A natural antisense transcript acts as a negative regulator for the maize drought stress response gene ZmNAC48

Identification and analysis of short-term and long-term salt-associated lncRNAs in the leaf of Avicennia marina

As a highly salt-resistant mangrove, Avicennia marina can thrive in the hypersaline water. The leaves of Avicennia marina play a crucial role in salinity stress adaptability by secreting salt. Although the functions of long non-coding RNAs (lncRNAs) in leaves remain unknown, they have emerged as regulators in leaf development, aging and salt response. In this study, we employed transcriptomic data of both short-term and long-term salt treated leaves to identify salt-associated lncRNAs of leaf tissue. As a result, 687 short-term and 797 long-term salt-associated lncRNAs were identified. Notably, both short-term and long-term salt-associated lncRNAs exhibited slightly longer lengths and larger exons, but smaller introns compared with salt-non-associated lncRNAs. Furthermore, salt-associated lncRNAs also displayed higher tissue-specificity than salt-non-associated lncRNAs. Most of the salt-associated lncRNAs were common to short- and long-term salt treatments. And about one fifth of the downregulated salt-associated lncRNAs identified both in two terms were leaf tissue-specific lncRNAs. Besides, these leaf-specific lncRNAs were found to be involved in the oxidation-reduction and photosynthesis processes, as well as several metabolic processes, suggesting the noticeable functions of salt-associated lncRNAs in regulating salt responses of Avicennia marina leaves.

Transcription factors as molecular switches regulating plant responses to drought stress

Plants often experience abiotic stress, which severely affects their growth. With the advent of global warming, drought stress has become a pivotal factor affecting crop yield and quality. Increasing numbers of studies have focused on elucidating the molecular mechanisms underlying plant responses to drought stress. As molecular switches, transcription factors (TFs) are key participants in drought-resistance regulatory networks in crops. TFs regulate the transcription of downstream genes and are regulated by various upstream regulatory factors. Therefore, understanding the mechanisms of action of TFs in regulating drought stress can help enhance the adaptive capacity of crops under drought conditions. In this review, we summarize the structural characteristics of several common TFs, their multiple drought-response pathways, and recently employed research strategies. We describe the application of new technologies such as analysis of stress granule dynamics and function, multi-omics data, gene editing, and molecular crosstalk between TFs in drought resistance. This review aims to familiarize readers with the regulatory network of TFs in drought resistance and to provide a reference for examining the molecular mechanisms of drought resistance in plants and improving agronomic traits.

Genome-wide identification of ZmMYC2 binding sites and target genes in maize

BACKGROUND

Jasmonate (JA) is the important phytohormone to regulate plant growth and adaption to stress signals. MYC2, an bHLH transcription factor, is the master regulator of JA signaling. Although MYC2 in maize has been identified, its function remains to be clarified.

RESULTS

To understand the function and regulatory mechanism of MYC2 in maize, the joint analysis of DAP-seq and RNA-seq is conducted to identify the binding sites and target genes of ZmMYC2. A total of 3183 genes are detected both in DAP-seq and RNA-seq data, potentially as the directly regulating genes of ZmMYC2. These genes are involved in various biological processes including plant growth and stress response. Besides the classic cis-elements like the G-box and E-box that are bound by MYC2, some new motifs are also revealed to be recognized by ZmMYC2, such as nGCATGCAnn, AAAAAAAA, CACGTGCGTGCG. The binding sites of many ZmMYC2 regulating genes are identified by IGV-sRNA.

CONCLUSIONS

All together, abundant target genes of ZmMYC2 are characterized with their binding sites, providing the basis to construct the regulatory network of ZmMYC2 and better understanding for JA signaling in maize.

Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L

Natural Antisense Transcripts (NATs) are a kind of complex regulatory RNAs that play crucial roles in gene expression and regulation. However, the NATs in Cannabis Sativa L., a widely economic and medicinal plant rich in cannabinoids remain unknown. In this study, we comprehensively predicted C. sativa NATs genome-wide using strand-specific RNA sequencing (ssRNA-Seq) data, and validated the expression profiles by strand-specific quantitative reverse transcription PCR (ssRT-qPCR). Consequently, a total of 307 NATs were predicted in C. sativa, including 104 cis- and 203 trans- NATs. Functional enrichment analysis demonstrated the potential involvement of the C. sativa NATs in DNA polymerase activity, RNA-DNA hybrid ribonuclease activity, and nucleic acid binding. Finally, 18 cis- and 376 trans- NAT-ST pairs were predicted to produce 621 cis- and 5,679 trans- small interfering RNA (nat-siRNAs), respectively. These nat-siRNAs were potentially involved in the biosynthesis of cannabinoids and cellulose. All these results will shed light on the regulation of NATs and nat-siRNAs in C. sativa.

LncRNA DANA1 promotes drought tolerance and histone deacetylation of drought responsive genes in Arabidopsis

Although many long noncoding RNAs have been discovered in plants, little is known about their biological function and mode of action. Here we show that the drought-induced long intergenic noncoding RNA DANA1 interacts with the L1p/L10e family member protein DANA1-INTERACTING PROTEIN 1 (DIP1) in the cell nucleus of Arabidopsis, and both DANA1 and DIP1 promote plant drought resistance. DANA1 and DIP1 increase histone deacetylase HDA9 binding to the CYP707A1 and CYP707A2 loci. DIP1 further interacts with PWWP3, a member of the PEAT complex that associates with HDA9 and has histone deacetylase activity. Mutation of DANA1 enhances CYP707A1 and CYP707A2 acetylation and expression resulting in impaired drought tolerance, in agreement with dip1 and pwwp3 mutant phenotypes. Our results demonstrate that DANA1 is a positive regulator of drought response and that DANA1 works jointly with the novel chromatin-related factor DIP1 on epigenetic reprogramming of the plant transcriptome during the response to drought.

The Functions of an NAC Transcription Factor, GhNAC2-A06, in Cotton Response to Drought Stress

Drought stress imposes severe constraints on crop growth and yield. The NAC transcription factors (TF) play a pivotal role in regulating plant stress responses. However, the biological functions and regulatory mechanisms of many cotton NACs have not been explored. In this study, we report the cloning and characterization of GhNAC2-A06, a gene encoding a typical cotton NAC TF. The expression of GhNAC2-A06 was induced by PEG treatment, drought stress, and ABA treatment. Furthermore, we investigated its function using the virus-induced gene silencing (VIGS) method. GhNAC2-A06 silenced plants exhibited a poorer growth status under drought stress conditions compared to the controls. The GhNAC2-A06 silenced cotton plants had a lower leaf relative water and chlorophyll content and a higher MDA content compared to the controls under the drought treatment. The levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) enzyme activity in the GhNAC2-A06 silenced plants were found to be lower compared to the controls when exposed to drought stress. Additionally, the downregulation of the drought stress-related genes, GhSAP12-D07, GhNCED1-A01, GhLEA14-A11, GhZAT10-D02, GhPROT2-A05, GhABF3-A03, GhABF2-D05, GhSAP3-D07, and GhCPK1-D04, was observed in the GhNAC2-A06 silenced cotton. Together, our research reveals that GhNAC2-A06 plays a role in the reaction of cotton to drought stress by affecting the expression of genes related to drought stress. The data obtained from this study lay the theoretical foundation for further in-depth research on the biological function and regulatory mechanisms of GhNAC2-A06.

Genetic and molecular exploration of maize environmental stress resilience: Toward sustainable agriculture

Global climate change exacerbates the effects of environmental stressors, such as drought, flooding, extreme temperatures, salinity, and alkalinity, on crop growth and grain yield, threatening the sustainability of the food supply. Maize (Zea mays) is one of the most widely cultivated crops and the most abundant grain crop in production worldwide. However, the stability of maize yield is highly dependent on environmental conditions. Recently, great progress has been made in understanding the molecular mechanisms underlying maize responses to environmental stresses and in developing stress-resilient varieties due to advances in high-throughput sequencing technologies, multi-omics analysis platforms, and automated phenotyping facilities. In this review, we summarize recent advances in dissecting the genetic factors and networks that contribute to maize abiotic stress tolerance through diverse strategies. We also discuss future challenges and opportunities for the development of climate-resilient maize varieties.

Global identification of natural antisense transcripts in Gossypium hirsutum and Gossypium barbadense under chilling stress

Natural antisense transcripts (NATs) in model plants have been recognized as important regulators of gene expression under abiotic stresses. However, the functional roles of NATs in crops under low temperature are still unclear. Here, we identified 815 and 689 NATs from leaves of Gossypium hirsutum and G. barbadense under chilling stress. Among those, 224 NATs were identified as interspecific homologs between the two species. The correlation coefficients for expression of NATs and their cognate sense genes (CSG) were 0.43 and 0.37 in G. hirsutum and G. barbadense, respectively. Furthermore, expression of interspecific NATs and CSGs alike was highly consistent under chilling stress with correlation coefficients of 0.90-0.91. Four cold-associated NATs were selected for functional validation using virus-induced gene silencing (VIGS). Our results suggest that CAN1 engage in the molecular regulation of chilling stress by regulating SnRK2.8 expression. This highly conserved NAT have valuable potential for applications in breeding cold-tolerant cotton.

The long non-coding RNA DANA2 positively regulates drought tolerance by recruiting ERF84 to promote JMJ29-mediated histone demethylation

Tens of thousands of long non-coding RNAs have been uncovered in plants, but few of them have been comprehensively studied for their biological function and molecular mechanism of their mode of action. Here, we show that the Arabidopsis long non-coding RNA DANA2 interacts with an AP2/ERF transcription factor ERF84 in the cell nucleus and then affects the transcription of JMJ29 that encodes a Jumonji C domain-containing histone H3K9 demethylase. Both RNA sequencing (RNA-seq) and genetic analyses demonstrate that DANA2 positively regulates drought stress responses through JMJ29. JMJ29 positively regulates the expression of ERF15 and GOLS2 by modulation of H3K9me2 demethylation. Accordingly, mutation of JMJ29 causes decreased ERF15 and GOLS2 expression, resulting in impaired drought tolerance, in agreement with drought-sensitive phenotypes of dana2 and erf84 mutants. Taken together, these results demonstrate that DANA2 is a positive regulator of drought response and works jointly with the transcriptional activator ERF84 to modulate JMJ29 expression in plant response to drought.

An insight into the roles of regulatory ncRNAs in plants: An abiotic stress and developmental perspective

Different environmental cues lead to changes in physiology, biochemistry and molecular status of plant's growth. Till date, various genes have been accounted for their role in regulating plant development and response to abiotic stress. Excluding genes that code for a functional protein in a cell, a large chunk of the eukaryotic transcriptome consists of non-coding RNAs (ncRNAs) which lack protein coding capacity but are still functional. Recent advancements in Next Generation Sequencing (NGS) technology have led to the unearthing of different types of small and large non-coding RNAs in plants. Non-coding RNAs are broadly categorised into housekeeping ncRNAs and regulatory ncRNAs which work at transcriptional, post-transcriptional and epigenetic levels. Diverse ncRNAs play different regulatory roles in nearly all biological processes including growth, development and response to changing environments. This response can be perceived and counteracted by plants using diverse evolutionarily conserved ncRNAs like miRNAs, siRNAs and lncRNAs to participate in complex molecular regimes by activating gene-ncRNA-mRNA regulatory modules to perform the downstream function. Here, we review the current understanding with a focus on recent advancements in the functional studies of the regulatory ncRNAs at the nexus of abiotic stresses and development. Also, the potential roles of ncRNAs in imparting abiotic stress tolerance and yield improvement in crop plants are also discussed with their future prospects.

AgMYB5, an MYB transcription factor from celery, enhanced β-carotene synthesis and promoted drought tolerance in transgenic Arabidopsis

BACKGROUND

Water shortage caused by global warming seriously affects the yield and quality of vegetable crops. β-carotene, the lipid-soluble natural product with important pharmacological value, is abundant in celery. Transcription factor MYB family extensively disperses in plants and plays regulatory roles in carotenoid metabolism and water scarcity response.

RESULTS

Here, the AgMYB5 gene encoding 196 amino acids was amplified from celery cv. 'Jinnanshiqin'. In celery, the expression of AgMYB5 exhibited transactivation activity, tissue specificity, and drought-condition responsiveness. Further analysis proved that ectopic expression of AgMYB5 increased β-carotene content and promoted drought tolerance in transgenic Arabidopsis thaliana. Moreover, AgMYB5 expression promoted β-carotene biosynthesis by triggering the expression of AtCRTISO and AtLCYB, which in turn increased antioxidant enzyme activities, and led to the decreased contents of H₂O₂ and MDA, and the inhibition of O₂^- generation. Meanwhile, β-carotene accumulation promoted endogenous ABA biosynthesis of transgenic Arabidopsis, which resulted in ABA-induced stomatal closing and delayed water loss. In addition, ectopic expression of AgMYB5 increased expression levels of AtERD1, AtP5CS1, AtRD22, and AtRD29.

CONCLUSIONS

The findings indicated that AgMYB5 up-regulated β-carotene biosynthesis and drought tolerance of Arabidopsis.

Maize transcription factor ZmNAC2 enhances osmotic stress tolerance in transgenic Arabidopsis

Osmotic stress seriously limits crop yield and quality. Among plant-specific transcription factors families, the NAC family of transcription factors is extensively involved in various growth, development and stress responses. Here we identified a maize NAC family transcription factor ZmNAC2 with inducible gene expression in response to osmotic stress. The subcellular localization showed that it was localized in the nucleus and overexpression of ZmNAC2 in Arabidopsis significantly promoted seed germination and elevated cotyledon greening under osmotic stress. ZmNAC2 also enhanced stomatal closure and decreased water loss in transgenic Arabidopsis. Overexpression of ZmNAC2 activated ROS scavenging and the transgenic lines accumulated less MDA and developed more lateral roots with drought or mannitol treatment. Further RNA-seq and qRT-PCR analysis showed that ZmNAC2 up-regulated a number of genes related to osmotic stress resistance, as well as plant hormone signaling genes. All together, ZmNAC2 enhances osmotic stress tolerance by regulating multiple physiological processes and molecular mechanisms, and exhibits potential as the target gene in crop breeding to increase osmotic stress resistance.

Transcription Factor ZmNAC20 Improves Drought Resistance by Promoting Stomatal Closure and Activating Expression of Stress-Responsive Genes in Maize

Drought is a major environmental threat that limits crop growth, development, and productivity worldwide. Improving drought resistance with genetic engineering methods is necessary to tackle global climate change. It is well known that NAC (NAM, ATAF and CUC) transcription factors play a critical role in coping with drought stress in plants. In this study, we identified an NAC transcription factor ZmNAC20, which regulates drought stress response in maize. ZmNAC20 expression was rapidly upregulated by drought and abscisic acid (ABA). Under drought conditions, the ZmNAC20-overexpressing plants had higher relative water content and survival rate than the wild-type maize inbred B104, suggesting that overexpression of ZmNAC20 improved drought resistance in maize. The detached leaves of ZmNAC20-overexpressing plants lost less water than those of wild-type B104 after dehydration. Overexpression of ZmNAC20 promoted stomatal closure in response to ABA. ZmNAC20 was localized in the nucleus and regulated the expression of many genes involved in drought stress response using RNA-Seq analysis. The study indicated that ZmNAC20 improved drought resistance by promoting stomatal closure and activating the expression of stress-responsible genes in maize. Our findings provide a valuable gene and new clues on improving crop drought resistance.

SbNAC9 Improves Drought Tolerance by Enhancing Scavenging Ability of Reactive Oxygen Species and Activating Stress-Responsive Genes of Sorghum

Drought stress severely threatens the yield of cereal crops. Therefore, understanding the molecular mechanism of drought stress response of plants is crucial for developing drought-tolerant cultivars. NAC transcription factors (TFs) play important roles in abiotic stress of plants, but the functions of NAC TFs in sorghum are largely unknown. Here, we characterized a sorghum NAC gene, SbNAC9, and found that SbNAC9 can be highly induced by polyethylene glycol (PEG)-simulated dehydration treatments. We therefore investigated the function of SbNAC9 in drought stress response. Sorghum seedlings overexpressing SbNAC9 showed enhanced drought-stress tolerance with higher chlorophyll content and photochemical efficiency of PSII, stronger root systems, and higher reactive oxygen species (ROS) scavenging capability than wild-type. In contrast, sorghum seedlings with silenced SbNAC9 by virus-induced gene silencing (VIGS) showed weakened drought stress tolerance. Furthermore, SbNAC9 can directly activate a putative peroxidase gene SbC5YQ75 and a putative ABA biosynthesis gene SbNCED3. Silencing SbC5YQ75 and SbNCED3 led to compromised drought tolerance and reduced ABA content of sorghum seedlings, respectively. Therefore, our findings revealed the important role of SbNAC9 in response to drought stress in sorghum and may shed light on genetic improvement of other crop species under drought-stress conditions.

Transcriptome analysis in contrasting maize inbred lines and functional analysis of five maize NAC genes under drought stress treatment

Drought substantially influences crop growth and development. NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) have received much attention for their critical roles in drought stress responses. To explore the maize NAC genes in response to drought stress, the transcriptome sequencing data of NAC TFs in two maize inbred lines, the drought tolerance line H082183 and the sensitive line Lv28, were used to screen the differentially expressed genes (DEGs). There were 129 maize NAC protein-coding genes identified, of which 15 and 20 NAC genes were differentially expressed between the two genotypes under MD and SD treatments, respectively. Meanwhile, the phylogenetic relationship of 152 non-redundant NAC family TFs in maize was generated. The maize NAC family proteins were grouped into 13 distinct subfamilies. Five drought stress-responsive NAC family members, which were designed as ZmNAP, ZmNAC19, ZmNAC4, ZmJUB1(JUBGBRUNNEN1), and ZmNAC87, were selected for further study. The expression of ZmNAP, ZmNAC19, ZmNAC4, ZmJUB1, and ZmNAC87 were significantly induced by drought, dehydration, polyethylene glycol (PEG) stress, and abscisic acid (ABA) treatments. The overexpressing Arabidopsis of these five NAC genes was generated for functional characterization, respectively. Under different concentrations of NaCl, D-mannitol stress, and ABA treatments, the sensitivity of ZmNAP-, ZmNAC19-, ZmNAC4-, ZmJUB1-, and ZmNAC87-overexpressing lines was significantly increased at the germination stage compared to the wild-type lines. The overexpression of these five NAC members significantly improved the drought stress tolerance in transgenic Arabidopsis. Yeast two-hybrid screening analysis revealed that ZmNAP may cooperatively interact with 11 proteins including ZmNAC19 to activate the drought stress response. The above results inferred that ZmNAP, ZmNAC19, ZmNAC4, ZmJUB1, and ZmNAC87 may play important roles in the plant response to drought stress and may be useful in bioengineering breeding and drought tolerance improvement.

Molecular Characterization and Drought Resistance of GmNAC3 Transcription Factor in Glycine max (L.) Merr

Soybean transcription factor GmNAC plays important roles in plant resistance to environmental stresses. In this study, GmNAC3 was cloned in the drought tolerant soybean variety “Jiyu47”, with the molecular properties of GmNAC3 characterized to establish its candidacy as a NAC transcription factor. The yeast self-activation experiments revealed the transcriptional activation activity of GmNAC3, which was localized in the nucleus by the subcellular localization analysis. The highest expression of GmNAC3 was detected in roots in the podding stage of soybean, and in roots of soybean seedlings treated with 20% PEG6000 for 12 h, which was 16 times higher compared with the control. In the transgenic soybean hairy roots obtained by the Agrobacterium-mediated method treated with 20% PEG6000 for 12 h, the activities of superoxide dismutase, peroxidase, and catalase and the content of proline were increased, the malondialdehyde content was decreased, and the expressions of stress resistance-related genes (i.e., APX2, LEA14, 6PGDH, and P5CS) were up-regulated. These expression patterns were confirmed by transgenic Arabidopsis thaliana with the overexpression of GmNAC3. This study provided strong scientific evidence to support further investigation of the regulatory function of GmNAC3 in plant drought resistance and the molecular mechanisms regulating the plant response to environmental stresses.

Genome-Wide Survey and Functional Verification of the NAC Transcription Factor Family in Wild Emmer Wheat

The NAC transcription factor (TF) family is one of the largest TF families in plants, which has been widely reported in rice, maize and common wheat. However, the significance of the NAC TF family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of NAC genes was conducted in the wild emmer genome and 249 NAC family members (TdNACs) were identified. The results showed that all of these genes contained NAM/NAC-conserved domains and most of them were predicted to be located on the nucleus. Phylogenetic analysis showed that these 249 TdNACs can be classified into seven clades, which are likely to be involved in the regulation of grain protein content, starch synthesis and response to biotic and abiotic stresses. Expression pattern analysis revealed that TdNACs were highly expressed in different wheat tissues such as grain, root, leaves and shoots. We found that TdNAC8470 was phylogenetically close to NAC genes that regulate either grain protein or starch accumulation. Overexpression of TdNAC8470 in rice showed increased grain starch concentration but decreased grain Fe, Zn and Mn contents compared with wild-type plants. Protein interaction analysis indicated that TdNAC8470 might interact with granule-bound starch synthase 1 (TdGBSS1) to regulate grain starch accumulation. Our work provides a comprehensive understanding of the NAC TFs family in wild emmer wheat and establishes the way for future functional analysis and genetic improvement of increasing grain starch content in wheat.

Genome-wide identification of foxtail millet's TRX family and a functional analysis of SiNRX1 in response to drought and salt stresses in transgenic Arabidopsis

Thioredoxins (TRXs) are small-molecule proteins with redox activity that play very important roles in the growth, development, and stress resistance of plants. Foxtail millet (Setaria italica) gradually became a model crop for stress resistance research because of its advantages such as its resistance to sterility and its small genome. To date, the thioredoxin (TRX) family has been identified in Arabidopsis thaliana, rice and wheat. However, studies of the TRX family in foxtail millet have not been reported, and the biological function of this family remains unclear. In this study, 35 SiTRX genes were identified in the whole genome of foxtail millet through bioinformatic analysis. According to phylogenetic analysis, 35 SiTRXs can be divided into 13 types. The chromosome distribution, gene structure, cis-elements and conserved protein motifs of 35 SiTRXs were characterized. Three nucleoredoxin (NRX) members were further identified by a structural analysis of TRX family members. The expression patterns of foxtail millet's SiNRX members under abiotic stresses showed that they have different stress-response patterns. In addition, subcellular localization revealed that SiNRXs were localized to the nucleus, cytoplasm and membrane. Further studies demonstrated that the overexpression of SiNRX1 enhanced Arabidopsis' tolerance to drought and salt stresses, resulting in a higher survival rate and better growth performance. Moreover, the expression levels of several known stress-related genes were generally higher in overexpressed lines than in the wild-type. Thus, this study provides a general picture of the TRX family in foxtail millet and lay a foundation for further research on the mechanism of the action of TRX proteins on abiotic stresses.

miR398b and AtC2GnT form a negative feedback loop to regulate Arabidopsis thaliana resistance against Phytophthora parasitica

Oomycetes are diploid eukaryotic microorganisms that seriously threaten sustainable crop production. MicroRNAs (miRNAs) and corresponding natural antisense transcripts (NATs) are important regulators of multiple biological processes. However, little is known about their roles in plant immunity against oomycete pathogens. In this study, we report the identification and functional characterization of miR398b and its cis-NAT, the core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase gene (AtC2GnT), in plant immunity. Gain- and loss-of-function assays revealed that miR398b mediates Arabidopsis thaliana susceptibility to Phytophthora parasitica by targeting Cu/Zn-Superoxidase Dismutase1 (CSD1) and CSD2, leading to suppressed expression of CSD1 and CSD2 and decreased plant disease resistance. We further showed that AtC2GnT transcripts could inhibit the miR398b-CSDs module via inhibition of pri-miR398b expression, leading to elevated plant resistance to P. parasitica. Furthermore, quantitative reverse transcription PCR, RNA ligase-mediated 5'-amplification of cDNA ends (RLM-5' RACE), and transient expression assays indicated that miR398b suppresses the expression of AtC2GnT. We generated AtC2GnT-silenced A. thaliana plants by CRISPR/Cas9 or RNA interference methods, and the Nicotiana benthamiana NbC2GnT-silenced plants by virus-induced gene silencing. Pathogenicity assays showed that the C2GnT-silenced plants were more susceptible, while AtC2GnT-overexpressing plants exhibited elevated resistance to P. parasitica. AtC2GnT encodes a Golgi-localized protein, and transient expression of AtC2GnT enhanced N. benthamiana resistance to Phytophthora pathogens. Taken together, our results revealed a positive role of AtC2GnT and a negative regulatory loop formed by miR398b and AtC2GnT in regulating plant resistance to P. parasitica.

Salvianolic Acid Modulates Physiological Responses and Stress-Related Genes That Affect Osmotic Stress Tolerance in Glycine max and Zea mays

Drought is a serious threat worldwide to soybean and maize production. This study was conducted to discern the impact of salvianolic acid treatment on osmotic-stressed soybean (Glycine max L.) and maize (Zea mays L.) seedlings from the perspective of physiochemical and molecular reactions. Examination of varied salvianolic acid concentrations (0, 0.1, 1, 5, 10, and 25 μM) on soybean and maize seedling growth confirmed that the 0.1 and 1 μM concentrations, respectively, showed an improvement in agronomic traits. Likewise, the investigation ascertained how salvianolic acid application could retrieve osmotic-stressed plants. Soybean and maize seedlings were irrigated with water or 25% PEG for 8 days. The results indicated that salvianolic acid application promoted the survival of the 39-day-old osmotic-stressed soybean and maize plants. The salvianolic acid-treated plants retained high photosynthetic pigments, protein, amino acid, fatty acid, sugar, and antioxidant contents, and demonstrated low hydrogen peroxide and lipid contents under osmotic stress conditions. Gene transcription pattern certified that salvianolic acid application led to an increased expression of GmGOGAT, GmUBC2, ZmpsbA, ZmNAGK, ZmVPP1, and ZmSCE1d genes, and a diminished expression of GmMIPS2, GmSOG1, GmACS, GmCKX, ZmPIS, and ZmNAC48 genes. Together, our results indicate the utility of salvianolic acid to enhance the osmotic endurance of soybean and maize plants.

Analysis of Physiological and Transcriptomic Differences between a Premature Senescence Mutant (GSm) and Its Wild-Type in Common Wheat (Triticum aestivum L.)

Simple Summary

Early leaf senescence is an important agronomic trait that affects crop yield and quality. To understand the molecular mechanism of early leaf senescence, a wheat (Triticum aestivum L.) premature leaf senescence mutant (GSm) and its wild type were employed in this study. We compared the physiological characteristics and transcriptome of wheat leaves between the wild type (WT) and the mutant at two-time points. Physiological characteristics and differentially expressed gene (DEG) analysis revealed many genes and metabolic pathways that were closely related to senescence. These results will not only support further gene cloning and functional analysis of GSm, but also facilitate the study of leaf senescence in wheat.

Abstract

Premature leaf senescence has a profound influence on crop yield and quality. Here, a stable premature senescence mutant (GSm) was obtained from the common wheat (Triticum aestivum L.) cultivar Chang 6878 by mutagenesis with ethyl methanesulfonate. The differences between the GSm mutant and its wild-type (WT) were analyzed in terms of yield characteristics, photosynthetic fluorescence indices, and senescence-related physiological parameters. RNA sequencing was used to reveal gene expression differences between GSm and WT. The results showed that the yield of GSm was considerably lower than that of WT. The net photosynthetic rate, transpiration rate, maximum quantum yield, non-photochemical quenching coefficient, photosynthetic electron transport rate, soluble protein, peroxidase activity, and catalase activity all remarkably decreased in flag leaves of GSm, whereas malondialdehyde content distinctively increased compared with those of WT. The analysis of differentially expressed genes indicated blockade of chlorophyll and carotenoid biosynthesis, accelerated degradation of chlorophyll, and diminished photosynthetic capacity in mutant leaves; brassinolide might facilitate chlorophyll breakdown and consequently accelerate leaf senescence. NAC genes positively regulated the senescence process. Compared with NAC genes, expression of WRKY and MYB genes was induced earlier in the mutant possibly due to increased levels of reactive oxygen species and plant hormones (e.g., brassinolide, salicylic acid, and jasmonic acid), thereby accelerating leaf senescence. Furthermore, the antioxidant system played a role in minimizing oxidative damage in the mutant. These results provides novel insight into the molecular mechanisms of premature leaf senescence in crops.

Regulation of small RNA-mediated high temperature stress responses in crop plants

Small RNAs have emerged as key players of gene expression regulation. Several lines of evidences highlight their role in modulating high temperature stress responsiveness in plants. Throughout their life cycle, plants have to regulate their gene expression at various developmental phases, physiological changes, and in response to biotic or environmental stress. High temperature is one the most common abiotic stress for crop plants, that results in impaired morphology, physiology, and yield. However, plants have certain mechanisms that enable them to withstand such conditions by modulating the expression of stress-related genes. Small RNA (sRNA)-regulated gene expression is one such mechanism which is ubiquitous in all eukaryotes. The sRNAs mainly include micro RNAs (miRNAs) and small interfering RNAs (siRNAs). They are primarily associated with the gene silencing either through translation inhibition, mRNA degradation, or DNA methylation. During high temperature stress the increased or decreased level of miRNAs altered the protein accumulation of target transcripts and, therefore, regulate stress responses. Several reports are available in plants which are genetically engineered through expressing artificial miRNAs resulted in thermotolerance. sRNAs have also been reported to bring the epigenetic changes on chromatin region through RNA-dependent DNA methylation (RdDM). The present article draws a brief illustration of sRNA origin, their functional mechanisms, role in high temperature stress, and possible application for developing stress tolerant crop plants.

Global identification of full-length cassava lncRNAs unveils the role of cold-responsive intergenic lncRNA 1 in cold stress response

Long noncoding RNAs (lncRNAs) have been considered to be important regulators of gene expression in a range of biological processes in plants. A large number of lncRNAs have been identified in plants. However, most of their biological functions still remain to be determined. Here, we identified a total of 3004 lncRNAs in cassava under normal or cold-treated conditions from Iso-seq data. We further characterized a cold-responsive intergenic lncRNA 1 (CRIR1) as a novel positive regulator of the plant response to cold stress. CRIR1 can be significantly induced by cold treatment. Ectopic expression of CRIR1 in cassava enhanced the cold tolerance of transgenic plants. Transcriptome analysis demonstrated that CRIR1 regulated a range of cold stress-related genes in a CBF-independent pathway. We further found that CRIR1 RNA can interact with cassava cold shock protein 5 (MeCSP5), which acts as an RNA chaperone, indicating that CRIR1 may recruit MeCSP5 to improve the translation efficiency of messenger RNA. In summary, our study extends the repertoire of lncRNAs in plants as well as their role in cold stress responses. Moreover, it reveals a mechanism by which CRIR1 affected cold stress response by modulating the expression of stress-responsive genes and increasing their translational yield.

Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

Background

Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance.

Results

The whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF.

Conclusions

The contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08286-7.

Exploitation of Drought Tolerance-Related Genes for Crop Improvement

Drought has become a major threat to food security, because it affects crop growth and development. Drought tolerance is an important quantitative trait, which is regulated by hundreds of genes in crop plants. In recent decades, scientists have made considerable progress to uncover the genetic and molecular mechanisms of drought tolerance, especially in model plants. This review summarizes the evaluation criteria for drought tolerance, methods for gene mining, characterization of genes related to drought tolerance, and explores the approaches to enhance crop drought tolerance. Collectively, this review illustrates the application prospect of these genes in improving the drought tolerance breeding of crop plants.