Jute (Corchorus spp.) is an important natural bast-fibre crop, but its productivity is severely affected by abiotic stresses such as drought, salinity, and waterlogging. Improvement of stress resilience in jute requires functional molecular markers directly linked to regulatory genes governing stress responses. The present study aimed to develop such resources through an integrated transcriptome-driven approach in the two cultivated species, Corchorus capsularis and C. olitorius. Analysis of publicly available RNA sequencing datasets identified 1889-6376 and 808-6259 stress-responsive differentially expressed genes under various abiotic stress conditions in C. capsularis and C. olitorius, respectively. From these datasets, 370 differentially expressed transcription factor genes harboring microsatellite motifs were identified in C. capsularis, while 348 such genes were identified in C. olitorius. A total of 728 and 702 simple sequence repeat markers were developed from these transcription factor genes in C. capsularis and C. olitorius, respectively. The majority of markers (77% in C. capsularis and 74% in C. olitorius) were located in regulatory untranslated regions, predominantly enriched with A/T-rich di- and tri-nucleotide motifs. Major stress-responsive transcription factor families, including MYB, basic helix-loop-helix, NAC, WRKY, AP2/ethylene-responsive factor, and homeobox, were highly represented. Synteny analysis revealed 173 conserved syntenic transcription factor-simple sequence repeats gene pairs within collinear chromosomal regions, indicating strong evolutionary conservation of regulatory frameworks between the two species. Population structure analysis revealed three genetic clusters (K = 3) broadly corresponding to species identity, with some admixture in C. olitorius, which may reflect shared ancestry or limited marker resolution rather than definitive gene flow. Pairwise genetic distance values ranged from 0.091(CIN-540 and CEX-39) to 0.773 (CIN-534 and OIN-578), reflecting substantial intraspecific diversity. This study provides a comprehensive set of transcription factor-derived simple sequence repeat markers tightly associated with stress-responsive regulatory genes in jute. They offer potential advantages over anonymous genomic markers and represent valuable genomic resources for marker-assisted breeding, genomic selection, and the development of climate-resilient jute cultivars.

CaNAC67, a stress-responsive NAC transcription factor-encoding gene from chickpea (Cicer arietinum), improves drought tolerance in transgenic Arabidopsis thaliana.

BcNAC55.2 activates BcFBA8 to enhance abiotic stress tolerance in Wucai.

Evidence for a JA-responsive SNAC1-ASMT1 regulatory module contributing to melatonin-mediated salinity stress tolerance in Barley.

The SNAC (Stress-responsive NAC) subfamily, a key branch of the conserved NAC transcription factor family, plays a central role in regulating plant stress response. However, systematic characterization of the SNAC family in cotton (Gossypium spp.) remains unclear. Employing a genome-wide screening approach, this study characterized 75 distinct SNAC transcription factor genes across ten Gossypium species, with tetraploid cottons harboring twice as many as their diploid progenitors. Phylogenetic analysis categorized the genes into three subgroups, with members of the same subgroup exhibiting conserved motif compositions and gene structures. Chromosomal localization revealed a conserved distribution pattern of SNAC genes between the Dt and At subgenomes in tetraploid cotton. Genomic collinearity analysis suggested that the primary driver of SNAC family expansion was segmental duplication. Promoter analysis predicted 2974 cis-regulatory elements, including cold- and hormone-responsive motifs, indicating their potential involvement in stress regulation. These GhSNAC genes indicated significant induced expressions under stress conditions, and GhSNAC3D exhibited the most significant up-regulated expression under low temperature stress. Genetic function studies displayed that VIGS-mediated GhSNAC3D-silencing significantly reduced the cold tolerance in cotton. This study systematically analyzed the genomic characteristics of the cotton SNAC family and functionally validated the molecular mechanism of GhSNAC3D-mediated cryogenic response, which lays a foundation for subsequent research on cold resistance in cotton and stress-resistant breeding.

Drought stress can damage crop growth and lead to a decline in yield, thereby affecting food security, especially in regions vulnerable to climate change. SNAC1 (stress-responsive NAC1), the NAC transcription factor family member, plays a crucial role in stomatal movement regulation. Effective regulation of stomatal movement is essential for protecting plants from water loss during adverse conditions. Our hypothesis revolves around altering HvSNAC1 activity by introducing a point mutation in its encoding gene, thereby influencing stomatal dynamics in barley. Two TILLING mutants, each harboring missense mutations in the NAC domain, exhibited higher stomatal density after drought stress compared to the parent cultivar 'Sebastian'. These mutants also demonstrated distinct patterns of ABA-induced stomatal movement compared to the wild-type (WT). To delve deeper, we conducted a comprehensive analysis of the transcriptomes of these mutants and the parent cultivar 'Sebastian' under both optimal watering conditions and 10days of drought stress treatment. We identified differentially expressed genes (DEGs) between the mutants and WT plants under control and drought conditions. Furthermore, we pinpointed DEGs specifically expressed in both mutants under drought conditions. Our experiments revealed that the cis-regulatory motif CACG, previously identified in Arabidopsis and rice, is recognized by HvSNAC1 in vitro. Enrichment analysis led to the identification of the cell wall organization category and potential target genes, such as HvEXPA8 (expansin 8), HvXTH (xyloglucan endotransglucosylase/hydrolase), and HvPAE9 (pectin acetylesterase 9), suggesting their regulation by HvSNAC1. These findings suggest that HvSNAC1 may play a role in regulating genes associated with stomatal density, size and reopening.

Drought stress profoundly hampers both plant growth and crop yield. To combat this, plants have evolved intricate transcriptional regulation mechanisms as a pivotal strategy. Through a genetic screening with rice genome-scale mutagenesis pool under drought stress, we identified an APETALA2/Ethylene Responsive Factor, namely OsERF103, positively responds to drought tolerance in rice. Combining chromatin immunoprecipitation sequencing and RNA sequencing analyses, we pinpointed c. 1000 genes directly influenced by OsERF103. Further results revealed that OsERF103 interacts with Stress-responsive NAC1 (SNAC1), a positive regulator of drought tolerance in rice, to synergistically regulate the expression of key drought-related genes, such as OsbZIP23. Moreover, we found that OsERF103 recruits a Su(var)3-9,enhancer of zeste and trithorax-domain group protein 705, which encodes a histone 3 lysine 4 (H3K4)-specific methyltransferase to specifically affect the deposition of H3K4me3 at loci like OsbZIP23 and other genes linked to dehydration responses. Additionally, the natural alleles of OsERF103 are selected during the domestication of both indica and japonica rice varieties and exhibit significant geographic distribution. Collectively, our findings have unfurled a comprehensive mechanistic framework underlying the OsERF103-mediated cascade regulation of drought response. This discovery not only enhances our understanding of drought signaling but also presents a promising avenue for the genetic improvement of drought-tolerant rice cultivars.

Abiotic stress tolerance in plants is often induced by activation of transcription factors. An increased stress tolerance was observed in indica rice cultivar BRRI dhan55 after transforming with the transcription factor SNAC1 (stress responsive NAC1) under stress inducible promoter rd29A that minimized unexpected phenotype and metabolic burden in transgenic lines. Tissue culture independent Agrobacterium-mediated in planta transformation method was used. Molecular analyses confirmed the successful integration of the SNAC1 gene and significantly higher gene expression level in the transgenic lines. The transgenic lines showed 3:1 segregation ratio at T2 generation following the Mendelian law of inheritance. Assays for leaf disk senescence and chlorophyll content at 100 mM and 200 mM salt and survival rates at 200 mM salt and drought conditions at 12 days of water withdrawal and after recovery under water showed significantly increased stress tolerance in the transgenics lines at seedling stage compared to the wild type. Enhanced yield, spikelet fertility, and 100 grain weight were observed at the reproductive stage compared to wild type under both salinity and drought stress conditions. Thus, SNAC1 expression in plants under inducible promoter is a better choice to enhance stress tolerance and yield under salinity and drought conditions. Plant Tissue Cult. & Biotech. 33(2): 115-133, 2023 (December)

Nitrogen (N) is a critical factor for crop growth and yield. Improving nitrogen use efficiency (NUE) in agricultural systems is crucial for sustainable food production. However, the underlying regulation of N uptake and utilization in crops is not well known. Here, we identified OsSNAC1 (stress-responsive NAC 1) as an upstream regulator of OsNRT2.1 (nitrate transporter 2.1) in rice (Oryza sativa) by yeast one-hybridization screening. OsSNAC1 was mainly expressed in roots and shoots and induced by N deficiency. We observed similar expression patterns of OsSNAC1, OsNRT2.1/2.2, and OsNRT1.1A/B in response to NO3- supply. Overexpression of OsSNAC1 resulted in increased concentrations of free NO3- in roots and shoots, as well as higher N uptake, higher NUE and nitrogen use index (NUI) in rice plants, which conferred increased plant biomass and grain yield. On the contrary, mutation of OsSNAC1 resulted in decreased N uptake and lower NUI, which inhibited plant growth and yield. OsSNAC1 overexpression significantly upregulated OsNRT2.1/2.2 and OsNRT1.1A/B expression, while the mutation of OsSNAC1 significantly downregulated OsNRT2.1/2.2 and OsNRT1.1A/B expression. Y1H, transient co-expression and ChIP assays showed OsSNAC1 directly binds to the upstream promoter region of OsNRT2.1/2.2 and OsNRT1.1A/1.1B. In conclusion, we identified a NAC transcription factor in rice, OsSNAC1, with a positive role in regulating NO3- uptake through directly binding to the upstream promoter region of OsNRT2.1/2.2 and OsNRT1.1A/1.1B and activating their expression. Our results provide a potential genetic approach for improving crop NUE in agriculture.

How mitochondria regulate the expression of their genes is poorly understood, partly because methods have not been developed for stably transforming mitochondrial genomes. In recent years, the disruption of mitochondrial genes has been achieved in several plant species using mitochondria-localized TALEN (mitoTALEN). In this study, we attempted to disrupt the NADH dehydrogenase subunit7 (NAD7) gene, a subunit of respiratory chain complex I, in Arabidopsis (Arabidopsis thaliana) using the mitoTALEN method. In some of the transformants, disruption of NAD7 was accompanied by severe growth inhibition and lethality, suggesting that NAD7 has an essential function in Arabidopsis. In addition, the mitochondrial genome copy number and overall expression of genes encoding mitochondrial proteins were generally increased by nad7 knockout. Similar increases were also observed in mutants with decreased NAD7 transcripts and with dysfunctions of other mitochondrial respiratory complexes. In these mutants, the expression of nuclear genes involved in mitochondrial translation or protein transport was induced in sync with mitochondrial genes. Mitochondrial genome copy number was also partly regulated by the nuclear stress-responsive factors NAC domain containing protein 17 and Radical cell death 1. These findings suggest the existence of overall gene-expression control through mitochondrial genome copy number in Arabidopsis and that disruption of single mitochondrial genes can have additional broad consequences in both the nuclear and mitochondrial genomes.

Three stress-responsive NAC transcription factors, Pp-SNACs, differentially and synergistically regulate abiotic stress in pear

Evolution and functional diversity of abiotic stress-responsive NAC transcription factor genes in Linum usitatissimum L

Overexpressing the NAC transcription factor LpNAC13 from Lilium pumilum in tobacco negatively regulates the drought response and positively regulates the salt response

Being master regulators of gene expression, transcription factors (TFs) play important roles in determining plant growth, development and reproduction. To date, many TFs have been shown to positively mediate plant responses to environmental stresses. In the current study, the biological functions of a stress-responsive NAC [NAM (No Apical Meristem), ATAF1/2 (Arabidopsis Transcription Activation Factor1/2), CUC2 (Cup-shaped Cotyledon2)]-TF encoding gene isolated from soybean (GmNAC019) in relation to plant drought tolerance and abscisic acid (ABA) responses were investigated. By using a heterologous transgenic system, we revealed that transgenic Arabidopsis plants constitutively expressing the GmNAC019 gene exhibited higher survival rates in a soil-drying assay, which was associated with lower water loss rate in detached leaves, lower cellular hydrogen peroxide content and stronger antioxidant defense under water-stressed conditions. Additionally, the exogenous treatment of transgenic plants with ABA showed their hypersensitivity to this phytohormone, exhibiting lower rates of seed germination and green cotyledons. Taken together, these findings demonstrated that GmNAC019 functions as a positive regulator of ABA-mediated plant response to drought, and thus, it has potential utility for improving plant tolerance through molecular biotechnology.

Recent studies have demonstrated melatonin protects various crops against abiotic stresses. However, the effects of melatonin on the photosynthetic apparatus of stressed plants is poorly characterized. We investigated the effects of melatonin pretreatment on photosynthesis and tolerance to salinity stress in Avena sativa (oat) plants. Oat plants were exposed to four treatments (three replicate pots per treatment): well-watered (WW; control); watered with 300 mM salt solution for 10 days (NaCl); pretreated with 100 µM melatonin solution for 7 days then watered normally for 10 days (Mel+W); or pretreated with 100 µM melatonin for 7 days then 300 mM salt for 10 days (Mel+NaCl). Considerable differences in growth parameters, chlorophyll content, stomatal conductance, proline accumulation, lipid peroxidation, electrolyte leakage, and growth parameters were observed between groups. Genes encoding three major antioxidant enzymes were upregulated in the Mel+NaCl group compared to the other groups. Chlorophyll-a fluorescence kinetic analyses revealed that almost all photosynthetic parameters were improved in Mel+NaCl plants compared to the other treatments. Analysis of genes encoding the major extrinsic proteins of photosystem II (PSII) revealed that PsbA, PsbB, PsbC, and PsbD (but not PsbO) were highly upregulated in Mel+NaCl plants compared to the other groups, indicating melatonin positively influenced photosynthesis under control conditions and salt stress. In addition, melatonin upregulated stress-responsive NAC transcription factor genes in plants exposed to salt stress. These findings suggest melatonin pretreatment improves photosynthesis and enhances salt tolerance in oat plants.

Differential regulation of the banana stress NAC family by individual and combined stresses of drought and heat in susceptible and resistant genotypes

Plant steroid hormones brassinosteroids (BRs) regulate plant growth and development at many different levels. Recent research has revealed that stress-responsive NAC (petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) transcription factor RD26 is regulated by BR signaling and antagonizes BES1 in the interaction between growth and drought stress signaling. However, the upstream signaling transduction components that activate RD26 during drought are still unknown. Here, we demonstrate that the function of RD26 is modulated by GSK3-like kinase BIN2 and protein phosphatase 2C ABI1. We show that ABI1, a negative regulator in abscisic acid (ABA) signaling, dephosphorylates and destabilizes BIN2 to inhibit BIN2 kinase activity. RD26 protein is stabilized by ABA and dehydration in a BIN2-dependent manner. BIN2 directly interacts and phosphorylates RD26 in vitro and in vivo. BIN2 phosphorylation of RD26 is required for RD26 transcriptional activation on drought-responsive genes. RD26 overexpression suppressed the brassinazole (BRZ) insensitivity of BIN2 triple mutant bin2 bil1 bil2, and BIN2 function is required for the drought tolerance of RD26 overexpression plants. Taken together, our data suggest a drought signaling mechanism in which drought stress relieves ABI1 inhibition of BIN2, allowing BIN2 activation. Sequentially, BIN2 phosphorylates and stabilizes RD26 to promote drought stress response.

Drought stress can cause huge crop production losses. Drought resistance consists of complex traits, and is regulated by arrays of unclear networks at the molecular level. A stress-responsive NAC transcription factor gene SNAC1 has been reported for its function in the positive regulation of drought resistance in rice, and several downstream SNAC1 targets have been identified. However, a complete regulatory network mediated by SNAC1 in drought response remains unknown. In this study, we performed Chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq of SNAC1-overexpression transgenic rice (SNAC1-OE) lines and wild-type under normal and moderate drought stress conditions, to identify all SNAC1 target genes at a genome-wide scale by RNA-Seq analyses. We detected 980 differentially expressed genes (DEGs) in the SNAC1-OE lines compared to the wild-type control under drought stress conditions. By ChIP-Seq analyses, we identified 4,339 SNAC1-binding genes under drought stress conditions (SNAC1BGDs). By combining the DEGs and SNAC1BGDs, we identified 93 SNAC1-targeted genes involved in drought responses (SNAC1TGDs). Most SNAC1TGDs are involved in transcriptional regulation, response to water loss, and other processes related to stress responses. Moreover, the major motifs in the SNAC1BGDs promoters include a NAC recognition sequence (NACRS) and an ABA responsive element (ABRE). SNAC1-OE lines are more sensitive to ABA than wild-type. SNAC1 can bind to the OsbZIP23 promoter, an important ABA signaling regulator, and positively regulate the expression of several ABA signaling genes.

BackgroundNAC (NAM, ATAF and CUC) transcriptional factors constitute a large family with more than 150 members in rice and several members of this family have been demonstrated to play crucial roles in rice abiotic stress response. In the present study, we report the function of a novel stress-responsive NAC gene, ONAC066, in rice drought and oxidative stress tolerance.ResultsONAC066 was localized in nuclei of cells when transiently expressed in Nicotiana benthamiana and is a transcription activator with the binding ability to NAC recognition sequence (NACRS) and AtJUB1 binding site (JBS). Expression of ONAC066 was significantly induced by PEG, NaCl, H2O2 and abscisic acid (ABA). Overexpression of ONAC066 in transgenic rice improved drought and oxidative stress tolerance and increased ABA sensitivity, accompanied with decreased rate of water loss, increased contents of proline and soluble sugars, decreased accumulation of reactive oxygen species (ROS) and upregulated expression of stress-related genes under drought stress condition. By contrast, RNAi-mediated suppression of ONAC066 attenuated drought and oxidative stress tolerance and decreased ABA sensitivity, accompanied with increased rate of water loss, decreased contents of proline and soluble sugars, elevated accumulation of ROS and downregulated expression of stress-related genes under drought stress condition. Furthermore, yeast one hybrid and chromatin immunoprecipitation-PCR analyses revealed that ONAC066 bound directly to a JBS-like cis-elements in OsDREB2A promoter and activated the transcription of OsDREB2A.ConclusionONAC066 is a nucleus-localized transcription activator that can respond to multiple abiotic stress factors. Functional analyses using overexpression and RNAi-mediated suppression transgenic lines demonstrate that ONAC066 is a positive regulator of drought and oxidative stress tolerance in rice.

Drought and cold are the primary factors limiting plant growth worldwide. The Ammopiptanthus mongolicus NAC11 (AmNAC11) gene encodes a stress-responsive transcription factor. Expression of the AmNAC11 gene was induced by drought, cold and high salinity. The AmNAC11 protein was localized in the nucleus and plays an important role in tolerance to drought, cold and salt stresses. We also found that differential expression of AmNAC11 was induced in the early stages of seed germination and was related to root growth. When the AmNAC11 gene was introduced into Arabidopsis thaliana by an Agrobacterium-mediated method, the transgenic lines expressing AmNAC11 displayed significantly enhanced tolerance to drought and freezing stresses compared to wild-type Arabidopsis thaliana plants. These results indicated that over-expression of the AmNAC11 gene in Arabidopsis could significantly enhance its tolerance to drought and freezing stresses. Our study provides a promising approach to improve the tolerance of crop cultivars to abiotic stresses through genetic engineering.