Genome-wide analysis of AP2/ERF transcription factors in carrot (Daucus carota L.) reveals evolution and expression profiles under abiotic stress

A novel AP2/ERF transcription factor, NtERF10, positively regulates plant height in tobacco

Ethylene response factors have been shown to be involved in the effects of plant developmental processes and to regulate stress tolerance. The aim of this study was to recognize the regulatory mechanisms of ethylene response factors on tobacco plant height. In this study, a gene-edited mutant (ERF10-KO) and wild type (WT) were utilized as experimental materials. Transcriptome and metabolome analyses were used to investigate the regulatory mechanism of NtERF10 gene editing on plant height in tobacco. Here, through the analysis of differentially expressed genes (DEGs), 2051 genes were upregulated and 1965 genes were downregulated. We characterized the different ERF10-KO and WT plant heights and identified key genes for photosynthesis, the plant hormone signal transduction pathway and the terpene biosynthesis pathway. NtERF10 was found to affect the growth and development of tobacco by regulating the expression levels of the PSAA, PSBA, GLY17 and GGP3 genes. Amino acid metabolism was analyzed by combining analyses of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). In addition, we found that members of the bHLH, NAC, MYB, and WRKY transcription factor families have vital roles in regulating plant height. This study not only provides important insights into the positive regulation of the ethylene response factor NtERF10 on plant height during plant growth and development but also provides new research ideas for tobacco molecular breeding.

Identification of the ERF gene family of Mangifera indica and the defense response of MiERF4 to Xanthomonas campestris pv. mangiferaeindicae

An important regulatory role for ethylene-responsive transcription factors (ERFs) is in plant growth and development, stress response, and hormone signaling. However, AP2/ERF family genes in mango have not been systematically studied. In this study, a total of 113 AP2/ERF family genes were identified from the mango genome and phylogenetically classified into five subfamilies: AP2 (28 genes), DREB (42 genes), ERF (33 genes), RAV (6 genes), and Soloist (4 genes). Of these, the ERF family, in conjunction with Arabidopsis and rice, forms a phylogenetic tree divided into seven groups, five of which have MiERF members. Analysis of gene structure and cis-elements showed that each MiERF gene contains only one AP2 structural domain, and that MiERF genes contain a large number of cis-elements associated with hormone signaling and stress response. Collinearity tests revealed a high degree of homology between MiERFs and CsERFs. Tissue-specific and stress-responsive expression profiling revealed that MiERF genes are primarily involved in the regulation of reproductive growth and are differentially and positively expressed in response to external hormones and pathogenic bacteria. Physiological results from a gain-of-function analysis of MiERF4 transiently overexpressed in tobacco and mango showed that transient expression of MiERF4 resulted in decreased colony count and callose deposition, as well as varying degrees of response to hormonal signals such as ETH, JA, and SA. Thus, MiERF4 may be involved in the JA/ETH signaling pathway to enhance plant defense against pathogenic bacteria. This study provides a basis for further research on the function and regulation of MiERF genes and lays a foundation for the selection of disease-resistant genes in mango.

Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.)

The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

AP2XII-1 and AP2XI-2 Suppress Schizogony Gene Expression in Toxoplasma gondii

Toxoplasma gondii is an intracellular parasite that is important in medicine and veterinary science and undergoes distinct developmental transitions in its intermediate and definitive hosts. The switch between stages of T. gondii is meticulously regulated by a variety of factors. Previous studies have explored the role of the microrchidia (MORC) protein complex as a transcriptional suppressor of sexual commitment. By utilizing immunoprecipitation and mass spectrometry, constituents of this protein complex have been identified, including MORC, Histone Deacetylase 3 (HDAC3), and several ApiAP2 transcription factors. Conditional knockout of MORC or inhibition of HDAC3 results in upregulation of a set of genes associated with schizogony and sexual stages in T. gondii tachyzoites. Here, our focus extends to two primary ApiAP2s (AP2XII-1 and AP2XI-2), demonstrating their significant impact on the fitness of asexual tachyzoites and their target genes. Notably, the targeted disruption of AP2XII-1 and AP2XI-2 resulted in a profound alteration in merozoite-specific genes targeted by the MORC-HDAC3 complex. Additionally, considerable overlap was observed in downstream gene profiles between AP2XII-1 and AP2XI-2, with AP2XII-1 specifically binding to a subset of ApiAP2 transcription factors, including AP2XI-2. These findings reveal an intricate cascade of ApiAP2 regulatory networks involved in T. gondii schizogony development, orchestrated by AP2XII-1 and AP2XI-2. This study provides valuable insights into the transcriptional regulation of T. gondii growth and development, shedding light on the intricate life cycle of this parasitic pathogen.

Alteration in the callogenesis, tropane alkaloid formation, and gene expression in Hyoscyamus niger under clinorotation

This study aimed to investigate the effects of clinorotation induced by 2-D clinostat on the growth, tropane alkaloid production, gene expression, antioxidant capacity, and cellular defense responses in the callus tissue of Hyoscyamus niger. Callus induction was conducted by putting hypocotyl explants in the MS culture medium supplemented with 1 mgL-1 2,4-D and 1 mgL-1 BAP growth regulators. The sub-cultured calli were placed on a clinostat for 0, 3, 7, and 10 days (2.24 × 10-5 g on the edge of the callus ring). Clinorotation significantly increased callus fresh weight, dry weight, protein, carbohydrate, and proline contents compared to the control, and their maximum contents were obtained after 7 and 10 days. H2O2 level enhanced under clinorotation with a 76.3% rise after 10 days compared to control and positively affected the atropine (77.1%) and scopolamine (69.2%) productions. Hyoscyamine 6-beta hydroxylase and putrescine N-methyltransferase gene expression involved in the tropane alkaloid biosynthesis were upregulated markedly with 14.2 and 17.1-folds increase after 10 days of clinorotation, respectively. The expressions of jasmonic acid, mitogen-activated protein kinase, and ethylene-responsive element-binding transcription factor were upregulated, and the activity of peroxidase and catalase showed a 72.7 and 80% rise after 10 days. These findings suggest that microgravity can enhance callogenesis by stimulating the ROS level, which can impact the antioxidant enzymes, tropane alkaloid formation, and gene expression.

Differential Response of MYB Transcription Factor Gene Transcripts to Circadian Rhythm in Tea Plants (Camellia sinensis)

The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible 'clock' in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor is involved in plant growth and development. MYB is also inextricably correlated with the circadian rhythm. In this study, the transcriptome data of the tea plant 'Baiyeyihao' were measured at a photoperiod interval of 4 h (24 h). A total of 25,306 unigenes were obtained, including 14,615 unigenes that were annotated across 20 functional categories within the GO classification. Additionally, 10,443 single-gene clusters were annotated to 11 sublevels of metabolic pathways using KEGG. Based on the results of gene annotation and differential gene transcript analysis, 22 genes encoding MYB transcription factors were identified. The G10 group in the phylogenetic tree had 13 members, of which 5 were related to the circadian rhythm, accounting for 39%. The G1, G2, G8, G9, G15, G16, G18, G19, G20, G21 and G23 groups had no members associated with the circadian rhythm. Among the 22 differentially expressed MYB transcription factors, 3 members of LHY, RVE1 and RVE8 were core circadian rhythm genes belonging to the G10, G12 and G10 groups, respectively. Real-time fluorescence quantitative PCR was used to detect and validate the expression of the gene transcripts encoding MYB transcription factors associated with the circadian rhythm.

Heat, drought, and combined stress effect on transgenic potato plants overexpressing the StERF94 transcription factor

Despite their economic importance worldwide, potato plants are sensitive to various abiotic constraints, such as drought and high temperatures, which cause significant losses in yields and tuber quality. Moreover, because of the climate change phenomenon, plants are frequently subjected to combined stresses, mainly high temperatures and drought. In this context, breeding for tolerant varieties should consider not only plant response to drought or high temperature but also to combined stresses. In the current study, we studied transgenic potato plants overexpressing an ethylene response transcription factor (TF; StERF94) involved in abiotic stress response signaling pathways. Our previous results showed that these transgenic plants display tolerance to salt stress more than wildtype (WT). In this work, we aimed to investigate the effects of drought, heat, and combined stresses on transgenic potato plants overexpressing StERF94 TF under in vitro culture conditions. The obtained results revealed that StERF94 overexpression improved the tolerance of the transgenic plants to drought, heat, and combined stresses through better control of the leaf water and chlorophyll contents, activation of antioxidant enzymes, and an accumulation of proline, especially in the leaves. Indeed, the expression level of antioxidant enzyme-encoding genes (CuZnSOD, FeSOD, CAT1, and CAT2) was significantly induced by the different stress conditions in the transgenic potato plants compared with the WT plants. This study further confirms that StERF94 TF may be implicated in regulating the expression of target genes encoding antioxidant enzymes.

Relationships between some transcription factors and concordantly expressed drought stress-related genes in bread wheat

The challenge of climate change makes it mandatory to improve tolerance to drought stress in bread wheat (Triticum aestivum) via biotechnological approaches. Drought stress experiment was conducted followed by RNA-Seq analysis for leaves of two wheat cultivars namely Giza 168 and Gemmiza 10 with contrasting genotypes. Expression patterns of the regulated stress-related genes and concordantly expressed TFs were detected, then, validated via qPCR for two loss-of-function mutants in Arabidopsis background harboring mutated genes analogue to those in wheat. Drought-stress related genes were searched for concordantly expressed TFs and a total of eight TFs were shown to coexpress with 14 stress-related genes. Among these genes, one TF belongs to the zinc finger protein CONSTANS family and proved via qPCR to drive expression of a gene encoding a speculative TF namely zinc transporter 3-like and two other stress related genes encoding tryptophan synthase alpha chain and asparagine synthetase. Known functions of the two TFs under drought stress complement those of the two concordantly expressed stress-related genes, thus, it is likely that they are related. This study highlights the possibility to utilize metabolic engineering approaches to decipher and incorporate existing regulatory frameworks under drought stress in future breeding programs of bread wheat.

The Role of Plant Transcription Factors in the Fight against Plant Viruses

Plants are vulnerable to the challenges of unstable environments and pathogen infections due to their immobility. Among various stress conditions, viral infection is a major threat that causes significant crop loss. In response to viral infection, plants undergo complex molecular and physiological changes, which trigger defense and morphogenic pathways. Transcription factors (TFs), and their interactions with cofactors and cis-regulatory genomic elements, are essential for plant defense mechanisms. The transcriptional regulation by TFs is crucial in establishing plant defense and associated activities during viral infections. Therefore, identifying and characterizing the critical genes involved in the responses of plants against virus stress is essential for the development of transgenic plants that exhibit enhanced tolerance or resistance. This article reviews the current understanding of the transcriptional control of plant defenses, with a special focus on NAC, MYB, WRKY, bZIP, and AP2/ERF TFs. The review provides an update on the latest advances in understanding how plant TFs regulate defense genes expression during viral infection.

Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs

Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.

Genome-Wide Identification of the ERF Transcription Factor Family for Structure Analysis, Expression Pattern, and Response to Drought Stress in Populus alba × Populus glandulosa

The Ethylene Responsive Factor (ERF) transcription factor family is important for regulating plant growth and stress responses. Although the expression patterns of ERF family members have been reported in many plant species, their role in Populus alba × Populus glandulosa, an important model plant for forest research, remains unclear. In this study, we identified 209 PagERF transcription factors by analyzing the P. alba × P. glandulosa genome. We analyzed their amino acid sequences, molecular weight, theoretical pI (Isoelectric point), instability index, aliphatic index, grand average of hydropathicity, and subcellular localization. Most PagERFs were predicted to localize in the nucleus, with only a few PagERFs localized in the cytoplasm and nucleus. Phylogenetic analysis divided the PagERF proteins into ten groups, Class I to X, with those belonging to the same group containing similar motifs. Cis-acting elements associated with plant hormones, abiotic stress responses, and MYB binding sites were analyzed in the promoters of PagERF genes. We used transcriptome data to analyze the expression patterns of PagERF genes in different tissues of P. alba × P. glandulosa, including axillary buds, young leaves, functional leaves, cambium, xylem, and roots, and the results indicated that PagERF genes are expressed in all tissues of P. alba × P. glandulosa, especially in roots. Quantitative verification results were consistent with transcriptome data. When P. alba × P. glandulosa seedlings were treated with 6% polyethylene glycol 6000 (PEG6000), the results of RT-qRCR showed that nine PagERF genes responded to drought stress in various tissues. This study provides a new perspective on the roles of PagERF family members in regulating plant growth and development, and responses to stress in P. alba × P. glandulosa. Our study provides a theoretical basis for ERF family research in the future.

Genome-Wide Identification of ERF Transcription Factor Family and Functional Analysis of the Drought Stress-Responsive Genes in Melilotus albus

As an important forage legume with high values in feed and medicine, Melilotus albus has been widely cultivated. The AP2/ERF transcription factor has been shown to play an important regulatory role in plant drought resistance, but it has not been reported in the legume forage crop M. albus. To digger the genes of M. albus in response to drought stress, we identified and analyzed the ERF gene family of M. albus at the genome-wide level. A total of 100 MaERF genes containing a single AP2 domain sequence were identified in this study, named MaERF001 to MaERF100, and bioinformatics analysis was performed. Collinearity analysis indicated that segmental duplication may play a key role in the expansion of the M. albus ERF gene family. Cis-acting element predictions suggest that MaERF genes are involved in various hormonal responses and abiotic stresses. The expression patterns indicated that MaERFs responded to drought stress to varying degrees. Furthermore, four up-regulated ERFs (MaERF008, MaERF037, MaERF054 and MaERF058) under drought stress were overexpressed in yeast and indicated their biological functions to confer the tolerance to drought. This work will advance the understanding of the molecular mechanisms underlying the drought response in M. albus. Further study of the promising potential candidate genes identified in this study will provide a valuable resource as the next step in functional genomics studies and improve the possibility of improving drought tolerance in M. albus by transgenic approaches.

The transcription factors VaERF16 and VaMYB306 interact to enhance resistance of grapevine to Botrytis cinerea infection

Botrytis cinerea is a fungus that infects cultivated grape (Vitis vinifera); the identification and characterization of resistance mechanisms in the host is of great importance for the grape industry. Here, we report that a transcription factor in the ethylene-responsive factor (ERF) family (VaERF16) from Chinese wild grape (Vitis amurensis 'Shuang You') is expressed during B. cinerea infection and in response to treatments with the hormones ethylene and methyl jasmonate. Heterologous overexpression of VaERF16 in Arabidopsis thaliana substantially enhanced resistance to B. cinerea and the bacterium Pseudomonas syringae DC3000 via the salicylic acid and jasmonate/ethylene signalling pathways. Yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays indicated that VaERF16 interacts with the MYB family transcription factor VaMYB306. Overexpression of VaERF16 or VaMYB306 in grape leaves increased resistance to B. cinerea and caused an up-regulation of the defence-related gene PDF1.2, which encodes a defensin-like protein. Conversely, silencing of either gene resulted in increased susceptibility to B. cinerea. Yeast one-hybrid and dual-luciferase assays indicated that VaERF16 increased the transcript levels of VaPDF1.2 by binding directly to the GCC box in its promoter. Notably, VaMYB306 alone did not bind to the VaPDF1.2 promoter, but the VaERF16-VaMYB306 transcriptional complex resulted in higher transcript levels of VaPDF1.2, suggesting that the proteins function through their mutual interaction. Elucidation of this regulatory module may be of value in enhancing resistance of grapevine to B. cinerea infection.

Genomic Regions Associated With Salinity Stress Tolerance in Tropical Maize (Zea Mays L.)

Being a widely cultivated crop globally under diverse climatic conditions and soil types, maize is often exposed to an array of biotic and abiotic stresses. Soil salinity is one of the challenges for maize cultivation in many parts of lowland tropics that significantly affects crop growth and reduces economic yields. Breeding strategies integrated with molecular approach might accelerate the process of identifying and developing salinity-tolerant maize cultivars. In this study, an association mapping panel consisting of 305 diverse maize inbred lines was phenotyped in a managed salinity stress phenotyping facility at International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates (UAE). Wide genotypic variability was observed in the panel under salinity stress for key phenotypic traits viz., grain yield, days to anthesis, anthesis-silking interval, plant height, cob length, cob girth, and kernel number. The panel was genotyped following the genome-based sequencing approach to generate 955,690 SNPs. Total SNPs were filtered to 213,043 at a call rate of 0.85 and minor allele frequency of 0.05 for association analysis. A total of 259 highly significant (P ≤ 1 × 10^-5) marker-trait associations (MTAs) were identified for seven phenotypic traits. The phenotypic variance for MTAs ranged between 5.2 and 9%. A total of 64 associations were found in 19 unique putative gene expression regions. Among them, 12 associations were found in gene models with stress-related biological functions.

Genome-Wide Identification, Characterization, and Expression Profiling of AP2/ERF Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (Carya illinoinensis)

The ethylene-responsive element (AP2/ERF) is one of the keys and conserved transcription factors (TFs) in plants that play a vital role in regulating plant growth, development, and stress response. A total of 202 AP2/ERF genes were identified from the pecan genome and renamed according to the chromosomal distribution of the CiAP2/ERF genes. They were divided into four subfamilies according to the domain and phylogenetic analysis, including 26 AP2, 168 ERF, six RAV, and two Soloist gene family members. These genes were distributed randomly across the 16 chromosomes, and we found 19 tandem and 146 segmental duplications which arose from ancient duplication events. The gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements, which were related to light responsiveness, stress, and defense responses, were identified in the promoter regions of AP2/ERFs. The expression profiling of 202 CiAP2/ERF genes was assessed by using RNA-Seq data and qRT-PCR during development (pistillate flowering development, graft union development, and kernel development) and under abiotic stresses (waterlogging, drought). Moreover, the results suggested that the ERF-VII members may play a critical role in waterlogging stress. These findings provided new insights into AP2/ERF gene evolution and divergence in pecan and can be considered a valuable resource for further functional validation, as well as for utilization in a stress-resistance-variety development program.

Identification of StAP2/ERF genes of potato (Solanum tuberosum) and their multiple functions in detoxification and accumulation of cadmium in yest: Implication for Genetic-based phytoremediation

The discovery of genes responsible for the tolerance to heavy metals is critical for genome-based phytotechnologies. In this study, we exposed potato (Solanum tuberosum L.) to Cd/Pb/Zn/Ni/Cu as an approach to explore the potential genes associated with stress tolerance. Using genome-wide analysis, we identified 181 potential StAP2/ERF genes that were classified into three subgroups. These StAP2/ERF genes were significantly related to heavy metal stress and are more specifically related to Cd tolerance in yeast. Yeast complementation tests showed that the StAP2/ERF129/139 genes (Subgroup 1) decreased Cd accumulation (Cd reduction-type), whilst the StAP2/ERF044/180 genes (Subgroup 2) promoted Cd accumulation in yeast which showed inhibited growth (Cd accumulation-type). The StAP2/ERF075/077/126 genes (Subgroup 3) promoted Cd accumulation and yeast growth (Cd detoxification-type). We used phylogenetic analysis to classify the 181 genes into three Cd tolerant types defined above in which the numbers of Cd reduction, accumulation, and detoxification type genes were 81, 65 and 35 respectively. Also, we performed tandem duplication, phylogenetic, and conserved motifs analysis to characterization the StAP2/ERF genes and results supported their functions in Cd tolerance. Our study showed that StAP2/ERFs is indispensable in Cd uptake and tolerance, and may be useful towards designing gene-modified plants with improved Cd tolerances.

CaAIL1 Acts Positively in Pepper Immunity against Ralstonia solanacearum by Repressing Negative Regulators

APETALA2 (AP2) subfamily transcription factors participate in plant growth and development, but their roles in plant immunity remain unclear. Here, we discovered that the AP2 transcription factor CaAIL1 functions in immunity against Ralstonia solanacearum infection (RSI) in pepper (Capsicum annuum). CaAIL1 expression was upregulated by RSI, and loss- and gain-of-function assays using virus-induced gene silencing and transient overexpression, respectively, revealed that CaAIL1 plays a positive role in immunity to RSI in pepper. Chromatin immunoprecipitation sequencing (ChIP-seq) uncovered a subset of transcription-factor-encoding genes, including CaRAP2-7, CaGATA17, CaGtf3a and CaTCF25, that were directly targeted by CaAIL1 via their cis-elements, such as GT or AGGCA motifs. ChIP-qPCR and electrophoretic mobility shift assays confirmed these findings. These genes, encoding transcription factors with negative roles in immunity, were repressed by CaAIL1 during pepper response to RSI, whereas genes encoding positive immune regulators such as CaEAS were derepressed by CaAIL1. Importantly, we showed that the atypical EAR motif (LXXLXXLXX) in CaAIL1 is indispensable for its function in immunity. These findings indicate that CaAIL1 enhances the immunity of pepper against RSI by repressing a subset of negative immune regulators during the RSI response through its binding to several cis-elements in their promoters.

Transcriptome-based identification and expression profiling of AP2/ERF members in Caragana intermedia and functional analysis of CiDREB3

BACKGROUND

The AP2/ERF transcription factor family plays important roles in regulation of plant growth and development as well as the response of plants to stress. However, there are currently few studies focusing on the function of the AP2/ERF-type transcription factors in Caragana intermedia Kuang et H. C. Fu. Here, the expression pattern of AP2/ERF transcription factors family in different tissues and under four stress treatments were evaluated, and the function of CiDREB3 was examined.

METHODS AND RESULTS

In this study, the genes encoding the AP2/ERF family of transcription factors were screened from the C. intermedia drought transcriptome database and subjected to bioinformatic analysis using the online tool and software. The expression pattern of the members of AP2/ERF transcription factors in C. intermedia were detected via quantitative real-time PCR (qRT-PCR). The function of CiDREB3 on growth, development and drought tolerance was evaluated by transgenic Arabidopsis. As a result, 22 sequences with complete ORFs were obtained and all sequences were divided into 13 sub-groups. Most of the AP2/ERF transcription factors exhibited tissue-specific expression and were induced by cold, heat, NaCl and mannitol treatments. Furthermore, heterologous expression of CiDREB3 altered the morphology of the transgenic Arabidopsis thaliana L. Heynh and improved its drought tolerance during seedlings development.

CONCLUSIONS

Taken together, the results of the present study helped to better understand the function of the AP2/ERF family transcription factors in response to multiple abiotic stresses and uncovered the role of CiDREB3 in affecting the morphology and abiotic stress tolerance of Arabidopsis.

Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

Background

In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato.

Results

Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results.

Conclusions

This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08043-w.

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.

Transcriptional Factor-Mediated Regulation of Active Component Biosynthesis in Medicinal Plants

Plants produce thousands of chemically diverse secondary metabolites, many of which have valuable pharmaceutical properties. There is much interest in the synthesis of these pharmaceuticallyvaluable compounds, including the key enzymes and the transcription factors involved. The function and regulatory mechanism of transcription factors in biotic and abiotic stresses have been studied in depth. However, their regulatory roles in the biosynthesis of bioactive compounds, especially in medicinal plants, have only begun. Here, we review what is currently known about how transcription factors contribute to the synthesis of bioactive compounds (alkaloids, terpenoids, flavonoids, and phenolic acids) in medicinal plants. Recent progress has been made in the cloning and characterization of transcription factors in medicinal plants on the genome scale. So far, several large transcription factors have been identified in MYB, WRKY, bHLH, ZIP, AP2/ERF transcription factors. These transcription factors have been predicted to regulate bioactive compound production. These transcription factors positively or negatively regulate the expression of multiple genes encoding key enzymes, and thereby control the metabolic flow through the biosynthetic pathway. Although the research addressing this niche topic is in its infancy, significant progress has been made, and advances in high-throughput sequencing technology are expected to accelerate the discovery of key regulatory transcription factors in medicinal plants. This review is likely to be useful for those interested in the synthesis of pharmaceutically- valuable plant compounds, especially those aiming to breed or engineer plants that produce greater yields of these compounds.

Overexpression of the Apple (Malus × domestica) MdERF100 in Arabidopsis Increases Resistance to Powdery Mildew

APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play important roles in plant development and stress response. Although AP2/ERF genes have been extensively investigated in model plants such as Arabidopsis thaliana, little is known about their role in biotic stress response in perennial fruit tree crops such as apple (Malus × domestica). Here, we investigated the role of MdERF100 in powdery mildew resistance in apple. MdERF100 localized to the nucleus but showed no transcriptional activation activity. The heterologous expression of MdERF100 in Arabidopsis not only enhanced powdery mildew resistance but also increased reactive oxygen species (ROS) accumulation and cell death. Furthermore, MdERF100-overexpressing Arabidopsis plants exhibited differential expressions of genes involved in jasmonic acid (JA) and salicylic acid (SA) signaling when infected with the powdery mildew pathogen. Additionally, yeast two-hybrid and bimolecular fluorescence complementation assays confirmed that MdERF100 physically interacts with the basic helix-loop-helix (bHLH) protein MdbHLH92. These results suggest that MdERF100 mediates powdery mildew resistance by regulating the JA and SA signaling pathways, and MdbHLH92 is involved in plant defense against powdery mildew. Overall, this study enhances our understanding of the role of MdERF genes in disease resistance, and provides novel insights into the molecular mechanisms of powdery mildew resistance in apple.

Comprehensive identification and characterization of simple sequence repeats based on the whole-genome sequences of 14 forest and fruit trees

Simple sequence repeats (SSRs) are popular and important molecular markers that exist widely in plants. Here, we conducted a comprehensive identification and comparative analysis of SSRs in 14 tree species. A total of 16, 298 SSRs were identified from 429, 449 genes, and primers were successfully designed for 99.44% of the identified SSRs. Our analysis indicated that tri-nucleotide SSRs were the most abundant, with an average of ~834 per species. Functional enrichment analysis by combining SSR-containing genes in all species, revealed 50 significantly enriched terms, with most belonging to transcription factor families associated with plant development and abiotic stresses such as Myeloblastosis_DNA-bind_4 (Myb_DNA-bind_4), APETALA2 (AP2), and Fantastic Four meristem regulator (FAF). Further functional enrichment analysis showed that 48 terms related to abiotic stress regulation and floral development were significantly enriched in ten species, whereas no significantly enriched terms were found in four species. Interestingly, the largest number of enriched terms was detected in Citrus sinensis (L.) Osbeck, accounting for 54.17% of all significantly enriched functional terms. Finally, we analyzed AP2 and trihelix gene families (Myb_DNA-bind_4) due to their significant enrichment in SSR-containing genes. The results indicated that whole-genome duplication (WGD) and whole genome triplication (WGT) might have played major roles in the expansion of the AP2 gene family but only slightly affected the expansion of the trihelix gene family during evolution. In conclusion, the identification and comprehensive characterization of SSR markers will greatly facilitate future comparative genomics and functional genomics studies.

TaAP2-15, An AP2/ERF Transcription Factor, Is Positively Involved in Wheat Resistance to Puccinia striiformis f. sp. tritici

AP2 transcription factors play a crucial role in plant development and reproductive growth, as well as response to biotic and abiotic stress. However, the role of TaAP2-15, in the interaction between wheat and the stripe fungus, Puccinia striiformis f. sp. tritici (Pst), remains elusive. In this study, we isolated TaAP2-15 and characterized its function during the interaction. TaAP2-15 was localized in the nucleus of wheat and N. benthamiana. Silencing of TaAP2-15 by barley stripe mosaic virus (BSMV)-mediated VIGS (virus-induced gene silencing) increased the susceptibility of wheat to Pst accompanied by enhanced growth of the pathogen (number of haustoria, haustorial mother cells and hyphal length). We confirmed by quantitative real-time PCR that the transcript levels of pathogenesis-related genes (TaPR1 and TaPR2) were down-regulated, while reactive oxygen species (ROS)-scavenging genes (TaCAT3 and TaFSOD3D) were induced accompanied by reduced accumulation of H₂O₂. Furthermore, we found that TaAP2-15 interacted with a zinc finger protein (TaRZFP34) that is a homolog of OsRZFP34 in rice. Together our findings demonstrate that TaAP2-15 is positively involved in resistance of wheat to the stripe rust fungus and provides new insights into the roles of AP2 in the host-pathogen interaction.

Digital gene expression analysis of the response to Ralstonia solanacearum between resistant and susceptible tobacco varieties

Tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum is the most serious soil-borne disease of tobacco. However, molecular mechanism information of R. solanacearum resistance is limited to tobacco, hindering better breeding of resistant tobacco. In this study, the expression profiles of the rootstalks of Yunyan87 (susceptible cultivar) and Fandi3 (resistant cultivar) at different stages after R. solanacearum infection were compared to explore molecular mechanisms of tobacco resistance against the bacterium. Findings from gene-expression profiling indicated that the number of upregulated differentially expressed genes (DEGs) at 3 and 7 days post-inoculation (dpi) increased significantly in the resistant cultivar. WRKY6 and WRKY11 family genes in WRKY transcription factors, ERF5 and ERF15 family genes in ERFs transcription factors, and genes encoding PR5 were significantly upregulated in the resistant cultivar response to the infection. For the first time, WRKY11 and ERF15 were found to be possibly involved in disease-resistance. The Kyoto Encyclopedia of Genes and Genomes analysis demonstrated glutathione metabolism and phenylpropane pathways as primary resistance pathways to R. solanacearum infection. In the resistant cultivar, DEGs encoding CYP450, TCM, CCoAOMT, 4CL, PAL, CCR, CSE, and CADH, involved in the synthesis of plant antitoxins such as flavonoids, stilbenoids, and lignins, enriched in the phenylpropane pathway were upregulated at 3 and 7 dpi. Furthermore, a pot experiment was performed to verify the role of flavonoids in controlling TBW. This study will strongly contribute to a better understanding of molecular interactions between tobacco plants and R. solanacearum.

In-depth analysis of potential PaAP2/ERF transcription factor related to fatty acid accumulation in avocado (Persea americana Mill.) and functional characterization of two PaAP2/ERF genes in transgenic tomato

Fatty acids in avocado fruit are crucial components influencing taste as well as fruit quality and nutritional value. Changes to fatty acid contents and concentrations in avocado fruit are important because of the associated effects on sensory properties. Hence, plant physiologists and molecular biologists interested in elucidating the influence of transcription factors on fatty acid accumulation in avocado fruit. In this study, APETALA2/ethylene-responsive factor (AP2/ERF) family members in avocado (Persea americana Mill.) were systematically and comprehensively analyze to identify potential PaAP2/ERF genes related to fatty acid accumulation. The results of bioinformatics analysis and the expression profiles of the AP2/ERF members suggested that 10 highly expressed PaAP2/ERF genes may encode transcription factors with functions related to the fatty acid accumulation in the avocado mesocarp. Furthermore, PaWRI1 and PaWRI2, two AP2/ERF transcription factor genes in avocado, were functionally characterized regarding their effects on fatty acid accumulation. The transcriptome and biochemical analyses of PaWRI1-2-overexpressing transgenic tomato plants revealed the up-regulated expression of 17 unigenes related to fatty acid synthesis and triacylglycerol assembly as well as increased fatty acid contents relative to the corresponding levels in the wild-type plants. In contrast, the overexpression of PaWRI2 in transgenic tomato plants up-regulated the expression of only six unigenes associated with fatty acid synthesis and triacylglycerol assembly and negligibly affected fatty acid accumulation when compared with wild-type plants. This systematic analysis provides a foundation for future studies regarding AP2/ERF functions associated with fatty acid accumulation.

De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense

Screening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.

A celery transcriptional repressor AgERF8 negatively modulates abscisic acid and salt tolerance

Ethylene response factors (ERFs) widely exist in plants and have been reported to be an important regulator of plant abiotic stress. Celery, a common economic vegetable of Apiaceae, contains lots of ERF transcription factors (TFs) with various functions. AP2/ERF TFs play positive or negative roles in plant growth and stress response. Here, AgERF8, a gene encoding EAR-type AP2/ERF TF, was identified. The AgERF8 mRNA accumulated in response to both abscisic acid (ABA) signaling and salt treatment. AgERF8 was proving to be a nucleus-located protein and could bind to GCC-box. The overexpression of AgERF8 in Arabidopsis repressed the transcription of downstream genes, AtBGL and AtBCH. Arabidopsis overexpressing AgERF8 gene showed inhibited root growth under ABA and NaCl treatments. AgERF8 transgenic lines showed low tolerance to ABA and salt stress than wild-type plants. Low increment in SOD and POD activities, increased accumulation of MDA, and significantly decreased plant fresh weights and chlorophyll levels were detected in AgERF8 hosting lines after treated with ABA and NaCl. Furthermore, the overexpression of AgERF8 also inhibited the levels of ascorbic acid and antioxidant-related genes (AtCAT1, AtSOD1, AtPOD, AtSOS1, AtAPX1, and AtP5CS1) expression in transgenic Arabidopsis. This finding indicated that AgERF8 negatively affected the resistance of transgenic Arabidopsis to ABA and salt stress through regulating downstream genes expression and relevant physiological changes. It will provide a potential sight to further understand the functions of ERF TFs in celery.

Genome-wide identification of AP2/ERF transcription factor-encoding genes in California poppy (Eschscholzia californica) and their expression profiles in response to methyl jasmonate

With respect to the biosynthesis of plant alkaloids, that of benzylisoquinoline alkaloids (BIAs) has been the most investigated at the molecular level. Previous investigations have shown that the biosynthesis of BIAs is comprehensively regulated by WRKY and bHLH transcription factors, while promoter analyses of biosynthesis enzyme-encoding genes have also implicated the involvement of members of the APETALA2/ethylene responsive factor (AP2/ERF) superfamily. To investigate the physiological roles of AP2/ERF transcription factors in BIA biosynthesis, 134 AP2/ERF genes were annotated using the draft genome sequence data of Eschscholzia californica (California poppy) together with transcriptomic data. Phylogenetic analysis revealed that these genes could be classified into 20 AP2, 5 RAV, 47 DREB, 60 ERF and 2 Soloist family members. Gene structure, conserved motif and orthologous analyses were also carried out. Gene expression profiling via RNA sequencing in response to methyl jasmonate (MeJA) indicated that approximately 20 EcAP2/ERF genes, including 10 group IX genes, were upregulated by MeJA, with an increase in the expression of the transcription factor-encoding gene EcbHLH1 and the biosynthesis enzyme-encoding genes Ec6OMT and EcCYP719A5. Further quantitative RT-PCR confirmed the MeJA responsiveness of the EcAP2/ERF genes, i.e., the increased expression of 9 group IX, 2 group X and 2 group III ERF subfamily genes. Transactivation activity of group IX EcAP2/ERFs was also confirmed by a luciferase reporter assay in conjunction with the promoters of the Ec6OMT and EcCYP719A5 genes. The physiological roles of AP2/ERF genes in BIA biosynthesis and their evolution in the regulation of alkaloid biosynthesis are discussed.

Advances in AP2/ERF super-family transcription factors in plant

In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.

NAC Family Transcription Factors in Carrot: Genomic and Transcriptomic Analysis and Responses to Abiotic Stresses

Carrot is an annual or biennial herbaceous plant of the Apiaceae family. Carrot is an important vegetable, and its fresh taproot, which contains rich nutrients, is the main edible part. In the life cycle of carrot, NAC family transcription factors (TFs) are involved in almost all physiological processes. The function of NAC TFs in carrot remains unclear. In this study, 73 NAC family TF members in carrot were identified and characterized using transcriptome and genome databases. These members were divided into 14 subfamilies. Multiple sequence alignment was performed, and the conserved domains, common motifs, phylogenetic tree, and interaction network of DcNAC proteins were predicted and analyzed. Results showed that the same group of NAC proteins of carrot had high similarity. Eight DcNAC genes were selected to detect their expression profiles under abiotic stress treatments. The expression levels of the selected DcNAC genes significantly increased under treatments with low temperature, high temperature, drought, and salt stress. Results provide potentially useful information for further analysis of the roles of DcNAC transcription factors in carrot.

Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate in Panax ginseng C.A. Meyer

The APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng C.A. Meyer), an important medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189, were identified and these PgERF genes were spliced into 397 transcripts. The 93 PgERF genes that have complete AP2 domains in open reading frame were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered into four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis thaliana. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation, and they have been especially enriched for the subcategory of nucleic acid binding transcription factor activity. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. The expressions of the PgERF genes also significantly varied, when ginseng was subjected to cold stress, as tested using six PgERF genes, PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128, randomly selected from the DREB subfamily. This result suggests that the DREB subfamily genes play an important role in plant response to cold stress. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). We found that 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results, therefore, provide new resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.

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.

Temporal restriction of salt inducibility in expression of salinity-stress related gene by the circadian clock in Solanum lycopersicum

Exposure to salinity causes plants to trigger transcriptional induction of a particular set of genes for initiating salinity-stress responses. Recent transcriptome analyses reveal that expression of a population of salinity-inducible genes also exhibits circadian rhythms. However, since the analyses were performed independently from those with salinity stress, it is unclear whether the observed circadian rhythms simply represent their basal expression levels independently from their induction by salinity, or these rhythms demonstrate the function of the circadian clock to actively limit the timing of occurrence of the salinity induction to particular times in the day. Here, by using tomato, we demonstrate that salt inducibility in expression of particular salinity-stress related genes is temporally controlled in the day. Occurrence of salinity induction in expression of SlSOS2 and P5CS, encoding a sodium/hydrogen antiporter and an enzyme for proline biosynthesis, is limited specifically to the morning, whereas that of SlDREB2, which encodes a transcription factor involved in tomato responses to several abiotic stresses such as salinity and drought, is restricted specifically to the evening. Our findings not only demonstrate potential importance in further investigating the basis and significance of circadian gated salinity stress responses under fluctuating day/night conditions, but also provide the potential to exploit an effective way for improving performance of salinity resistance in tomato.

Association of transcription factor WRKY56 gene from Populus simonii × P. nigra with salt tolerance in Arabidopsis thaliana

The WRKY transcription factor family is one of the largest groups of transcription factor in plants, playing important roles in growth, development, and biotic and abiotic stress responses. Many WRKY genes have been cloned from a variety of plant species and their functions have been analyzed. However, the studies on WRKY transcription factors in tree species under abiotic stress are still not well characterized. To understand the effects of the WRKY gene in response to abiotic stress, mRNA abundances of 102 WRKY genes in Populus simonii × P. nigra were identified by RNA sequencing under normal and salt stress conditions. The expression of 23 WRKY genes varied remarkably, in a tissue-specific manner, under salt stress. Since the WRKY56 was one of the genes significantly induced by NaCl treatment, its cDNA fragment containing an open reading frame from P. simonii × P. nigra was then cloned and transferred into Arabidopsis using the floral dip method. Under salt stress, the transgenic Arabidopsis over-expressed the WRKY56 gene, showing an increase in fresh weight, germination rate, proline content, and peroxidase and superoxide dismutase activity, when compared with the wild type. In contrast, transgenic Arabidopsis displayed a decrease in malondialdehyde content under salt stress. Overall, these results indicated that the WRKY56 gene played an important role in regulating salt tolerance in transgenic Arabidopsis.

Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube

The Ethylene response factor (ERF) belongs to the APETALA2/ethylene response factor (AP2/ERF) superfamily, located at the end of the ethylene signalling pathway, and has important roles in regulating the ethylene-related response genes. Thus, identifying and charactering this transcription factor would be helpful to elucidate ethylene related fruit ripening regulation in Chinese jujube (Ziziphus jujuba Mill.). In the present study, 119 AP2/ERF genes, including 5 Related to ABI3/VPs (RAV), 17 AP2s, 57 ERFs, 39 dehydration-responsive element-binding (DREB) factors and 1 soloist gene, were identified from the jujube genome sequences. Genome localization, gene duplication, phylogenetic relationships and conserved motifs were simultaneously analysed. Using available transcriptomic data, 85 genes with differential transcripts in the flower, leaf and fruit were detected, suggesting a broad regulation of AP2/ERF genes in the growth and development of jujube. Among them, 44 genes were expressed in the fruit. As assessed by quantitative PCR, 15 up- and 23 downregulated genes corresponding to fruit full maturity were found, while in response to 100 μl l^-1 ethylene, 6 up- and 16 downregulated genes were generated. By comparing the output, ZjERF54 and DREB39 were found to be the best candidate genes that positively participated in jujube fruit ripening, while ZjERF25 and ZjERF36, which had an ERF-associated amphiphilic repression (EAR) motif, were ripening repressors. These findings help to gain insights into AP2/ERF gene evolution and provide a useful resource to further understand the ethylene regulatory mechanisms underlying Chinese jujube fruit ripening.

RAV transcription factors are essential for disease resistance against cassava bacterial blight via activation of melatonin biosynthesis genes

With 1 AP2 domain and 1 B3 domain, 7 MeRAVs in apetala2/ethylene response factor (AP2/ERF) gene family have been identified in cassava. However, the in vivo roles of these remain unknown. Gene expression assays showed that the transcripts of MeRAVs were commonly regulated after Xanthomonas axonopodis pv manihotis (Xam) and MeRAVs were specifically located in plant cell nuclei. Through virus-induced gene silencing (VIGS) in cassava, we found that MeRAV1 and MeRAV2 are essential for plant disease resistance against cassava bacterial blight, as shown by the bacterial propagation of Xam in plant leaves. Through VIGS in cassava leaves and overexpression in cassava leave protoplasts, we found that MeRAV1 and MeRAV2 positively regulated melatonin biosynthesis genes and the endogenous melatonin level. Further investigation showed that MeRAV1 and MeRAV2 are direct transcriptional activators of 3 melatonin biosynthesis genes in cassava, as evidenced by chromatin immunoprecipitation-PCR in cassava leaf protoplasts and electrophoretic mobility shift assay. Moreover, cassava melatonin biosynthesis genes also positively regulated plant disease resistance. Taken together, this study identified MeRAV1 and MeRAV2 as common and upstream transcription factors of melatonin synthesis genes in cassava and revealed a model of MeRAV1 and MeRAV2-melatonin biosynthesis genes-melatonin level in plant disease resistance against cassava bacterial blight.

Hormone dependent survival mechanisms of plants during post-waterlogging stress

Waterlogging stress has two phases like waterlogging phase and post-waterlogging phase where both are injurious to plants. Susceptible plants normally die at post-waterlogging phase due to damaged root system, sudden rexoygenation, dehydration and photoinhibition of the desubmerged tissues. Formation of reactive oxygen species (ROS) is the main result of reoxygenation stress that can cause oxidative damage of the functional tissues responsible for normal physiological activities. There are almost all types of hormones responsible to recover plants from these destructive phenomenons. Among these hormones ethylene and abscisic acid (ABA) are the main regulators to overcome the reoxygenation and drought like stresses in plants at post-waterlogging condition. The balanced crosstalk among the hormones is highly important for the survival of plants at these stresses. So this paper is completely a precise summary of hormonal homeostasis of post-waterlogged plants through physiological, biochemical and signaling pathways.

Transcriptomic changes reveal gene networks responding to the overexpression of a blueberry DWARF AND DELAYED FLOWERING 1 gene in transgenic blueberry plants

BACKGROUND

Constitutive expression of the CBF/DREB1 for increasing freezing tolerance in woody plants is often associated with other phenotypic changes including dwarf plant and delayed flowering. These phenotypic changes have been observed when Arabidopsis DWARF AND DELAYED FLOWERING 1 (DDF1) was overexpressed in A. thaliana plants. To date, the DDF1 orthologues have not been studied in woody plants. The aim of this study is to investigate transcriptomic responses to the overexpression of blueberry (Vaccinium corymbosum) DDF1 (herein, VcDDF1-OX).

RESULTS

The VcDDF1-OX resulted in enhanced freezing tolerance in tetraploid blueberry plants and did not result in significant changes in plant size, chilling requirement, and flowering time. Comparative transcriptome analysis of transgenic 'Legacy-VcDDF1-OX' plants containing an overexpressed VcDDF1 with non-transgenic highbush blueberry 'Legacy' plants revealed the VcDDF1-OX derived differentially expressed (DE) genes and transcripts in the pathways of cold-response, plant flowering, DELLA proteins, and plant phytohormones. The increase in freezing tolerance was associated to the expression of cold-regulated genes (CORs) and the ethylene pathway genes. The unchanged plant size, dormancy and flowering were due to the minimal effect of the VcDDF1-OX on the expression of DELLA proteins, flowering pathway genes, and the other phytohormone genes related to plant growth and development. The DE genes in auxin and cytokinin pathways suggest that the VcDDF1-OX has also altered plant tolerance to drought and high salinity.

CONCLUSION

A DDF1 orthologue in blueberry functioned differently from the DDF1 reported in Arabidopsis. The overexpression of VcDDF1 or its orthologues is a new approach to increase freezing tolerance of deciduous woody plant species with no obvious effect on plant size and plant flowering time.

Regulation of Apetala2/Ethylene Response Factors in Plants

Multiple environmental stresses affect growth and development of plants. Plants try to adapt under these unfavorable condition through various evolutionary mechanisms like physiological and biochemical alterations connecting various network of regulatory processes. Transcription factors (TFs) like APETALA2/ETHYLENE RESPONSE FACTORS (AP2/ERFs) are an integral component of these signaling cascades because they regulate expression of a wide variety of down stream target genes related to stress response and development through different mechanism. This downstream regulation of transcript does not always positively or beneficially affect the plant but also they display some developmental defects like senescence and reduced growth under normal condition or sensitivity to stress condition. Therefore, tight auto/cross regulation of these TFs at transcriptional, translational and domain level is crucial to understand. The present manuscript discuss the multiple regulation and advantage of plasticity and specificity of these family of TFs to a wide or single downstream target(s) respectively. We have also discussed the concern which comes with the unwanted associated traits, which could only be averted by further study and exploration of these AP2/ERFs.

Genome-wide identification of cassava R2R3 MYB family genes related to abscission zone separation after environmental-stress-induced abscission

Cassava plants (Manihot esculenta Crantz) resist environmental stresses by shedding leaves in leaf pulvinus abscission zones (AZs), thus leading to adaptation to new environmental conditions. Little is known about the roles of cassava R2R3 MYB factors in regulating AZ separation. Herein, 166 cassava R2R3 MYB genes were identified. Evolutionary analysis indicated that the 166 R2R3 MYB genes could be divided into 11 subfamilies. Transcriptome analysis indicated that 26 R2R3 MYB genes were expressed in AZs across six time points during both ethylene- and water-deficit stress-induced leaf abscission. Comparative expression profile analysis of similar SOTA (Self Organizing Tree Algorithm) clusters demonstrated that 10 R2R3 MYB genes had similar expression patterns at six time points in response to both treatments. GO (Gene Ontology) annotation confirmed that all 10 R2R3 MYB genes participated in the responses to stress and ethylene and auxin stimuli. Analysis of the putative 10 R2R3 MYB promoter regions showed that those genes primarily contained ethylene- and stress-related cis-elements. The expression profiles of the genes acting downstream of the selected MYBs were confirmed to be involved in cassava abscission zone separation. All these results indicated that R2R3 MYB plays an important regulatory role in AZ separation.

Exposure to various abscission-promoting treatments suggests substantial ERF subfamily transcription factors involvement in the regulation of cassava leaf abscission

BACKGROUND

Cassava plants (Manihot esculenta Crantz) have obvious abscission zone (AZ) structures in their leaf pulvinus-petioles. Cassava leaf abscission can be triggered by either 17 days of water-deficit stress or 4 days of ethylene treatment. To date, little is known about cassava AP2/ERF factors, and less is known regarding their roles in regulating abscission zone development.

RESULTS

Here, the cassava and Arabidopsis AP2/ERF genes were compared, finding that the cassava genome contains approximately 1.54-fold more ERF subfamily than the Arabidopsis genome. Microarray analysis was used to identify the AP2/ERF genes that are expressed in cassava leaf pulvinus-petiole abscission zones by comparing the AP2/ERF gene expression profiles of ethylene- and water-deficit stress-induced leaf abscission. In total, 99 AP2/ERF genes were identified as expressed in AZs across six time points during both ethylene- and water-deficit stress-induced leaf abscission. Comparative expression profile analysis of similar SOTA (Self Organizing Tree Algorithm) clusters at six time points during ethylene- and water-deficit stress-induced leaf abscission demonstrated that 20 ERF subfamily genes had similar expression patterns in response to both treatments. GO (Gene Ontology) annotation confirmed that all 20 ERF subfamily genes participate in ethylene-mediated signalling. Analysis of the putative ERF promoter regions shown that the genes contained primarily ethylene- and stress-related cis-elements. Further analysis of ACC oxidase activity in AZs across six time points during abscission shown increased ethylene production in response to both ethylene and water-deficit stress; however, the difference was more dramatic for water-deficit stress. Finally, the expression ratios of 20 ERF subfamily genes were analysed in two cassava cultivars, 'KU50' and 'SC5', that exhibit different levels of leaf abscission when challenged with the same water-deficit stress. The analysis indicated that most of the ERF genes were expressed at higher levels in the precocious abscission 'KU50' cultivar than in the delayed abscission 'SC5' cultivar.

CONCLUSION

Ccomparative analysis of both ethylene- and water-deficit stress-induced leaf abscission shown that the ERF subfamily functions in the regulation of cassava abscission zone development.

Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean

Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the AP2-ERF genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (Phaseolus vulgaris). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of AP2-ERF genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all PvAP2-ERF genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were PvAP2/ERF-20-25-62-78-113-173. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor PvAP2-ERF78, an ortholog of Arabidopsis At2G28550, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.

Genome-Wide Analysis of the AP2/ERF Superfamily Genes and their Responses to Abiotic Stress in Medicago truncatula

The AP2/ERF superfamily is a large, plant-specific transcription factor family that is involved in many important processes, including plant growth, development, and stress responses. Using Medicago truncatula genome information, we identified and characterized 123 putative AP2/ERF genes, which were named as MtERF1-123. These genes were classified into four families based on phylogenetic analysis, which is consistent with the results of other plant species. MtERF genes are distributed throughout all chromosomes but are clustered on various chromosomes due to genomic tandem and segmental duplication. Using transcriptome, high-throughput sequencing data, and qRT-PCR analysis, we assessed the expression patterns of the MtERF genes in tissues during development and under abiotic stresses. In total, 87 MtERF genes were expressed in plant tissues, most of which were expressed in specific tissues during development or under specific abiotic stress treatments. These results support the notion that MtERF genes are involved in developmental regulation and environmental responses in M. truncatula. Furthermore, a cluster of DREB subfamily members on chromosome 6 was induced by both cold and freezing stress, representing a positive gene regulatory response under low temperature stress, which suggests that these genes might contribute to freezing tolerance to M. truncatula. In summary, our genome-wide characterization, evolutionary analysis, and expression pattern analysis of MtERF genes in M. truncatula provides valuable information for characterizing the molecular functions of these genes and utilizing them to improve stress tolerance in plants.