Identification of ERF genes in peanuts and functional analysis of AhERF008 and AhERF019 in abiotic stress response

Water-deficit stress induces prenylated stilbenoid production and affects biomass in peanut hairy roots: Exploring the role of stilbenoid prenyltransferase downregulation

The peanut plant is one of the most economically important crops around the world. Abiotic stress, such as drought, causes over five hundred million dollars in losses in peanut production per year. Peanuts are known to produce prenylated stilbenoids to counteract biotic stress. However, their role in abiotic stress tolerance has not been elucidated. To address this issue, hairy roots with the capacity to produce prenylated stilbenoids were established. An RNA-interference (RNAi) molecular construct targeting the stilbenoid-specific prenyltransferase AhR4DT-1 was designed and expressed via Agrobacterium rhizogenes-mediated transformation in hairy roots of peanut cultivar Georgia Green. Two transgenic hairy roots with the RNAi molecular construct were established, and the downregulation of AhR4DT-1 was validated using reverse transcriptase quantitative PCR. To determine the efficacy of the RNAi-approach in modifying the levels of prenylated stilbenoids, the hairy roots were co-treated with methyl jasmonate, hydrogen peroxide, cyclodextrin, and magnesium chloride to induce the production of stilbenoids and then the stilbenoids were analyzed in extracts of the culture medium. Highly reduced levels of prenylated stilbenoids were observed in the RNAi hairy roots. Furthermore, the hairy roots were evaluated in a polyethylene glycol (PEG) assay to assess the role of prenylated stilbenoids on water-deficit stress. Upon PEG treatment, stilbenoids were induced and secreted into the culture medium of RNAi and wild-type hairy roots. Additionally, the biomass of the RNAi hairy roots decreased by a higher amount as compared to the wild-type hairy roots suggesting that prenylated stilbenoids might play a role against water-deficit stress.

Unveiling growth-promoting attributes of peanut root endophyte Micromonospora sp

In this study, 20 endophytic actinobacteria were isolated from different parts of peanut plants growing in cropland with low and high salt in West Bengal, India. The endophytes underwent a rigorous morphological, biochemical, and genetic screening process to evaluate their effectiveness in enhancing plant growth. About 20% of these isolates were identified as potential plant growth-promoting endophytic actinobacteria, which showed high 16S rRNA gene sequence similarity (up to 99-100%) with different species of Micromonospora. Among these isolates, Micromonospora sp. ASENR15 produced the highest levels of indole acetic acid (IAA) and gibberellic acid (GA), while Micromonospora sp. ASENL2, Micromonospora sp. ANENR4, and Micromonospora sp. ASENR12 produced the highest level of siderophore. Among these leaf and root endophytic Micromonospora, strain ANENR4 was tested for its plant growth-promoting attributes. ANENR4 can be transmitted into the roots of a healthy peanut plant, enhances growth, and colonize the roots in abundance, suggesting the potential agricultural significance of the strain. Moreover, the study is the first report of endophytic Micromonospora in peanuts with PGP effects. The outcomes of this study open avenues for further research on harnessing the benefits of this endophytic Micromonospora for optimizing plant growth in agriculture.

The genus Arachis: an excellent resource for studies on differential gene expression for stress tolerance

Peanut Arachis hypogaea is a segmental allotetraploid in the section Arachis of the genus Arachis along with the Section Rhizomataceae. Section Arachis has several diploid species along with Arachis hypogaea and A. monticola. The section Rhizomataceae comprises polyploid species. Several species in the genus are highly tolerant to biotic and abiotic stresses and provide excellent sets of genotypes for studies on differential gene expression. Though there were several studies in this direction, more studies are needed to identify more and more gene combinations. Next generation RNA-seq based differential gene expression study is a powerful tool to identify the genes and regulatory pathways involved in stress tolerance. Transcriptomic and proteomic study of peanut plants under biotic stresses reveals a number of differentially expressed genes such as R genes (NBS-LRR, LRR-RLK, protein kinases, MAP kinases), pathogenesis related proteins (PR1, PR2, PR5, PR10) and defense related genes (defensin, F-box, glutathione S-transferase) that are the most consistently expressed genes throughout the studies reported so far. In most of the studies on biotic stress induction, the differentially expressed genes involved in the process with enriched pathways showed plant-pathogen interactions, phenylpropanoid biosynthesis, defense and signal transduction. Differential gene expression studies in response to abiotic stresses, reported the most commonly expressed genes are transcription factors (MYB, WRKY, NAC, bZIP, bHLH, AP2/ERF), LEA proteins, chitinase, aquaporins, F-box, cytochrome p450 and ROS scavenging enzymes. These differentially expressed genes are in enriched pathways of transcription regulation, starch and sucrose metabolism, signal transduction and biosynthesis of unsaturated fatty acids. These identified differentially expressed genes provide a better understanding of the resistance/tolerance mechanism, and the genes for manipulating biotic and abiotic stress tolerance in peanut and other crop plants. There are a number of differentially expressed genes during biotic and abiotic stresses were successfully characterized in peanut or model plants (tobacco or Arabidopsis) by genetic manipulation to develop stress tolerance plants, which have been detailed out in this review and more concerted studies are needed to identify more and more gene/gene combinations.

A MYB-related transcription factor from peanut, AhMYB30, improves freezing and salt stress tolerance in transgenic Arabidopsis through both DREB/CBF and ABA-signaling pathways

Abiotic stresses such as salinity and low temperature have serious impact on peanut growth and yield. The present work investigated the function of a MYB-related transcription factor gene AhMYB30 obtained from peanut under salt and low temperature stresses by transgenic methods. The results indicated that the overexpression of AhMYB30 in Arabidopsis could enhance the resistance of transgenic plants to freezing and salt stresses. The expression of stress-response genes RD29A (Response-to-Dehydration 29A), COR15A (Cold-Regulated 15A), KIN1 (Kinesin 1) and ABI2 (Abscisic acid Insensitive 2) increased in transgenic plants compared with in wild-type. Subcellular localization and transcriptional autoactivation validation demonstrated that AhMYB30 has essential features of transcription factors. Therefore, AhMYB30 may increase salt and freezing stress tolerance as the transcription factor (TF) in Arabidopsis through both DREB/CBF and ABA-signaling pathways. Our results lay the theoretical foundation for exploring stress resistance mechanisms of peanut and offering novel genetic resources for molecular breeding.

Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses

Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.

Ethylene Response Factor LlERF110 Mediates Heat Stress Response via Regulation of LlHsfA3A Expression and Interaction with LlHsfA2 in Lilies (Lilium longiflorum)

Heat stress seriously affects the quality of cut lily flowers. The ethylene response factors (ERFs) participate in heat stress response in many plants. In this study, heat treatment increased the production of ethylene in lily leaves, and exogenous ethylene treatment enhanced the heat resistance of lilies. LlERF110, an important transcription factor in the ethylene signaling pathway, was found in the high-temperature transcriptome. The coding region of LlERF110 (969 bp) encodes 322 amino acids and LlERF110 contains an AP2/ERF typical domain belonging to the ERF subfamily group X. LlERF110 was induced by ethylene and was expressed constitutively in all tissues. LlERF110 is localized in the nucleus and has transactivation activity. Virus-induced gene silencing of LlERF110 in lilies reduced the basal thermotolerance phenotypes and significantly decreased the expression of genes involved in the HSF-HSP pathway, such as LlHsfA2, LlHsfA3A, and LlHsfA5, which may activate other heat stress response genes; and LlHsp17.6 and LlHsp22, which may protect proteins under heat stress. LlERF110 could directly bind to the promoter of LlHsfA3A and activate its expression according to the yeast one hybrid and dual-luciferase reporter assays. LlERF110 interacts with LlHsfA2 in the nucleus according to BiFC and the yeast two-hybrid assays. In conclusion, these results indicate that LlERF110 plays an important role in the basal thermotolerance of lilies via regulation of the HSF-HSP pathway, which could be the junction of the heat stress response pathway and the ethylene signaling pathway.

Genome-Wide Characterization of Ascorbate Peroxidase Gene Family in Peanut (Arachis hypogea L.) Revealed Their Crucial Role in Growth and Multiple Stress Tolerance

Ascorbate peroxidase (APX), an important antioxidant enzyme, plays a significant role in ROS scavenging by catalyzing the decrease of hydrogen peroxide under various environmental stresses. Nevertheless, information about the APX gene family and their evolutionary and functional attributes in peanut (Arachis hypogea L.) was not reported. Therefore, a comprehensive genome-wide study was performed to discover the APX genes in cultivated peanut genome. This study identified 166 AhAPX genes in the peanut genome, classified into 11 main groups. The gene duplication analysis showed that AhAPX genes had experienced segmental duplications and purifying selection pressure. Gene structure and motif investigation indicated that most of the AhAPX genes exhibited a comparatively well-preserved exon-intron pattern and motif configuration contained by the identical group. We discovered five phytohormones-, six abiotic stress-, and five growth and development-related cis-elements in the promoter regions of AhAPX. Fourteen putative ah-miRNAs from 12 families were identified, targeting 33 AhAPX genes. Furthermore, we identified 3,257 transcription factors from 38 families (including AP2, ARF, B3, bHLH, bZIP, ERF, MYB, NAC, WRKY, etc.) in 162 AhAPX genes. Gene ontology and KEGG enrichment analysis confirm the role of AhAPX genes in oxidoreductase activity, catalytic activity, cell junction, cellular response to stimulus and detoxification, biosynthesis of metabolites, and phenylpropanoid metabolism. Based on transcriptome datasets, some genes such as AhAPX4/7/17/77/82/86/130/133 and AhAPX160 showed significantly higher expression in diverse tissues/organs, i.e., flower, leaf, stem, roots, peg, testa, and cotyledon. Likewise, only a few genes, including AhAPX4/17/19/55/59/82/101/102/137 and AhAPX140, were significantly upregulated under abiotic (drought and cold), and phytohormones (ethylene, abscisic acid, paclobutrazol, brassinolide, and salicylic acid) treatments. qRT-PCR-based expression profiling presented the parallel expression trends as generated from transcriptome datasets. Our discoveries gave new visions into the evolution of APX genes and provided a base for further functional examinations of the AhAPX genes in peanut breeding programs.

Identification, expression, and association analysis of calcineurin B-like protein–interacting protein kinase genes in peanut

Plants usually respond to the external environment by initiating a series of signal transduction processes mediated by protein kinases, especially calcineurin B-like protein–interacting protein kinases (CIPKs). In this study, 54 CIPKs were identified in the peanut genome, of which 26 were from cultivated species (named AhCIPKs) and 28 from two diploid progenitors (Arachis duranensis—AdCIPKs and Arachis ipaensis—AiCIPKs). Evolution analysis revealed that the 54 CIPKs were composed of two different evolutionary branches. The CIPK members were unevenly distributed at different chromosomes. Synteny analysis strongly indicated that whole-genome duplication (allopolyploidization) contributed to the expansion of CIPK. Comparative genomics analysis showed that there was only one common collinear CIPK pairs among peanut, Arabidopsis, rice, grape, and soybean. The prediction results of cis-acting elements showed that AhCIPKs, AdCIPKs, and AiCIPKs contained different proportions of transcription factor binding motifs involved in regulating plant growth, abiotic stress, plant hormones, and light response elements. Spatial expression profiles revealed that almost all AhCIPKs had tissue-specific expression patterns. Furthermore, association analysis identified one polymorphic site in AdCIPK12 (AhCIPK11), which was significantly associated with pod length, seed length, hundred seed weight, and shoot root ratio. Our results provide valuable information of CIPKs in peanut and facilitate better understanding of their biological functions.

The AP2/ERF GmERF113 Positively Regulates the Drought Response by Activating GmPR10-1 in Soybean

Ethylene response factors (ERFs) are involved in biotic and abiotic stress; however, the drought resistance mechanisms of many ERFs in soybeans have not been resolved. Previously, we proved that GmERF113 enhances resistance to the pathogen Phytophthora sojae in soybean. Here, we determined that GmERF113 is induced by 20% PEG-6000. Compared to the wild-type plants, soybean plants overexpressing GmERF113 (GmERF113-OE) displayed increased drought tolerance which was characterized by milder leaf wilting, less water loss from detached leaves, smaller stomatal aperture, lower Malondialdehyde (MDA) content, increased proline accumulation, and higher Superoxide dismutase (SOD) and Peroxidase (POD) activities under drought stress, whereas plants with GmERF113 silenced through RNA interference were the opposite. Chromatin immunoprecipitation and dual effector-reporter assays showed that GmERF113 binds to the GCC-box in the GmPR10-1 promoter, activating GmPR10-1 expression directly. Overexpressing GmPR10-1 improved drought resistance in the composite soybean plants with transgenic hairy roots. RNA-seq analysis revealed that GmERF113 downregulates abscisic acid 8′-hydroxylase 3 (GmABA8’-OH 3) and upregulates various drought-related genes. Overexpressing GmERF113 and GmPR10-1 increased the abscisic acid (ABA) content and reduced the expression of GmABA8’-OH3 in transgenic soybean plants and hairy roots, respectively. These results reveal that the GmERF113-GmPR10-1 pathway improves drought resistance and affects the ABA content in soybean, providing a theoretical basis for the molecular breeding of drought-tolerant soybean.

Genome-wide characterization and identification of candidate ERF genes involved in various abiotic stress responses in sesame (Sesamum indicum L.)

BACKGROUND

The adverse effects of climate change on crop production are constraining breeders to develop high-quality environmentally stable varieties. Hence, efforts are being made to identify key genes that could be targeted for enhancing crop tolerance to environmental stresses. ERF transcription factors play an important role in various abiotic stresses in plants. However, the roles of the ERF family in abiotic stresses tolerance are still largely unknown in sesame, the "queen" of oilseed crops.

RESULTS

In total, 114 sesame ERF genes (SiERFs) were identified and characterized. 96.49% of the SiERFs were distributed unevenly on the 16 linkage groups of the sesame genome. The phylogenetic analysis with the Arabidopsis ERFs (AtERFs) subdivided SiERF subfamily proteins into 11 subgroups (Groups I to X; and VI-L). Genes in the same subgroup exhibited similar structure and conserved motifs. Evolutionary analysis showed that the expansion of ERF genes in sesame was mainly induced by whole-genome duplication events. Moreover, cis-acting elements analysis showed that SiERFs are mostly involved in environmental responses. Gene expression profiles analysis revealed that 59 and 26 SiERFs are highly stimulated under drought and waterlogging stress, respectively. In addition, qRT-PCR analyses indicated that most of SiERFs are also significantly up-regulated under osmotic, submerge, ABA, and ACC stresses. Among them, SiERF23 and SiERF54 were the most induced by both the abiotic stresses, suggesting their potential for targeted improvement of sesame response to multiple abiotic stresses.

CONCLUSION

This study provides a comprehensive understanding of the structure, classification, evolution, and abiotic stresses response of ERF genes in sesame. Moreover, it offers valuable gene resources for functional characterization towards enhancing sesame tolerance to multiple abiotic stresses.

Global Survey, Expressions and Association Analysis of CBLL Genes in Peanut

Cystathionine γ-synthase (CGS), methionine γ-lyase (MGL), cystathionine β-lyase (CBL) and cystathionine γ-lyase (CGL) share the Cys_Met_Meta_PP domain and play important roles in plant stress response and development. In this study, we defined the genes containing the Cys_Met_Meta_PP domain (PF01053.20) as CBL-like genes (CBLL). Twenty-nine CBLL genes were identified in the peanut genome, including 12 from cultivated peanut and 17 from wild species. These genes were distributed unevenly at the ends of different chromosomes. Evolution, gene structure, and motif analysis revealed that CBLL proteins were composed of five different evolutionary branches. Chromosome distribution pattern and synteny analysis strongly indicated that whole-genome duplication (allopolyploidization) contributed to the expansion of CBLL genes. Comparative genomics analysis showed that there were three common collinear CBLL gene pairs among peanut, Arabidopsis, grape, and soybean, but no collinear CBLL gene pairs between peanut and rice. The prediction results of cis-acting elements showed that AhCBLLs, AdCBLLs, and AiCBLLs contained different proportions of plant growth, abiotic stress, plant hormones, and light response elements. Spatial expression profiles revealed that almost all AhCBLLs had significantly higher expression in pods and seeds. All AhCBLLs could respond to heat stress, and some of them could be rapidly induced by cold, salt, submergence, heat and drought stress. Furthermore, one polymorphic site in AiCBLL7 was identified by association analysis which was closely associated with pod length (PL), pod width (PW), hundred pod weight (HPW) and hundred seed weight (HSW). The results of this study provide a foundation for further research on the function of the CBLL gene family in peanut.

Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.)

APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogenetic relationship, intron-exon structure, and chromosomal location of AhAP2/ERF were further characterized. All of these AhAP2/ERF genes were distributed unevenly across the 20 chromosomes, and 14 tandem and 85 segmental duplicated gene pairs were identified which originated from ancient duplication events. Gene evolution analysis showed that A. hypogaea cv. Tifrunner were separated 64.07 and 66.44 Mya from Medicago truncatula L. and Glycine max L., respectively. Promoter analysis discovered many cis-acting elements related to light, hormones, tissues, and stress responsiveness process. The protein interaction network predicted the exitance of functional interaction among families or subgroups. Expression profiles showed that genes from AP2, ERF, and dehydration-responsive-element-binding subfamilies were significantly upregulated under drought stress conditions. Our study laid a foundation and provided a panel of candidate AP2/ERF TFs for further functional validation to uplift breeding programs of drought-resistant peanut cultivars.

Plant Transcription Factors Involved in Drought and Associated Stresses

Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.

Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars

Jujube (Ziziphus jujuba Mill.) is an economically and agriculturally significant fruit crop and is widely cultivated throughout the world. Heat stress has recently become a primary abiotic stressor limiting the productivity and growth of jujube, as well as other crops. There are few studies, however, that have performed transcriptome profiling of jujube when it is exposed to heat stress. In this study, we observed the physiochemical changes and analyzed gene expression profiles in resistant jujube cultivar ‘HR’ and sensitive cultivar ‘HS’ subjected to heat stress for 0, 1, 3, and 5d. Twenty-four cDNA libraries from ‘HR’ and ‘HS’ leaves were built with a transcriptome assay. A total of 6887 and 5077 differentially expressed genes were identified in ‘HR’ and ‘HS’ after 1d, 3d, and 5d of heat stress compared with the control treatment, GO and KEGG enrichment analysis revealed that some of the genes were highly enriched in oxidation-reduction process, response to stress, response to water deprivation, response to heat, carbon metabolism, protein processing in endoplasmic reticulum, and plant hormone signal transduction and may play vital roles in the heat stress response in jujube plants. Differentially expressed genes were identified in the two cultivars, including heat shock proteins, transcriptional factors, and ubiquitin-protein ligase genes. And the expression pattern of nine genes was also validated by qRT-PCR. These results will provide useful information for elucidating the molecular mechanism underlying heat stress in different jujube cultivars.

An AP2/ERF Gene, HuERF1, from Pitaya (Hylocereus undatus) Positively Regulates Salt Tolerance

Pitaya (Hylocereus undatus) is a high salt-tolerant fruit, and ethylene response factors (ERFs) play important roles in transcription-regulating abiotic tolerance. To clarify the function of HuERF1 in the salt tolerance of pitaya, HuERF1 was heterogeneously expressed in Arabidopsis. HuERF1 had nuclear localization when HuERF1::GFP was expressed in Arabidopsis protoplasts and had transactivation activity when HuERF1 was expressed in yeast. The expression of HuERF1 in pitaya seedlings was significantly induced after exposure to ethylene and high salinity. Overexpression of HuERF1 in Arabidopsis conferred enhanced tolerance to salt stress, reduced the accumulation of superoxide (O₂·¯) and hydrogen peroxide (H₂O₂), and improved antioxidant enzyme activities. These results indicate that HuERF1 is involved in ethylene-mediated salt stress tolerance, which may contribute to the salt tolerance of pitaya.

Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut (Arachis hypogaea L.) Cultivars

Background: Exposure of seeds to high salinity can cause reduced germination and poor seedling establishment. Improving the salt tolerance of peanut (Arachis hypogaea L.) seeds during germination is an important breeding goal of the peanut industry. Bacterial communities in the spermosphere soils may be of special importance to seed germination under salt stress, whereas extant results in oilseed crop peanut are scarce. Methods: Here, bacterial communities colonizing peanut seeds with salt stress were characterized using 16S rRNA gene sequencing. Results: Peanut spermosphere was composed of four dominant genera: Bacillus, Massilia, Pseudarthrobacter, and Sphingomonas. Comparisons of bacterial community structure revealed that the beneficial bacteria (Bacillus), which can produce specific phosphatases to sequentially mineralize organic phosphorus into inorganic phosphorus, occurred in relatively higher abundance in salt-treated spermosphere soils. Further soil enzyme activity assays showed that phosphatase activity increased in salt-treated spermosphere soils, which may be associated with the shift of Bacillus. Conclusion: This study will form the foundation for future improvement of salt tolerance of peanuts at the seed germination stage via modification of the soil microbes.

Genome-wide identification, expression, and association analysis of the monosaccharide transporter (MST) gene family in peanut (Arachis hypogaea L.)

In this study, we reported the genome-wide analysis of the whole sugar transporter gene family of a legume species, peanut (Arachis hypogaea L.), including the chromosome locations, gene structures, phylogeny, expression patterns, as well as comparative genomic analysis with Arabidopsis, rice, grape, and soybean. A total of 76 AhMST genes (AhMST1-76) were identified from the peanut genome and located unevenly in 20 chromosomes. Phylogeny analysis indicated that the AhMSTs can be divided into eight groups including two undefined peanut-specific groups. Transcriptional profiles revealed that many AhMST genes showed tissue-specific expression, the majority of the AhMST genes mainly expressed in sink organs and floral organ of peanut. Chromosome distribution pattern and synteny analysis strongly indicated that genome-wide segmental and tandem duplication contributed to the expansion of peanut MST genes. Four common orthologs (AhMST9, AhMST13, AhMST40, and AhMST43) between peanut and the other four species were identified by comparative genomic analysis, which might play important roles in maintaining the growth and development of plant. Furthermore, four polymorphic sites in AhMST11, AhMST13, and AhMST60 were significantly correlated with hundred pod weight (HPW) and hundred seed weight (HSW) by association analysis. In a word, these results will provide new insights for understanding the functions of AhMST family members to sugar transporting and the potential for yield improvement in peanut.

Influence of salt stress on the rhizosphere soil bacterial community structure and growth performance of groundnut (Arachis hypogaea L.)

Soil salinity is regarded as severe environmental stress that can change the composition of rhizosphere soil bacterial community and import a plethora of harms to crop plants. However, relatively little is known about the relationship between salt stress and root microbial communities in groundnuts. The goal of this study was to assess the effect of salt stress on groundnut growth performance and rhizosphere microbial community structure. Statistical analysis exhibited that salt stress indeed affected groundnut growth and pod yield. Further taxonomic analysis showed that the bacterial community predominantly consisted of phyla Proteobacteria, Actinobacteria, Saccharibacteria, Chloroflexi, Acidobacteria, and Cyanobacteria. Among these bacteria, numbers of Cyanobacteria and Acidobacteria mainly increased, while that of Actinobacteria and Chloroflexi decreased after salt treatment via taxonomic and qPCR analysis. Moreover, Sphingomonas and Microcoleus as the predominant genera in salt-treated rhizosphere soils might enhance salt tolerance as plant growth-promoting rhizobacteria. Metagenomic profiling showed that series of sequences related to signaling transduction, posttranslational modification, and chaperones were enriched in the salt-treated soils, which may have implications for plant survival and salt tolerance. These data will help us better understand the symbiotic relationship between the dominant microbial community and groundnuts and form the foundation for further improvement of salt tolerance of groundnuts via modification of soil microbial community.

Transcriptomic and metabolomic analyses reveal that melatonin promotes melon root development under copper stress by inhibiting jasmonic acid biosynthesis

Melatonin has been shown to alleviate the effects of abiotic stress and to regulate plant development. Copper, a common heavy metal and soil pollutant, can suppress plant growth and development. In this work, we explored the protective effects of exogenous melatonin on lateral root formation in response to copper stress using melon seeds subjected to three germination treatments: CK1 (control), CK2 (300 μmol/L CuSO₄), and MT3 (300 μmol/L melatonin + 300 μmol/L CuSO₄). Melatonin pretreatment increased the antioxidant enzyme activities and root vigor, and decreased the proline and malondialdehyde (MDA) contents in the roots of copper-stressed melon seedlings. We then used transcriptomic and metabolomic analyses to explore the mechanisms by which exogenous melatonin protects against copper stress. There were 70 significant differentially expressed genes (DEGs) (28 upregulated, 42 downregulated) and 318 significantly differentially expressed metabolites (DEMs) (168 upregulated, 150 downregulated) between the MT3 and CK2 treatments. Melatonin pretreatment altered the expression of genes related to redox and cell wall formation processes. In addition, we found that members of the AP2/ERF, BBR/BPC, GRAS, and HD-ZIP transcription factor families may have vital roles in lateral root development. Melatonin also increased the level of Glutathione (GSH), which chelates excess Cu²⁺. The combined transcriptomic and metabolomic analysis revealed DEGs and DEMs involved in jasmonic acid (JA) biosynthesis, including four lipoxygenase-related genes and two metabolites (linoleic acid and lecithin) related to melatonin's alleviation effect on copper toxicity. This research elucidated the molecular mechanisms of melatonin's protective effects in copper-stressed melon.

Comparative Transcriptomics Analysis and Functional Study Reveal Important Role of High-Temperature Stress Response Gene GmHSFA2 During Flower Bud Development of CMS-Based F1 in Soybean

High-temperature (HT) is one of the most important environmental factors that negatively impact the yield of some soybean cytoplasmic male sterility (CMS)-based hybrid (F₁) combinations. The response of soybean to HT, especially at the male organ development stage, is poorly understood. To investigate the molecular mechanisms of the response from soybean CMS-based F₁ male organ to HT, a detailed transcriptomics analysis was performed during flower bud development of soybean HT-tolerant and HT-sensitive CMS-based F₁ combinations (NF₁ and YF₁) under normal-temperature and HT conditions. Obvious HT damage was observed by subjecting YF₁ with HT, such as indehiscent anthers and decreased pollen fertility, whereas the male fertility of NF₁ was normal. In total, 8,784 differentially expressed genes (DEGs) were found to respond to HT stress, which were mainly associated with anther/pollen wall development, carbohydrate metabolism and sugar transport, and auxin signaling. The quantitative real-time PCR (qRT-PCR) analysis and substance content detection also revealed that HT caused male fertility defects in YF₁ by altering pectin metabolism, auxin, and sugar signaling pathways. Most importantly, the sugar signaling-PIF-auxin signaling pathway may underlie the instability of male fertility in YF₁ under HT. Furthermore, HT induced the expression of heat shock factor (HSF) and heat shock protein (HSP) gene families. Overexpression of GmHSFA2 in Arabidopsis can promote the expression of HT protective genes (such as HSP20) by binding to the HSE motifs in their promoters, so as to improve the HT tolerance during flowering. Our results indicated that GmHSFA2 acted as a positive regulator, conferring HT tolerance improvement in soybean CMS-based F₁. GmHSFA2 may be directly involved in the activation of male fertility protection mechanism in the soybean CMS-based F₁ under HT stress.

Osmoprotection in plants under abiotic stresses: new insights into a classical phenomenon

Plant osmoprotectants protect against abiotic stresses. Introgression of osmoprotectant genes into crop plants via genetic engineering is an important strategy in developing more productive plants. Plants employ adaptive mechanisms to survive various abiotic stresses. One mechanism, the osmoprotection system, utilizes various groups of low molecular weight compounds, collectively known as osmoprotectants, to mitigate the negative effect of abiotic stresses. Osmoprotectants may include amino acids, polyamines, quaternary ammonium compounds and sugars. These nontoxic compounds stabilize cellular structures and enzymes, act as metabolic signals, and scavenge reactive oxygen species produced under stressful conditions. The advent of recent drastic fluctuations in the global climate necessitates the development of plants better adapted to abiotic stresses. The introgression of genes related to osmoprotectant biosynthesis from one plant to another by genetic engineering is a unique strategy bypassing laborious conventional and classical breeding programs. Herein, we review recent literature related to osmoprotectants and transgenic plants engineered with specific osmoprotectant properties.

The ABA-induced soybean ERF transcription factor gene GmERF75 plays a role in enhancing osmotic stress tolerance in Arabidopsis and soybean

BACKGROUND

Ethylene-responsive factors (ERFs) play important roles in plant growth and development and the response to adverse environmental factors, including abiotic and biotic stresses.

RESULTS

In the present study, we identified 160 soybean ERF genes distributed across 20 chromosomes that could be clustered into eight groups based on phylogenetic relationships. A highly ABA-responsive ERF gene, GmERF75, belonging to Group VII was further characterized. Subcellular localization analysis showed that the GmERF75 protein is localized in the nucleus, and qRT-PCR results showed that GmERF75 is responsive to multiple abiotic stresses and exogenous hormones. GmERF75-overexpressing Arabidopsis lines showed higher chlorophyll content compared to WT and mutants under osmotic stress. Two independent Arabidopsis mutations of AtERF71, a gene homologous to GmERF75, displayed shorter hypocotyls, and overexpression of GmERF75 in these mutants could rescue the short hypocotyl phenotypes. Overexpressing GmERF75 in soybean hairy roots improved root growth under exogenous ABA and salt stress.

CONCLUSIONS

These results suggested that GmERF75 is an important plant transcription factor that plays a critical role in enhancing osmotic tolerance in both Arabidopsis and soybean.

The expanding roles of APETALA2/Ethylene Responsive Factors and their potential applications in crop improvement

Understanding the molecular basis of the gene-regulatory networks underlying agronomic traits or plant responses to abiotic/biotic stresses is very important for crop improvement. In this context, transcription factors, which either singularly or in conjugation directly control the expression of many target genes, are suitable candidates for improving agronomic traits via genetic engineering. In this regard, members of one of the largest class of plant-specific APETALA2/Ethylene Response Factor (AP2/ERF) superfamily, which is implicated in various aspects of development and plant stress adaptation responses, are considered high-value targets for crop improvement. Besides their long-known regulatory roles in mediating plant responses to abiotic stresses such as drought and submergence, the novel roles of AP2/ERFs during fruit ripening or secondary metabolites production have also recently emerged. The astounding functional plasticity of AP2/ERF members is considered to be achieved by their interplay with other regulatory networks and signalling pathways. In this review, we have integrated the recently accumulated evidence from functional genomics studies and described their newly emerged functions in plants. The key structural features of AP2/ERF proteins and the modes of their action are briefly summarized. The importance of AP2/ERFs in plant development and stress responses and a summary of the event of their successful applications in crop improvement programs are also provided. Altogether, we envisage that the synthesized information presented in this review will be useful to design effective strategies for improving agronomic traits in crop plants.

Genome-wide identification and expression analysis reveal the potential function of ethylene responsive factor gene family in response to Botrytis cinerea infection and ovule development in grapes (Vitis vinifera L.)

The prevention of Botrytis cinerea infection and the study of grape seedlessness are very important for grape industries. Finding correlated regulatory genes is an important approach towards understanding their molecular mechanisms. Ethylene responsive factor (ERF) gene family play critical roles in defence networks and the growth of plants. To date, no large-scale study of the ERF proteins associated with pathogen defence and ovule development has been performed in grape (Vitis vinifera L.). In the present study, we identified 113 ERF genes (VvERF) and named them based on their chromosome locations. The ERF genes could be divided into 11 groups based on a multiple sequence alignment and a phylogenetic comparison with homologues from Arabidopsis thaliana. Synteny analysis and Ka/Ks ratio calculation suggested that segmental and tandem duplications contributed to the expansion of the ERF gene family. The evolutionary relationships between the VvERF genes were investigated by exon-intron structure characterisation, and an analysis of the cis-acting regulatory elements in their promoters suggested potential regulation after stress or hormone treatments. Expression profiling after infection with the fungus, B. cinerea, indicated that ERF genes function in responses to pathogen attack. In addition, the expression levels of most ERF genes were much higher during ovule development in seedless grapes, suggesting a role in ovule abortion related to seedlessness. Taken together, these results indicate that VvERF proteins are involved in responses to Botrytis cinerea infection and in grape ovule development. This information may help guide strategies to improve grape production.

Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil

Background: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts. Method: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts. Results: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance. Conclusion: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.

Ethylene Response Factor (ERF) Family Proteins in Abiotic Stresses and CRISPR-Cas9 Genome Editing of ERFs for Multiple Abiotic Stress Tolerance in Crop Plants: A Review

Abiotic stresses such as extreme heat, cold, drought, and salt have brought alteration in plant growth and development, threatening crop yield and quality leading to global food insecurity. Many factors plays crucial role in regulating various plant growth and developmental processes during abiotic stresses. Ethylene response factors (ERFs) are AP2/ERF superfamily proteins belonging to the largest family of transcription factors known to participate during multiple abiotic stress tolerance such as salt, drought, heat, and cold with well-conserved DNA-binding domain. Several extensive studies were conducted on many ERF family proteins in plant species through over-expression and transgenics. However, studies on ERF family proteins with negative regulatory functions are very few. In this review article, we have summarized the mechanism and role of recently studied AP2/ERF-type transcription factors in different abiotic stress responses. We have comprehensively discussed the application of advanced ground-breaking genome engineering tool, CRISPR/Cas9, to edit specific ERFs. We have also highlighted our on-going and published R&D efforts on multiplex CRISPR/Cas9 genome editing of negative regulatory genes for multiple abiotic stress responses in plant and crop models. The overall aim of this review is to highlight the importance of CRISPR/Cas9 and ERFs in developing sustainable multiple abiotic stress tolerance in crop plants.

An AP2/ERF gene, IbRAP2-12, from sweetpotato is involved in salt and drought tolerance in transgenic Arabidopsis

The manipulation of APETALA2/ethylene responsive factor (AP2/ERF) genes in plants makes great contributions on resistance to abiotic stresses. Here, we cloned an AP2/ERF gene from the salt-tolerant sweetpotato line ND98 and named IbRAP2-12. IbRAP2-12 protein expressed in nuclear revealed by transient expression in tobacco epidermal cells, and IbRAP2-12 exhibited transcriptional activation using heterologous expression assays in yeast. IbRAP2-12 was induced by NaCl (200 mM), 20% polyethylene glycol (PEG) 6000, 100 μM abscisic acid (ABA), 100 μM ethephon and 100 μM methyl jasmonate (MeJA). IbRAP2-12-overexpressing Arabidopsis lines were more tolerant to salt and drought stresses than wild type plants. Transcriptome analysis showed that genes involved in the ABA signalling, JA signalling, proline biosynthesis and reactive oxygen species (ROS) scavenging processes were up-regulated in IbRAP2-12 overexpression lines under salt and drought stresses. In comparing with WT, the contents of ABA, JA and proline were significantly increased, while hydrogen peroxide (H₂O₂) and the rate of water loss were significantly reduced in transgenic lines under salt and drought stresses. All these results demonstrated the roles of IbRAP2-12 in enhancing salt and drought tolerance in transgenic Arabidopsis lines. Thus, this IbRAP2-12 gene can be used to increase the tolerance ability during abiotic stresses in plants.

Research Progress in Membrane Lipid Metabolism and Molecular Mechanism in Peanut Cold Tolerance

Early sowing has been extensively used in high-latitude areas to avoid drought stress during sowing; however, cold damage has become the key limiting factor of early sowing. To relieve cold stress, plants develop a series of physiological and biochemical changes and sophisticated molecular regulatory mechanisms. The biomembrane is the barrier that protects cells from injury as well as the primary place for sensing cold signals. Chilling tolerance is closely related to the composition, structure, and metabolic process of membrane lipids. This review focuses on membrane lipid metabolism and its molecular mechanism, as well as lipid signal transduction in peanut (Arachis hypogaea L.) under cold stress to build a foundation for explicating lipid metabolism regulation patterns and physiological and molecular response mechanisms during cold stress and to promote the genetic improvement of peanut cold tolerance.

Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses

In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.

A Novel Soybean ERF Transcription Factor, GmERF113, Increases Resistance to Phytophthora sojae Infection in Soybean

Phytophthora root and stem rot of soybean caused by the oomycete Phytophthora sojae, is a destructive disease worldwide. Ethylene response factors (ERFs) play important roles in regulating plant biotic and abiotic stress tolerance. In this study, a new ERF gene, GmERF113, was isolated from the highly resistant soybean 'Suinong 10.' Sequence analysis suggested that the protein encoded by GmERF113 contained a conserved AP2/ERF domain of 58 amino acid and belonged to the B-4 subgroup of the ERF subfamily. Expression of GmERF113 was significantly induced by P. sojae, ethylene, and methyl jasmonate. GmERF113 protein localized to the nucleus when transiently expressed in Arabidopsis protoplasts, could bind to the GCC-box, and acted as a transcription activator. In addition, a region of the full-length GmERF113, GmERF113-II, interacted with a basic helix-loop-helix transcription factor (GmbHLH) in yeast cells. Full-length GmERF113 also interacted with GmbHLH in planta. GmERF113-overexpressing transgenic plants in susceptible cultivar 'Dongnong 50' soybean exhibited increased resistance to P. sojae and positively regulated the expression of the pathogenesis-related genes, PR1 and PR10-1. These results indicate that GmERF113 may play a crucial role in the defense of soybean against P. sojae infection.

Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea

APETALA2/ethylene response factor (AP2/ERF) and heat-shock protein 90 (HSP90) are two significant classes of transcription factor and molecular chaperone proteins which are known to be implicated under abiotic and biotic stresses. Comprehensive survey identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 131 in Medicago, 179 in common bean and 140 in Lotus, whereas the number of HSP90 genes ranged from 5 to 7 in five legumes. Sequence alignment and phylogenetic analyses distinguished AP2, ERF, DREB, RAV and soloist proteins, while HSP90 proteins segregated on the basis of their cellular localization. Deeper insights into the gene structure allowed ERF proteins to be classified into AP2s based on DNA-binding domains, intron arrangements and phylogenetic grouping. RNA-seq and quantitative real-time PCR (qRT-PCR) analyses in heat-stressed chickpea as well as Fusarium wilt (FW)- and sterility mosaic disease (SMD)-stressed pigeonpea provided insights into the modus operandi of AP2/ERF and HSP90 genes. This study identified potential candidate genes in response to heat stress in chickpea while for FW and SMD stresses in pigeonpea. For instance, two DREB genes (Ca_02170 and Ca_16631) and three HSP90 genes (Ca_23016, Ca_09743 and Ca_25602) in chickpea can be targeted as potential candidate genes. Similarly, in pigeonpea, a HSP90 gene, C.cajan_27949, was highly responsive to SMD in the resistant genotype ICPL 20096, can be recommended for further functional validation. Also, two DREB genes, C.cajan_41905 and C.cajan_41951, were identified as leads for further investigation in response to FW stress in pigeonpea.

Transcriptome-based discovery of AP2/ERF transcription factors related to temperature stress in tea plant (Camellia sinensis)

Tea plant (Camellia sinensis) is an important natural resource for the global supply of non-alcoholic beverage production. The extension of tea plant cultivation is challenged by biotic and abiotic stresses. Transcription factors (TFs) of the APETALA 2 (AP2)/ethylene-responsive factor (ERF) family are involved in growth and anti-stresses through multifaceted transcriptional regulation in plants. This study comprehensively analyzed AP2/ERF family TFs from C. sinensis on the basis of the transcriptome sequencing data of four tea plant cultivars, namely, 'Yunnanshilixiang', 'Chawansanhao', 'Ruchengmaoyecha', and 'Anjibaicha'. A total of 89 putative AP2/ERF transcription factors with full-length AP2 domain were identified from C. sinensis and classified into five subfamilies, namely, AP2, dehydration-responsive-element-binding (DREB), ERF, related to ABI3/VP (RAV), and Soloist. All identified CsAP2/ERF genes presented relatively stable expression levels in the four tea plant cultivars. Many groups also showed cultivar specificity. Five CsAP2/ERF genes from each AP2/ERF subfamily (DREB, ERF, AP2, and RAV) were related to temperature stresses; these results indicated that AP2/ERF TFs may play important roles in abnormal temperature stress response in C. sinensis.