irrespective of the stress treatments. Additionally, upregulated N metabolism genes were enriched upon drought, and downregulated photosynthesis genes were enriched under N starvation. We found 4,372 and 5,430 drought-responsive DEGs under normal N and N starvation conditions, respectively. N starvation may aggravate drought by downregulating transcripts in the “carbon metabolism”, “ribosome”, “arginine biosynthesis pathway”, “oxidative phosphorylation” and “aminoacyl-tRNA biosynthesis” pathways. We identified 78 genes related to N uptake and assimilation, 38 of which exhibited differential expression under stress. A total of 395 DEGs were categorized as transcription factors, of which AR2/ERF-ERF, WRKY, NAC, MYB, bHLH, C3H and C2C2-Dof families played key roles in drought and N starvation stresses. The transcriptome data obtained, and the genes identified facilitate our understanding of the mechanisms of S. japonica responses to drought and N starvation stresses and provide a molecular foundation for understanding the mechanisms of its long lifespan for breeding resistant varieties for greening.

Sulfur dioxide enhance drought tolerance of wheat seedlings through H2S signaling

Drought is one of the most common factors that limit plant growth and productivity. Sulfur dioxide (SO₂) has recently been found to play a benefical role in protection of plants against environmental stress. In this study, we investigated the effect of SO₂ on the physiological and molecular response of wheat seedlings to drought stress. Pretreatment with 10 mg/m³ SO₂ significantly increased the survival rate and relative water content (RWC) of wheat seedlings under drought stress, indicating that pre-exposure to appropriate level of SO₂ could enhance drought tolerance of plants. These responses were related to the enhanced proline accumulation in the drought-treated wheat seedlings that induced by SO₂ pretreatment. Meanwhile, SO₂ pretreatment increased the activities of superoxide dismutase (SOD) and peroxidase (POD), and effectively reduced the content of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) in drought-treated wheat seedlings, suggesting SO₂ could alleviate drought-induced oxidative damage by enhancing antioxidant defense system in plants. Expression analysis of transcription factor genes also showed that SO₂ pretreatment decreased the expression of TaNAC69, but the expression of TaERF1 and TaMYB30 changed slightly and maintained at higher levels in wheat seedlings in response to drought stress. Furthermore, SO₂ pretreatment triggered marked accumulation of hydrogen sulfide (H₂S) in wheat seedlings under drought stress. When scavenged H₂S by spraying Hypotaurine (HT), the activities of antioxidant enzymes and the expression of transcription factor genes were decreased, and the content of H₂O₂ and MDA increased to the level of drought treatment alone, suggesting a regulatory role of SO₂-induced H₂S in plant adaptation to drought stress. Together, this study indicated that SO₂ enhanced drought tolerance of wheat seedlings through H₂S signaling, and provided new strategy for enhancing plant tolerance to drought stress.

Hydrogen sulfide (H2S) signaling in plant development and stress responses

ABSTRACT

Hydrogen sulfide (H₂S) was initially recognized as a toxic gas and its biological functions in mammalian cells have been gradually discovered during the past decades. In the latest decade, numerous studies have revealed that H₂S has versatile functions in plants as well. In this review, we summarize H₂S-mediated sulfur metabolic pathways, as well as the progress in the recognition of its biological functions in plant growth and development, particularly its physiological functions in biotic and abiotic stress responses. Besides direct chemical reactions, nitric oxide (NO) and hydrogen peroxide (H₂O₂) have complex relationships with H₂S in plant signaling, both of which mediate protein post-translational modification (PTM) to attack the cysteine residues. We also discuss recent progress in the research on the three types of PTMs and their biological functions in plants. Finally, we propose the relevant issues that need to be addressed in the future research.

GRAPHIC ABSTRACT

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s42994-021-00035-4.

Hydrogen sulfide: A versatile gaseous molecule in plants

Hydrogen sulfide (H₂S) is a gasotransmitter and signaling molecule associated with seed germination, plant growth, organogenesis, photosynthesis, stomatal conductance, senescence, and post-harvesting. H₂S is produced in plants via both enzymatic and non-enzymatic pathways in different subcellular compartments. Exogenous application of H₂S facilitates versatile metabolic processes and antioxidant machinery in plants under normal and environmental stresses. This compound interacts with phytohormones like auxins, abscisic acid, gibberellins, ethylene, jasmonic acid, and salicylic acid. Furthermore, H₂S participates in signal transductions of other signaling molecules like nitric oxide, carbon monoxide, calcium, methylglyoxal, and hydrogen peroxide. It also mediates post-translational modification, which is a protective mechanism against oxidative damage of proteins. This review summarizes the roles of H₂S as intriguing molecule in plants.

H2S induces NO in the regulation of AsA-GSH cycle in wheat seedlings by water stress

In current study, we investigated the relationship between hydrogen sulfide (H₂S) and nitric oxide (NO) in the regulation of ascorbate-glutathione (AsA-GSH) cycle in wheat seedlings by water stress. Findings showed that water stress significantly stimulated the production of H₂S and NO, the transcript levels and activities of enzymes in AsA-GSH cycle, as well as malondialdehyde (MDA) production and electrolyte leakage, but significantly decreased AsA/DHA and GSH/GSSG. Meanwhile, water stress significantly decreased plant height and dry biomass. Except MDA and electrolyte leakage, above changes induced by water stress were reversed by H₂S synthesis inhibitor aminooxyacetic acid (AOA) and NO synthesis inhibitor N^G-nitro-L-arginine methyl ester (L-NAME). However, AOA and L-NAME significantly enhanced MDA production and electrolyte leakage, which further decreased plant height and dry biomass of wheat seedlings under water stress. Application of exogenous H₂S donor sodium hydrosulfide (NaHS) to AOA-treated plants and application of exogenous NO donor sodium nitroprusside (SNP) to L-NAME-treated plants reversed above effects of AOA and L-NAME, respectively. Application of L-NAME plus water stress significantly decreased NO production induced by water stress. However, application of L-NAME plus water stress had no obvious influence on H₂S production induced by water stress, while application of AOA plus water stress significantly reduced the production of H₂S and NO induced by water stress. Current findings suggested that H₂S acted upstream of NO in the regulation of AsA-GSH cycle in wheat seedlings by water stress.

Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng

Pseudotaxus chienii, a rare tertiary relict species with economic and ecological value, is a representative of the monotypic genus Pseudotaxus that is endemic to China. P. chienii can adapt well to habitat isolation and ecological heterogeneity under a variety of climate and soil conditions, and is able to survive in harsh environments. However, little is known about the molecular and genetic resources of this long-lived conifer. Herein, we sequenced the transcriptomes of four organs of P. chienii using the PacBio Isoform Sequencing and Illumina RNA Sequencing platforms. Based on the PacBio Iso-Seq data, we obtained 44,896, 58,082, 50,485, and 67,638 full-length unigenes from the root, stem, leaf, and strobilus, respectively, with a mean length of 2692 bp, and a mean N50 length of 3010.75 bp. We then comprehensively annotated these unigenes. The number of organ-specific expressed unigenes ranged from 4393 in leaf to 9124 in strobilus, suggesting their special roles in physiological processes, organ development, and adaptability in the different four organs. A total of 16,562 differentially expressed genes (DEGs) were identified among the four organs and clustered into six subclusters. The gene families related to biotic/abiotic factors, including the TPS, CYP450, and HSP families, were characterized. The expression levels of most DEGs in the phenylpropanoid biosynthesis pathway and plant–pathogen interactions were higher in the root than in the three other organs, suggesting that root constitutes the main organ of defensive compound synthesis and accumulation and has a stronger ability to respond to stress. The sequences were analyzed to predict transcription factors, long non-coding RNAs, and alternative splicing events. The expression levels of most DEGs of C2H2, C3H, bHLH, and bZIP families in the root and stem were higher than those in the leaf and strobilus, indicating that these TFs may play a crucial role in the survival of the root and stem. These results comprise the first comprehensive gene expression profiles obtained for different organs of P. chienii. Our findings will facilitate further studies on the functional genomics, adaptive evolution, and phylogeny of P. chienii, and lay the foundation for the development of conservation strategies for this endangered conifer.

Transcriptome analysis of near-isogenic lines for glume hairiness of wheat

Hairiness, which is a phenotypic trait common among land plants, primarily affects the stem, leaf, and floral organs. Plant hairiness is associated with complex functions. For example, glume hairiness in wheat is related to the resistance to biotic and abiotic stresses, and may also influence human health. In the present study, two pairs of near-isogenic lines (NILs) for glume hairiness, which were derived from a cross between a Tibetan semi-wild wheat accession (Triticum aestivum ssp. tibetanum Q1028) and a common wheat cultivar (T. aestivum 'Zhengmai 9023'), underwent a glume transcriptome analysis. We detected 27,935 novel genes, of which 18,027 were annotated. Additionally, 488 and 600 differentially expressed genes (DEGs) were detected in NIL1 and NIL2, respectively, with 37 DEGs detected in both NIL pairs. Moreover, 987 and 1584 single nucleotide polymorphisms (SNPs) were detected in NIL1 and NIL2, respectively, with 39 SNPs detected in both NIL pairs, of which most were located in the Hairy glume (Hg) gene region on chromosome arm 1AS. The annotation of the DEGs with gene ontology terms revealed that genes associated with hairiness in Arabidopsis and rice were similarly enriched. The possible functions of these genes related to glume hairiness were examined. The study results provide useful information for identifying candidate genes and the fine-mapping of Hg in the wheat genome.

Comparative Transcriptome Analysis of Two Aegilops tauschii with Contrasting Drought Tolerance by RNA-Seq

As the diploid progenitor of common wheat, Aegilops tauschii is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported concerning the molecular mechanism of drought tolerance in Ae. tauschii. In this work, the drought tolerance of 155 Ae. tauschii accessions was firstly screened on the basis of their coleoptile lengths under simulated drought stress. Subsequently, two accessions (XJ002 and XJ098) with contrasting coleoptile lengths were selected and intensively analyzed on rate of water loss (RWL) as well as physiological characters, confirming the difference in drought tolerance at the seedling stage. Further, RNA-seq was utilized for global transcriptome profiling of the two accessions seedling leaves under drought stress conditions. A total of 6969 differentially expressed genes (DEGs) associated with drought tolerance were identified, and their functional annotations demonstrated that the stress response was mediated by pathways involving alpha-linolenic acid metabolism, starch and sucrose metabolism, peroxisome, mitogen-activated protein kinase (MAPK) signaling, carbon fixation in photosynthetic organisms, and glycerophospholipid metabolism. In addition, DEGs with obvious differences between the two accessions were intensively analyzed, indicating that the expression level of DEGs was basically in alignment with the physiological changes of Ae. tauschii under drought stress. The results not only shed fundamental light on the regulatory process of drought tolerance in Ae. tauschii, but also provide a new gene resource for improving the drought tolerance of common wheat.

H2S signaling in plants and applications in agriculture

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Hydrogen sulfide (H₂S) plays a signaling role in higher plants.

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It mediates persulfidation, a post-translational modification.

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It regulates physiological functions ranging from seed germination to fruit ripening.

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The beneficial effects of exogenous H₂S are mainly caused by the stimulation of antioxidant systems.

The signaling properties of the gasotransmitter molecule hydrogen sulfide (H₂S), which is endogenously generated in plant cells, are mainly observed during persulfidation, a protein post-translational modification (PTM) that affects redox-sensitive cysteine residues. There is growing experimental evidence that H₂S in higher plants may function as a mechanism of response to environmental stress conditions. In addition, exogenous applications of H₂S to plants appear to provide additional protection against stresses, such as salinity, drought, extreme temperatures and heavy metals, mainly through the induction of antioxidant systems, in order to palliate oxidative cellular damage. H₂S also appears to be involved in regulating physiological functions, such as seed germination, stomatal movement and fruit ripening, as well as molecules that maintain post-harvest quality and rhizobium–legume symbiosis. These properties of H₂S open up new challenges in plant research to better understand its functions as well as new opportunities for biotechnological treatments in agriculture in a changing environment.

Stress responsive gene regulation in relation to hydrogen sulfide in plants under abiotic stress

Plants often face a variety of abiotic stresses, which affects them negatively and lead to yield loss. The antioxidant system efficiently removes excessive reactive oxygen species and maintains redox homeostasis in plants. With better understanding of these protective mechanisms, recently the concept of hydrogen sulfide (H₂ S) and its role in cell signaling has become the center of attention. H₂ S has been recognized as a third gasotransmitter and a potent regulator of growth and development processes such as germination, maturation, senescence and defense mechanism in plants. Because of its gaseous nature, H₂ S can diffuse to different part of the cells and balance the antioxidant pools by supplying sulfur to cells. H₂ S showed tolerance against a plethora of adverse environmental conditions like drought, salt, high temperature, cold, heavy metals and flood via changing in level of osmolytes, malonaldialdehyde, Na⁺ /K⁺ uptake, activities of H₂ S biosynthesis and antioxidative enzymes. It also promotes cross adaptation through persulfidation. H₂ S along with calcium, methylglyoxal and nitric oxide, and their cross talk induces the expression of mitogen activated protein kinases as well as other genes in response to stress. Therefore, it is sensible to evaluate and explore the stress responsive genes involved in H₂ S regulated homeostasis and stress tolerance. The current article is aimed to summarize the recent updates on H₂ S-mediated gene regulation in special reference to abiotic stress tolerance mechanism, and cross adaptation in plants. Moreover, new insights into the H₂ S-associated signal transduction pathway have also been explored.

Biochemical Characterization of the Fusarium graminearum Candidate ACC-Deaminases and Virulence Testing of Knockout Mutant Strains

Fusarium graminearum is a plant pathogenic fungus which is able to infect wheat and other economically important cereal crop species. The role of ethylene in the interaction with host plants is unclear and controversial. We have analyzed the inventory of genes with a putative function in ethylene production or degradation of the ethylene precursor 1-aminocyclopropane carboxylic acid (ACC). F. graminearum, in contrast to other species, does not contain a candidate gene encoding ethylene-forming enzyme. Three genes with similarity to ACC synthases exist; heterologous expression of these did not reveal enzymatic activity. The F. graminearum genome contains in addition two ACC deaminase candidate genes. We have expressed both genes in E. coli and characterized the enzymatic properties of the affinity-purified products. One of the proteins had indeed ACC deaminase activity, with kinetic properties similar to ethylene-stress reducing enzymes of plant growth promoting bacteria. The other candidate was inactive with ACC but turned out to be a d-cysteine desulfhydrase. Since it had been reported that ethylene insensitivity in transgenic wheat increased Fusarium resistance and reduced the content of the mycotoxin deoxynivalenol (DON) in infected wheat, we generated single and double knockout mutants of both genes in the F. graminearum strain PH-1. No statistically significant effect of the gene disruptions on fungal spread or mycotoxin content was detected, indicating that the ability of the fungus to manipulate the production of the gaseous plant hormones ethylene and H₂S is dispensable for full virulence.

Interactions between hydrogen sulphide and nitric oxide regulate two soybean citrate transporters during the alleviation of aluminium toxicity

Hydrogen sulphide (H2 S) is emerging as an important signalling molecule involved in plant resistance to various stresses. However, the underlying mechanism of H2 S in aluminium (Al) resistance and the crosstalk between H2 S and nitric oxide (NO) in Al stress signalling remain elusive. Citrate secretion is a wide-spread strategy for plants against Al toxicity. Here, two citrate transporter genes, GmMATE13 and GmMATE47, were identified and characterized in soybean. Functional analysis in Xenopus oocytes and transgenic Arabidopsis showed that GmMATE13 and GmMATE47 mediated citrate exudation and enhanced Al resistance. Al treatment triggered H2 S generation and citrate exudation in soybean roots. Pretreatment with an H2 S donor significantly elevated Al-induced citrate exudation, reduced Al accumulation in root tips, and alleviated Al-induced inhibition of root elongation, whereas application of an H2 S scavenger elicited the opposite effect. Furthermore, H2 S and NO mediated Al-induced GmMATE expression and plasma membrane (PM) H+ -ATPase activity and expression. Further investigation showed that NO induced H2 S production by regulating the key enzymes involved in biosynthesis and degradation of H2 S. These findings indicate that H2 S acts downstream of NO in mediating Al-induced citrate secretion through the upregulation of PM H+ -ATPase-coupled citrate transporter cotransport systems, thereby conferring plant resistance to Al toxicity.

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets

Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought responses in the field remain largely unknown. Here, we addressed this by utilizing an interdisciplinary approach involving field water status phenotyping, sampling, and gene expression analyses. Overall, changes at the transcriptional level were reflected in plant spectral traits amenable to field-level physiological measurements, although changes in photosynthesis-related pathways were found likely to be under more complex post-transcriptional control. Examining homoeologous genes with a 1:1:1 relationship across the A, B, and D genomes (triads), we revealed a complex genomic architecture for drought responses under field conditions, involving gene homoeolog specialization, multiple gene clusters, gene families, miRNAs, and transcription factors coordinating these responses. Our results provide a new focus for genomics-assisted breeding of drought-tolerant wheat cultivars.

The roles of H2S and H2O2 in regulating AsA-GSH cycle in the leaves of wheat seedlings under drought stress

This paper investigated the roles of hydrogen sulfide (H₂S) and hydrogen peroxide (H₂O₂) and the possible relationship between them in regulating the AsA-GSH cycle in wheat leaves under drought stress (DS). Results showed that DS markedly increased the production of H₂S and H₂O₂, the transcript levels and activities of ascorbate peroxidase (APX), glutathione reductase (GR), monodehydroascorbate reductase (MDHAR), and dehydroascorbate reductase (DHAR); malondialdehyde (MDA) content; and electrolyte leakage (EL). Meanwhile, DS markedly reduced plant height and biomass. Above increases induced by drought stress except MDA content and EL were all suppressed by pretreatments with H₂S synthesis inhibitor aminooxyaceticacid (AOA) and H₂O₂ synthesis inhibitor diphenylene iodonium (DPI). Besides, pretreatments with AOA and DPI further significantly increased MDA content and EL and significantly reduced plant height and biomass under DS. DPI reduced the production of H₂O₂ and H₂S induced by DS. AOA also reduced the production of H₂S and H₂O₂ induced by DS. Pretreatments with NaHS + AOA and H₂O₂ + DPI reversed above effects of AOA and DPI. Our results suggested that H₂S and H₂O₂ all participated in the up-regulation of AsA-GSH cycle in wheat leaves by DS and possibly affected each other.

Comparative analysis of root transcriptome profiles between drought-tolerant and susceptible wheat genotypes in response to water stress

Water deficit is one of the major factors limiting crop productivity worldwide. Plant roots play a key role in uptaking water, perceiving and transducing of water deficit signals to shoot. Although the mechanisms of drought-tolerance have been reported recently, the transcriptional regulatory network of wheat root response to water stress has not been fully understood. In this study, drought-tolerant cultivar JM-262 and susceptible cultivar LM-2 are planted to characterize the root transcriptional changes and physiological responses to water deficit. A total of 8197 drought tolerance-associated differentially expressed genes (DEGs) are identified, these genes are mainly mapped to carbon metabolism, flavonoid biosynthesis, and phytohormone signal transduction. The number and expression level of DEGs involved in antioxidative and antiosmotic stresses are more enhanced in JM-262 under water stress. Furthermore, we find the DEGs related to root development are much more induced in JM-262 in phytohormone signal transduction and carbon metabolism pathway. In conclusion, JM-262 may alleviate the damage of drought by producing more osmoprotectants, ROS scavengers, biomass and energy. Interestingly, hormone signaling and cross-talk probably play an important role in promoting JM-262 greater root systems to take up more water, higher capabilities to induce more drought-related DEGs and higher resisitance to oxidative stresse.

Drought Response in Wheat: Key Genes and Regulatory Mechanisms Controlling Root System Architecture and Transpiration Efficiency

Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars.