Isolation and molecular characterization of ERF1, an ethylene response factor gene from durum wheat (Triticum turgidum L. subsp. durum), potentially involved in salt-stress responses

Genome-wide identification of long non-coding RNAs and their potential functions in radish response to salt stress

Long non-coding RNAs (lncRNAs) are increasingly recognized as cis- and trans-acting regulators of protein-coding genes in plants, particularly in response to abiotic stressors. Among these stressors, high soil salinity poses a significant challenge to crop productivity. Radish (Raphanus sativus L.) is a prominent root vegetable crop that exhibits moderate susceptibility to salt stress, particularly during the seedling stage. Nevertheless, the precise regulatory mechanisms through which lncRNAs contribute to salt response in radish remain largely unexplored. In this study, we performed genome-wide identification of lncRNAs using strand-specific RNA sequencing on radish fleshy root samples subjected to varying time points of salinity treatment. A total of 7,709 novel lncRNAs were identified, with 363 of them displaying significant differential expression in response to salt application. Furthermore, through target gene prediction, 5,006 cis- and 5,983 trans-target genes were obtained for the differentially expressed lncRNAs. The predicted target genes of these salt-responsive lncRNAs exhibited strong associations with various plant defense mechanisms, including signal perception and transduction, transcription regulation, ion homeostasis, osmoregulation, reactive oxygen species scavenging, photosynthesis, phytohormone regulation, and kinase activity. Notably, this study represents the first comprehensive genome-wide analysis of salt-responsive lncRNAs in radish, to the best of our knowledge. These findings provide a basis for future functional analysis of lncRNAs implicated in the defense response of radish against high salinity, which will aid in further understanding the regulatory mechanisms underlying radish response to salt stress.

Transcription Factor GmERF105 Negatively Regulates Salt Stress Tolerance in Arabidopsis thaliana

The Ethylene Response Factor (ERF) transcription factors form a subfamily of the AP2/ERF family that is instrumental in mediating plant responses to diverse abiotic stressors. Herein, we present the isolation and characterization of the GmERF105 gene from Williams 82 (W82), which is rapidly induced by salt, drought, and abscisic acid (ABA) treatments in soybean. The GmERF105 protein contains an AP2 domain and localizes to the nucleus. GmERF105 was selectively bound to GCC-box by gel migration experiments. Under salt stress, overexpression of GmERF105 in Arabidopsis significantly reduced seed germination rate, fresh weight, and antioxidant enzyme activity; meanwhile, sodium ion content, malonic dialdehyde (MDA) content, and reactive oxygen species (ROS) levels were markedly elevated compared to the wild type. It was further found that the transcription levels of CSD1 and CDS2 of two SOD genes were reduced in OE lines. Furthermore, the GmERF105 transgenic plants displayed suppressed expression of stress response marker genes, including KIN1, LEA14, NCED3, RD29A, and COR15A/B, under salt treatment. Our findings suggest that GmERF105 can act as a negative regulator in plant salt tolerance pathways by affecting ROS scavenging systems and the transcription of stress response marker genes.

Chrysanthemum embryo development is negatively affected by a novel ERF transcription factor, CmERF12

Embryo abortion often occurs during distant hybridization events. Apetala 2/ethylene-responsive factor (AP2/ERF) proteins are key transcription factor (TF) regulators of plant development and stress resistance, but their roles in hybrid embryo development are poorly understood. In this study, we isolated a novel AP2/ERF TF, CmERF12, from chrysanthemum and show that it adversely affects embryo development during distant hybridization. Transcriptome and real-time quantitative PCR demonstrate that CmERF12 is expressed at significantly higher levels in aborted ovaries compared with normal ones. CmERF12 localizes to the cell nucleus and contains a conserved EAR motif that mediates its transcription repressor function in yeast and plant cells. We generated artificial microRNA (amiR) CmERF12 transgenic lines of Chrysanthemum morifolium var. 'Yuhualuoying' and conducted distant hybridization with the wild-type tetraploid, Chrysanthemum nankingense, and found that CmERF12-knock down significantly promoted embryo development and increased the seed-setting rates during hybridization. The expression of various genes related to embryo development was up-regulated in developing ovaries from the cross between female amiR-CmERF12 C. morifolium var. 'Yuhualuoying'× male C. nankingense. Furthermore, CmERF12 directly interacted with CmSUF4, which is known to affect flower development and embryogenesis, and significantly reduced its ability to activate its target gene CmEC1 (EGG CELL1). Our study provides a novel method to overcome barriers to distant hybridization in plants and reveals the mechanism by which CmERF12 negatively affects chrysanthemum embryo development.

Transcriptome analysis and functional identification of GmMYB46 in soybean seedlings under salt stress

Salinity is one of the major abiotic stress that limits crop growth and productivity. We investigated the transcriptomes of salt-treated soybean seedlings versus a control using RNA-seq to better understand the molecular mechanisms of the soybean (Glycine max L.) response to salt stress. Transcriptome analysis revealed 1,235 differentially expressed genes (DEGs) under salt stress. Several important pathways and key candidate genes were identified by KEGG enrichment. A total of 116 differentially expressed transcription factors (TFs) were identified, and 17 TFs were found to belong to MYB families. Phylogenetic analysis revealed that these TFs may be involved in salt stress adaptation. Further analysis revealed that GmMYB46 was up-regulated by salt and mannitol and was localized in the nucleus. The salt tolerance of transgenic Arabidopsis overexpressing GmMYB46 was significantly enhanced compared to wild-type (WT). GmMYB46 activates the expression of salt stress response genes (P5CS1, SOD, POD, NCED3) in Arabidopsis under salt stress, indicating that the GmMYB46 protein mediates the salt stress response through complex regulatory mechanisms. This study provides information with which to better understand the molecular mechanism of salt tolerance in soybeans and to genetically improve the crop.

Evaluation of drought resistance and transcriptome analysis for the identification of drought-responsive genes in Iris germanica

Iris germanica, a species with very high ornamental value, exhibits the strongest drought resistance among the species in the genus Iris, but the molecular mechanism underlying its drought resistance has not been evaluated. To investigate the gene expression profile changes exhibited by high-drought-resistant I. germanica under drought stress, 10 cultivars with excellent characteristics were included in pot experiments under drought stress conditions, and the changes in the chlorophyll (Chl) content, plasma membrane relative permeability (RP), and superoxide dismutase (SOD), malondialdehyde (MDA), free proline (Pro), and soluble protein (SP) levels in leaves were compared among these cultivars. Based on their drought-resistance performance, the 10 cultivars were ordered as follows: 'Little Dream' > 'Music Box' > 'X'Brassie' > 'Blood Stone' > 'Cherry Garden' > 'Memory of Harvest' > 'Immortality' > 'White and Gold' > 'Tantara' > 'Clarence'. Using the high-drought-resistant cultivar 'Little Dream' as the experimental material, cDNA libraries from leaves and rhizomes treated for 0, 6, 12, 24, and 48 h with 20% polyethylene glycol (PEG)-6000 to simulate a drought environment were sequenced using the Illumina sequencing platform. We obtained 1, 976, 033 transcripts and 743, 982 unigenes (mean length of 716 bp) through a hierarchical clustering analysis of the resulting transcriptome data. The unigenes were compared against the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and gene ontology (GO) databases for functional annotation, and the gene expression levels in leaves and rhizomes were compared between the 20% PEG-6000 stress treated (6, 12, 24, and 48 h) and control (0 h) groups using DESeq2. 7849 and 24,127 differentially expressed genes (DEGs) were obtained from leaves and rhizomes, respectively. GO and KEGG enrichment analyses of the DEGs revealed significantly enriched KEGG pathways, including ribosome, photosynthesis, hormone signal transduction, starch and sucrose metabolism, synthesis of secondary metabolites, and related genes, such as heat shock proteins (HSPs), transcription factors (TFs), and active oxygen scavengers. In conclusion, we conducted the first transcriptome sequencing analysis of the I. germanica cultivar 'Little Dream' under drought stress and generated a large amount of genetic information. This study lays the foundation for further exploration of the molecular mechanisms underlying the responses of I. germanica to drought stress and provides valuable genetic resources for the breeding of drought-resistant plants.

Transcriptome analysis reveals significant difference in gene expression and pathways between two peanut cultivars under Al stress

Aluminum (Al) toxicity is an important factor in limiting peanut growth on acidic soil. The molecular mechanisms underlying peanut responses to Al stress are largely unknown. In this study, we performed transcriptome analysis of the root tips (0-1 cm) of peanut cultivar ZH2 (Al-sensitive) and 99-1507 (Al-tolerant) respectively. Root tips of peanuts that treated with 100 μM Al for 8 h and 24 h were analyzed by RNA-Seq, and a total of 8,587 differentially expressed genes (DEGs) were identified. GO and KEGG pathway analysis excavated a group of important Al-responsive genes related to organic acid transport, metal cation transport, transcription regulation and programmed cell death (PCD). These homologs were promising targets to modulate Al tolerance in peanuts. It was found that the rapid transcriptomic response to Al stress in 99-1507 helped to activate effective Al tolerance mechanisms. Protein and protein interaction analysis indicated that MAPK signal transduction played important roles in the early response to Al stress in peanuts. Moreover, weighted correlation network analysis (WGCNA) identified a predicted EIL (EIN3-like) gene with greatly increased expression as an Al-associated gene, and revealed a link between ethylene signaling transduction and Al resistance related genes in peanut, which suggested the enhanced signal transduction mediated the rapid transcriptomic responses. Our results revealed key pathways and genes associated with Al stress, and improved the understanding of Al response in peanut.

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

Understanding salt tolerance mechanism using transcriptome profiling and de novo assembly of wild tomato Solanum chilense

Soil salinity affects the plant growth and productivity detrimentally, but Solanum chilense, a wild relative of cultivated tomato (Solanum lycopersicum L.), is known to have exceptional salt tolerance. It has precise adaptations against direct exposure to salt stress conditions. Hence, a better understanding of the mechanism to salinity stress tolerance by S. chilense can be accomplished by comprehensive gene expression studies. In this study 1-month-old seedlings of S. chilense and S. lycopersicum were subjected to salinity stress through application of sodium chloride (NaCl) solution. Through RNA-sequencing here we have studied the differences in the gene expression patterns. A total of 386 million clean reads were obtained through RNAseq analysis using the Illumina HiSeq 2000 platform. Clean reads were further assembled de novo into a transcriptome dataset comprising of 514,747 unigenes with N50 length of 578 bp and were further aligned to the public databases. Genebank non-redundant (Nr), Viridiplantae, Gene Ontology (GO), KOG, and KEGG databases classification suggested enrichment of these unigenes in 30 GO categories, 26 KOG, and 127 pathways, respectively. Out of 265,158 genes that were differentially expressed in response to salt treatment, 134,566 and 130,592 genes were significantly up and down-regulated, respectively. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in cytokinin, ethylene, auxin, abscisic acid, gibberellin, and Ca²⁺ mediated signaling pathways were up-regulated. Furthermore, GO enrichment analysis was performed using REVIGO and up-regulation of multiple genes involved in various biological processes in chilense under salinity were identified. Through pathway analysis of DEGs, “Wnt signaling pathway” was identified as a novel pathway for the response to the salinity stress. Moreover, key genes for salinity tolerance, such as genes encoding proline and arginine metabolism, ROS scavenging system, transporters, osmotic regulation, defense and stress response, homeostasis and transcription factors were not only salt-induced but also showed higher expression in S. chilense as compared to S. lycopersicum. Thus indicating that these genes may have an important role in salinity tolerance in S. chilense. Overall, the results of this study improve our understanding on possible molecular mechanisms underlying salt tolerance in plants in general and tomato in particular.

Functional characterization of LkERF-B2 for improved salt tolerance ability in Arabidopsis thaliana

The ethylene response factors have been reported to play critical roles in developmental and environmental responses in plants. In the present study, an ERF transcription factor gene was aimed to be identified from Larix kaempferi. Molecular characteristics and function of this gene were further explored. The result showed that a 1344 bp ERF transcription factor gene containing initiation and termination codon was obtained by RT-PCR and named LkERF-B2. LkERF-B2 gene encoded 447 amino acids containing a typical AP2/ERF domain. Alignment of predicted amino acid sequence of LkERF-B2 in various plant species showed that this ERF transcription factor was highly homologous (79.0%) with that of Picea sitchensi. To elucidate the function of LkERF-B2, LkERF-B2 overexpression vector was successfully constructed and transformed to Arabidopsis thaliana via dip flower. Compared with control plant, LkERF-B2 overexpressed transgenic A. thaliana showed a significantly higher survival rate under cold, heat, NaCl and drought stresses. NaCl stress analysis revealed that control and transgenic Arabidopsis were both flowering earlier under 100 and 150 mM/L NaCl treatment. While under 200-300 mM/L NaCl treatment, the growth of control plant was significantly inhibited compared with transgenic A. thaliana. Salt injury rate and salt injury index of transgenic Arabidopsis were lower than those of the control. Further investigation showed that transgenic Arabidopsis exhibited much higher content of chloroplast pigments under different NaCl concentration. Meanwhile, the activity of SOD and POD was also enhanced in transgenic A. thaliana. These results suggested that LkERF-B2 was a key transcription factor and could lead to enhanced salt stress tolerance.

Promoter deletion analysis reveals root-specific expression of the alkenal reductase gene (OsAER1) in Oryza sativa

Root-specific promoters are useful in plant genetic engineering, primarily to improve water and nutrient absorption. The aim of this study was to clone and characterise the promoter of the Oryza sativa L. alkenal reductase (OsAER1) gene encoding 2-alkenal reductase, an NADPH-dependent oxidoreductase. Expression analysis using quantitative real-time PCR confirmed the root-specific expression of the OsAER1 gene. Subsequently, a 3082-bp fragment of the OsAER1 promoter was isolated from a local Indonesian rice cultivar, Awan Kuning. Sequencing and further nucleotide sequence analysis of the 3082-bp promoter fragment (PA-5) revealed the presence of at least 10 root-specific cis-regulatory elements putatively responsible for OsAER1 root-specific expression. Using the 3082-bp promoter fragment to drive the expression of the GUS reporter transgene confirmed that the OsAER1 promoter is root-specific. Further, the analysis indicated that OsAER1 promoter activity was absent in leaves, petioles and shoots during sprouting, vegetative, booting and generative stages of rice development. In contrast, the promoter activity was present in anthers and aleurone layers of immature seeds 7-20 days after anthesis. Moreover, there was no promoter activity observed in the aleurone layers of mature seeds. The OsAER1 promoter activity is induced by Al-toxicity, NaCl and submergence stresses, indicating the OsAER1 promoter activity is induced by those stresses. Exogenous treatments of transgenic plants carrying the PA-5 promoter construct with abscisic acid and indoleacetic acid also induced expression of the GUS reporter transgene, indicating the role of plant growth regulators in controlling OsAER1 promoter activity. Promoter deletion analysis was conducted to identify the cis-acting elements of the promoter responsible for controlling root-specific expression. The GUS reporter gene was fused with various deletion fragments of the OsAER1 promoter and the resulting constructs were transformed in rice plants to generate transgenic plants. The results of this analysis indicated that cis-acting elements controlling root-specific expression are located between -1562 to -1026bp of the OsAER1 CDS. Here we discusses the results of the conducted analyses, the possible role of OsAER1 in rice growth and development, possible contributions and the potential usage of these findings in future plant research.

Cloning and molecular characterization of TaERF6, a gene encoding a bread wheat ethylene response factor

Ethylene response factor proteins are important for regulating gene expression under different stresses. Different isoforms for ERF have previously isolated from bread wheat (Triticum aestivum L.) and related genera and called from TaERF1 to TaERF5. We isolated, cloned and molecular characterized a novel one based on TdERF1, an isoform in durum wheat (Triticum turgidum L.) and called TaERF6. Its cDNA was synthesized, sequenced and compared with genomic sequence to figure out intron and exon regions and determine coding sequence region. The length of TdERF1 gene was 1939 bp and cDNA was 1065 bp including two exons, the first one 259 bp and the second one 806 bp separated by a 874 bp intron with a 111 bp 5'-UTR (untranslated region) and 401 bp 3'-UTR. TaERF6 encodes a 353 amino acids protein with nearly 99% identity to TdERF1. Hydrophobic cluster analysis revealed an N-terminal hydrophobic domain contains a highly conserved motif with the consensus sequence of M [C/L/Y] [G/R] [G/R/P] [A/G/V/L/R] [I/L/R/S/P/Q] [L/I/R/H] and hydrophobic clusters in AP2/ERF domain of which tends to form -sheet. Three monopartite nuclear localization signals also identified in TaERF6 that play important role in getting back into the nucleus. The results showed several putative phosphorylation sites in TaERF6 that a motif from residues 246 to 266, the CMVII-4 motif, was predicted to phosphorylate by different kinase proteins and play important roles in TaERF6 function. Phylogenetic analysis showed 7 clusters (I to VII) and 10 subclusters according to their relatedness in Poaceae family.

Influence of salinity and Fusarium oxysporum as the stress factors on morpho-physiological and yield attributes in onion

Occurrence of salt stress with the soil borne fungus Fusarium oxysporum f. sp. cepa (FOC) are potential threat to the crop yield. This investigation reports effect of the concurrent stresses (salinity and FOC) on morpho-physiological and yield attributes in onion. In vitro growth tests revealed proliferation of FOC biomass at different levels of salinity (2-8 dS m-1). A greenhouse pot experiment with the proposed levels of salinity (2.5, 3.5 and 4.5 dS m-1) in combination with FOC inoculation showed more drastic effect of combined stress on disease severity, plant growth and bulb as compared to the individual stress. In general, osmotic potential, total chlorophyll content, membrane stability index and total protein content of the leaf were decreased, while total phenolics were increased due to the given stress/s. Total sugar content decreased due to effect of the  individual stress of FOC, while it increased under the individual stress of salinity and in combination with FOC. FOC infection did not change activity of polyphenol oxidase (PPO), while it improved peroxidase (POX) and phenylalanine ammonia lyase (PAL) and decreased catalase (CAT) activity. Activities of POX and PPO increased, however PAL and CAT declined under individual as well as simultaneous stress of salinity  and  FOC. The research work concluded that FOC will be a more severe disease threat for onion cultivation in saline soils.

The chromatin remodeler ZmCHB101 impacts expression of osmotic stress-responsive genes in maize

The maize chromatin remodeler ZmCHB101 plays an essential role in the osmotic stress response. ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Drought and osmotic stresses are recurring conditions that severely constrain crop production. Evidence accumulated in the model plant Arabidopsis thaliana suggests that core components of SWI/SNF chromatin remodeling complexes play essential roles in abiotic stress responses. However, how maize SWI/SNF chromatin remodeling complexes function in osmotic and drought stress responses remains unknown. Here we show that ZmCHB101, a homolog of A. thaliana SWI3D in maize, plays essential roles in osmotic and dehydration stress responses. ZmCHB101-RNA interference (RNAi) transgenic plants displayed osmotic, salt and drought stress-sensitive phenotypes. Genome-wide RNA-sequencing analysis revealed that ZmCHB101 impacts the transcriptional expression landscape of osmotic stress-responsive genes. Intriguingly, ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Furthermore, we identified that ZmCHB101 associates with RNA polymerase II (RNAPII) in vivo and is a prerequisite for the proper occupancy of RNAPII on the proximal regions of transcription start sites of stress-response genes. Taken together, our findings suggest that ZmCHB101 affects gene expression by remodeling chromatin states and controls RNAPII occupancies in maize under osmotic stress.

The Tomato DOF Daily Fluctuations 1, TDDF1 acts as flowering accelerator and protector against various stresses

Adaptation to environmental changes is an important fitness trait for crop development. Photoperiod is an essential factor in seasonal control of flowering time. Sensing of day-length requires an interaction between the Photoperiod and the endogenous rhythms that is controlled by plant circadian clock. Thus, circadian clock is a critical regulator and internal molecular time-keeping mechanism, controlling key agricultural traits in crop plants such as the ability to adjust their growth and physiology to anticipate diurnal environmental changes. Here, we describe the gene Tomato Dof Daily Fluctuations 1 (TDDF1), which is involved in circadian regulation and stress resistance. Large daily oscillations in TDDF1 expression were retained after transferring to continuous dark (DD) or light (LL) conditions. Interestingly, overexpressing TDDF1 induce early flowering in tomato through up-regulation of the flowering-time control genes, moreover, by protein-protein interaction with the floral inducer SFT gene. Notably, overexpressing TDDF1 in tomato was associated with chlorophyll overaccumulation by up-regulating the related biosynthetic genes. TDDF1 expression results in improved drought, salt, various hormones stress tolerance alongwith resistance to late blight caused by Phytophthora infestans. This study can be a distinctive strategy to improve other economically important crops.

A novel AP2/ERF family transcription factor from Glycine soja, GsERF71, is a DNA binding protein that positively regulates alkaline stress tolerance in Arabidopsis

KEY MESSAGE

Here we first found that GsERF71, an ERF factor from wild soybean could increase plant alkaline stress tolerance by up-regulating H+-ATPase and by modifing the accumulation of Auxin. Alkaline soils are widely distributed all over the world and greatly limit plant growth and development. In our previous transcriptome analyses, we have identified several ERF (ethylene-responsive factor) genes that responded strongly to bicarbonate stress in the roots of wild soybean G07256 (Glycine soja). In this study, we cloned and functionally characterized one of the genes, GsERF71. When expressed in epidermal cells of onion, GsERF71 localized to the nucleus. It can activate the reporters in yeast cells, and the C-terminus of 170 amino acids is essential for its transactivation activity. Yeast one-hybrid and EMSA assays indicated that GsERF71 specifically binds to the cis-acting elements of the GCC-box, suggesting that GsERF71 may participate in the regulation of transcription of the relevant biotic and abiotic stress-related genes. Furthermore, transgenic Arabidopsis plants overexpressing GsERF71 showed significantly higher tolerance to bicarbonate stress generated by NaHCO3 or KHCO3 than the wild type (WT) plants, i.e., the transgenic plants had greener leaves, longer roots, higher total chlorophyll contents and lower MDA contents. qRT-PCR and rhizosphere acidification assays indicated that the expression level and activity of H+-ATPase (AHA2) were enhanced in the transgenic plants under alkaline stress. Further analysis indicated that the expression of auxin biosynthetic genes and IAA contents were altered to a lower extent in the roots of transgenic plants than WT plants under alkaline stress in a short-term. Together, our data suggest that GsERF71 enhances the tolerance to alkaline stress by up-regulating the expression levels of H+-ATPase and by modifying auxin accumulation in transgenic plants.

RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant

Salinity stress has become an increasing threat to food security worldwide and elucidation of the mechanism for salinity tolerance is of great significance. Induced mutation, especially spaceflight mutagenesis, is one important method for crop breeding. In this study, we show that a spaceflight-induced wheat mutant, named salinity tolerance 1 (st1), is a salinity-tolerant line. We report the characteristics of transcriptomic sequence variation induced by spaceflight, and show that mutations in genes associated with sodium ion transport may directly contribute to salinity tolerance in st1. Furthermore, GO and KEGG enrichment analysis of differentially expressed genes (DEGs) between salinity-treated st1 and wild type suggested that the homeostasis of oxidation-reduction process is important for salt tolerance in st1. Through KEGG pathway analysis, "Butanoate metabolism" was identified as a new pathway for salinity responses. Additionally, key genes for salinity tolerance, such as genes encoding arginine decarboxylase, polyamine oxidase, hormones-related, were not only salt-induced in st1 but also showed higher expression in salt-treated st1 compared with salt-treated WT, indicating that these genes may play important roles in salinity tolerance in st1. This study presents valuable genetic resources for studies on transcriptome variation caused by induced mutation and the identification of salt tolerance genes in crops.

RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant

Salinity stress has become an increasing threat to food security worldwide and elucidation of the mechanism for salinity tolerance is of great significance. Induced mutation, especially spaceflight mutagenesis, is one important method for crop breeding. In this study, we show that a spaceflight-induced wheat mutant, named salinity tolerance 1 (st1), is a salinity-tolerant line. We report the characteristics of transcriptomic sequence variation induced by spaceflight, and show that mutations in genes associated with sodium ion transport may directly contribute to salinity tolerance in st1. Furthermore, GO and KEGG enrichment analysis of differentially expressed genes (DEGs) between salinity-treated st1 and wild type suggested that the homeostasis of oxidation-reduction process is important for salt tolerance in st1. Through KEGG pathway analysis, "Butanoate metabolism" was identified as a new pathway for salinity responses. Additionally, key genes for salinity tolerance, such as genes encoding arginine decarboxylase, polyamine oxidase, hormones-related, were not only salt-induced in st1 but also showed higher expression in salt-treated st1 compared with salt-treated WT, indicating that these genes may play important roles in salinity tolerance in st1. This study presents valuable genetic resources for studies on transcriptome variation caused by induced mutation and the identification of salt tolerance genes in crops.

Transcriptome Analyses Reveal Candidate Genes Potentially Involved in Al Stress Response in Alfalfa

Alfalfa is the most extensively cultivated forage legume, yet most alfalfa cultivars are not aluminum tolerant, and the molecular mechanisms underlying alfalfa responses to Al stress are largely unknown. In this study, we aimed to understand how alfalfa responds to Al stress by identifying and analyzing Al-stress-responsive genes in alfalfa roots at the whole-genome scale. The transcriptome changes in alfalfa roots under Al stress for 4, 8, or 24 h were analyzed using Illumina high-throughput sequencing platforms. A total of 2464 differentially expressed genes (DEGs) were identified, and most were up-regulated at early (4 h) and/or late (24 h) Al exposure time points rather than at the middle exposure time point (8 h). Metabolic pathway enrichment analysis demonstrated that the DEGs involved in ribosome, protein biosynthesis, and process, the citrate cycle, membrane transport, and hormonal regulation were preferentially enriched and regulated. Biosynthesis inhibition and signal transduction downstream of auxin- and ethylene-mediated signals occur during alfalfa responses to root growth inhibition. The internal Al detoxification mechanisms play important roles in alfalfa roots under Al stress. These findings provide valuable information for identifying and characterizing important components in the Al signaling network in alfalfa and enhance understanding of the molecular mechanisms underlying alfalfa responses to Al stress.

A novel Ap2/ERF transcription factor from Stipa purpurea leads to enhanced drought tolerance in Arabidopsis thaliana

SpERF1 acts as a positive regulator, contributing to drought stress tolerance in A. thaliana through activating DRE/CRT elements in the promoters of abiotic stress-responsive genes. Stipa purpurea is an endemic perennial grass species in alpine arid and semi-arid meadows on the Qinghai-Xizang Plateau, which is highly tolerant against drought and cold. ERF transcription factors are known to regulate gene expression under abiotic and biotic treatments. Herein, we isolated a full-length ERF gene CDS from S. purpurea named SpERF1, which was induced by drought, cold, and jasmonic acid stresses. Subcellular localization revealed that SpERF1 is a nuclear protein, consistent with its roles as a transcription factor. Overexpression of SpERF1 enhanced drought tolerance of transgenic Arabidopsis thaliana via the activation of DRE/CRT elements in the promoters of abiotic stress-responsive genes. Furthermore, increased accumulation of proline indicated that SpERF1 might be involved in proline synthesis in the transgenic lines, allowing them to have a better buffering capacity and membrane protection under drought stress. This study indicated that SpERF1 might be an attractive target in the genetic engineering for improving stress tolerance in other crops. Moreover, SpERF1 protein function analysis increased our understanding of S. purpurea's ability to adapt to the adverse conditions of the Qinghai-Xizang Plateau.

Ethylene positively regulates cold tolerance in grapevine by modulating the expression of ETHYLENE RESPONSE FACTOR 057

Ethylene (ET) is a gaseous plant hormone that plays essential roles in biotic and abiotic stress responses in plants. However, the role of ET in cold tolerance varies in different species. This study revealed that low temperature promotes the release of ET in grapevine. The treatment of exogenous 1-aminocyclopropane-1-carboxylate increased the cold tolerance of grapevine. By contrast, the application of the ET biosynthesis inhibitor aminoethoxyvinylglycine reduced the cold tolerance of grapevine. This finding suggested that ET positively affected cold stress responses in grapevine. The expression of VaERF057, an ET signaling downstream gene, was strongly induced by low temperature. The overexpression of VaERF057 also enhanced the cold tolerance of Arabidopsis. Under cold treatment, malondialdehyde content was lower and superoxide dismutase, peroxidase, and catalase activities were higher in transgenic lines than in wild-type plants. RNA-Seq results showed that 32 stress-related genes, such as CBF1-3, were upregulated in VaERF057-overexpressing transgenic line. Yeast one-hybrid results further demonstrated that VaERF057 specifically binds to GCC-box and DRE motifs. Thus, VaERF057 may directly regulate the expression of its target stress-responsive genes by interacting with a GCC-box or a DRE element. Our work confirmed that ET positively regulates cold tolerance in grapevine by modulating the expression of VaERF057.

Future-proof crops: challenges and strategies for climate resilience improvement

Breeding for stress-resilient crops strongly depends on technological and biological advancements that have provided a wealth of information on genetic variants and their contribution to stress tolerance. In the context of the upcoming challenges for agriculture due to climate change, such as prolonged and/or increased stress intensities, CO2 increase and stress combinations, hierarchizing this information is key to accelerating crop improvement towards sustained or even increased productivity. We propose traits with high scalability to yield and crop performance that can be targeted for improvement and provide examples of recent discoveries with potential applicability in breeding. Critical to success is the integrated analysis of the phenotypes of genetic variants across different environmental variables using modelling approaches and high-throughput phenotyping.

Comparative Analysis of WRKY Genes Potentially Involved in Salt Stress Responses in Triticum turgidum L. ssp. durum

WRKY transcription factors are involved in multiple aspects of plant growth, development and responses to biotic stresses. Although they have been found to play roles in regulating plant responses to environmental stresses, these roles still need to be explored, especially those pertaining to crops. Durum wheat is the second most widely produced cereal in the world. Complex, large and unsequenced genomes, in addition to a lack of genomic resources, hinder the molecular characterization of tolerance mechanisms. This paper describes the isolation and characterization of five TdWRKY genes from durum wheat (Triticum turgidum L. ssp. durum). A PCR-based screening of a T. turgidum BAC genomic library using primers within the conserved region of WRKY genes resulted in the isolation of five BAC clones. Following sequencing fully the five BACs, fine annotation through Triannot pipeline revealed 74.6% of the entire sequences as transposable elements and a 3.2% gene content with genes organized as islands within oceans of TEs. Each BAC clone harbored a TdWRKY gene. The study showed a very extensive conservation of genomic structure between TdWRKYs and their orthologs from Brachypodium, barley, and T. aestivum. The structural features of TdWRKY proteins suggested that they are novel members of the WRKY family in durum wheat. TdWRKY1/2/4, TdWRKY3, and TdWRKY5 belong to the group Ia, IIa, and IIc, respectively. Enrichment of cis-regulatory elements related to stress responses in the promoters of some TdWRKY genes indicated their potential roles in mediating plant responses to a wide variety of environmental stresses. TdWRKY genes displayed different expression patterns in response to salt stress that distinguishes two durum wheat genotypes with contrasting salt stress tolerance phenotypes. TdWRKY genes tended to react earlier with a down-regulation in sensitive genotype leaves and with an up-regulation in tolerant genotype leaves. The TdWRKY transcripts levels in roots increased in tolerant genotype compared to sensitive genotype. The present results indicate that these genes might play some functional role in the salt tolerance in durum wheat.

TdERF1, an ethylene response factor associated with dehydration responses in durum wheat (Triticum turgidum L. subsp. durum)

Water deficit and increasing salinization reduce productivity of wheat, the leading crop for human diet. While the complete genome sequence of this crop has not been deciphered, a BAC library screening allowed the isolation of TdERF1, the first ethylene response factor gene from durum wheat. This gene is putatively involved in mediating salt stress tolerance and its characterization provides clues toward understanding the mechanisms underlying the adaptation/tolerance of durum wheat to suboptimal growth conditions. TdERF1 expression is differentially induced by high salt treatment in 2 durum wheat varieties, the salt-tolerant Grecale (GR) and the salt-sensitive Om Rabiaa (OR). To further extend these findings, we show here that the expression of this ERF is correlated with physiological parameters, such as the accumulation of osmo-regulators and membrane integrity, that discriminate between the 2 contrasted wheat genotypes. The data confirm that GR and OR are 2 contrasted wheat genotypes with regard to salt-stress and show that TdERF1 is also induced by water stress with an expression pattern clearly discriminating between the 2 genotypes. These findings suggest that TdERF1 might be involved in responses to salt and water stress providing a potential genetic marker discriminating between tolerant and sensitive wheat varieties.

Diverse roles of jasmonates and ethylene in abiotic stress tolerance

Jasmonates (JAs) and ethylene (ET), often acting cooperatively, play essential roles in regulating plant defense against pests and pathogens. Recent research reviewed here has revealed mechanistic new insights into the mode of action of these hormones in plant abiotic stress tolerance. During cold stress, JAs and ET differentially regulate the C-repeat binding factor (CBF) pathway. Major JA and ET signaling hubs such as JAZ proteins, CTR1, MYC2, components of the mediator complex, EIN2, EIN3, and several members of the AP2/ERF transcription factor gene family all have complex regulatory roles during abiotic stress adaptation. Better understanding the roles of these phytohormones in plant abiotic stress tolerance will contribute to the development of crop plants tolerant to a wide range of stressful environments.