Functions and application of the AP2/ERF transcription factor family in crop improvement

Upregulated expression of MYB4, DREB1 and AP37 transcription factors modulates cold stress response in high-altitude Himalayan rice via time-dependent ROS regulation

BACKGROUND

Cold stress is an upcoming challenge for rice (Oryza sativa L.) cultivation, especially at the seedling establishment stage. It causes serious constraints in its production and productivity as it is a thermophilic cereal crop. North-western Himalayan region has a rich repository of temperate rice genotypes, and there is a need to identify cold-tolerant rice varieties from these available genetic resources.

METHODS AND RESULTS

The present study screened 90 rice accessions (indica and japonica) grown in the high-altitude regions at 2200 m amsl for cold tolerance (5 °C) at the seedling stage, and found 14 highly cold-tolerant accessions. Almost eighty per cent of the indica types clustered into cold-sensitive class. One cold-tolerant japonica (GS-74) accession and one cold-susceptible (SR-4) accession were used to compare their biochemical and gene expression response during cold stress and after recovery. A wide range of differences was noticed at different time points in the accumulation of ROS scavengers, osmo-protectants and antioxidant enzymes, with significant differences between the contrasting genotypes. Similarly, gene expression of five transcription factors OsMYB4, OsAP37, OsDREB1A, OsDREB1B and OsDREB1D revealed their role in cold responsiveness at the seedling stage, critically modulating the cold-induced osmoprotectant-mediated tolerance mechanism.

CONCLUSION

This is the first study that explored the high-altitude Himalayan rice germplasm for cold tolerance at the critical S3 seedling stage under controlled conditions. It demonstrated that the upregulation of OsDREB1A, OsDREB1B, OsMYB4 and OsAP37 transcription factors modulates cold stress response in rice via a complex mechanism involving ROS scavengers and osmoprotectants.

A genomic variation map provides insights into potato evolution and key agronomic traits

Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop, which requires a deep understanding of potato domestication and differentiation. In the present study, we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants. Using the variome map, we discovered the reshaping of tuber transcriptome during potato domestication, characterized genome-wide differentiation between landrace groups Stenotomum and Phureja. We identified a jasmonic acid biosynthetic gene possibly affecting the tuber dormancy period. Genome-wide association studies revealed a UDP-glycosyltransferase gene for the biosynthesis of anti-nutritional steroidal glycoalkaloids (SGAs), and a Dehydration Responsive Element Binding (DREB) transcription factor conferring increased average tuber weight. In addition, genome similarity and group-specific SNP analyses indicated that tetraploid potatoes originated from the diploid Solanum tuberosum group Stenotomum. These findings shed light on the evolutionary trajectory of potato domestication and improvement, providing a solid foundation for advancing hybrid potato-breeding practices.

Time-series analysis reveals metabolic and transcriptional dynamics during mulberry fruit development and ripening

Understanding the global transcriptomic and metabolic changes during mulberry growth and development is essential for the enhancing fruit quality and optimizing breeding strategies. By integrating phenotypic, metabolomic, and transcriptomic data across 18 developmental and ripening stages of Da10 mulberry fruit, a global map of gene expression and metabolic changes was generated. Analysis revealed a gradual progression of morphological, metabolic, and transcriptional changes throughout the development and ripening phases. In this study, a new transcriptome transition, which was highly related to stress resistance, was observed after the full ripening stage. Moreover, a novel method was devised by integrating metabolome and phenotypic data to assess fruit quality and determine optimal harvest times early in the supply chain. Phase-specific co-expression networks involved in photosynthesis, quality regulation, and plant immunity were also constructed. Notably, eight flavonoids and six hub genes emerged as potential natural edible coatings or gene-editing targets for mulberry fruit to enhance resistance against biotic and abiotic stress. These findings should facilitate further research on stress resistance, post-harvest management, and sustainable agricultural development.

The AP2/ERF transcription factor MhERF113-like positively regulates drought tolerance in transgenic tomato and apple

Drought is a major abiotic stress in agriculture that severely affects crop growth, yield, and quality. The APETALA2/ethylene responsive factor (AP2/ERF) plays a crucial role in maintaining plant growth, development, as well as stress tolerance. Herein, we cloned and characterized the MhERF113-like gene from Malus hupehensis. MhERF113-like is significantly induced by drought and highly expressed in leaves. Overexpression of MhERF113-like positively regulated the drought tolerance of apple calli and plants, as judged by less electrolyte leakage, lower malonaldehyde (MDA) and hydrogen peroxide (H2O2) contents in OE than those of the WT apple calli and plants under drought stress. In addition, ectopic expression of MhERF113-like gene in tomatoes improved the drought tolerance, accompanied by enhanced expression of antioxidant genes (SlAPX1 and SlSOD) and stress responsive genes (SlDREB and SlRD29), and reduced H2O2 and O2- contents in OE tomatoes. Taken together, our study demonstrated that MhERF113-like may play an important role in the regulation of plant drought tolerance, which may provide a key factor for future biotechnology applications to improve drought stress tolerance in plants.

Genome-Wide Identification and Expression Profiling of Dehydration-Responsive Element-Binding Family Genes in Flax (Linum usitatissimum L.)

Dehydration-responsive element-binding (DREB) transcription factors are ubiquitous in plants and regulate plant growth, development, signal transduction, and responses to stress, particularly drought stress. However, DREB genes in flax have not previously been studied. This study conducted a comprehensive and systematic analysis of the DREB gene family in flax (Linum usitatissimum L.). A total of 59 LuDREB genes were identified in Longya-10 (a breeding variety), with an uneven distribution across all 15 chromosomes. Further analysis revealed significant variations among LuDREB members, with predictions indicating that these proteins are hydrophilic and localized in the nucleus and cytoplasm. A phylogenetic analysis classified the LuDREB genes into six subgroups, a classification further supported by gene structure and motif composition. Members within the same subgroup exhibited structural conservation, suggesting functional redundancy. The duplication analysis identified 30 pairs of segmentally duplicated LuDREB genes and one pair of tandemly duplicated genes, indicating that segmental duplication was the primary driver of LuDREB gene expansion. A comparative collinearity analysis revealed that most LuDREB genes had orthologs in other plant species, suggesting that this gene family has remained relatively conserved throughout evolution. Cis-acting element analysis identified numerous hormone- and stress-responsive elements in LuDREB promoters, and the quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) results confirmed the role of all LuDREB genes in drought stress response. In addition, transcriptome analysis revealed that LuDREB49 and LuDREB56 exhibited high expression levels in the capsules, whereas LuDREB3 and LuDREB36 showed significantly higher expression levels in the stems, suggesting that these LuDREB genes may have specialized functions in capsule or stem development. Collectively, this study provides a comprehensive overview of LuDREB genes, offering valuable insights into their roles in flax growth, development, and stress responses.

Ethylene modulates wheat response to phosphate deficiency

Ethylene is involved in the response to P deficiency in some model plants such as Arabidopsis and rice, but its role in wheat remains unclear. Following our recent study demonstrating the role of differentially expressed genes encoding ethylene response factors (ERFs) in response to P starvation in wheat, this study aims to investigate remodeling of the ethylene pathway and the physiological roles of ethylene in wheat under P deficiency using transcriptome analysis and the addition of the exogenous ethylene analogue, ethephon, or ethylene inhibitors. ERFs with at least a 2-fold expression change upon P deficiency had a distribution biased towards chromosome 4B. A group of genes encoding aminocyclopropane-1-carboxylic acid (ACC) synthase and ACC oxidase were up-regulated under P starvation, suggesting an increase in ACC and ethylene content, which was verified by biochemical measurements and gas chromatography-mass spectrometry analysis. Under P deficiency, both root and shoot biomass decreased with application of exogenous ethephon or ethylene inhibitors, while root fork numbers and root surface area decreased upon ethephon treatment. Phosphate (Pi) concentrations in roots and old leaves increased with ethephon treatment, and Pi redistribution in roots and younger leaves was altered under Pi starvation. Our findings can guide breeding of germplasm with high Pi efficiency.

Moss-pathogen interactions: a review of the current status and future opportunities

In complex and diverse environments, plants face constant challenges from various pathogens, including fungi, bacteria, and viruses, which can severely impact their growth, development, and survival. Mosses, representing early divergent lineages of land plants, lack traditional vascular systems yet demonstrate remarkable adaptability across diverse habitats. While sharing the fundamental innate immune systems common to all land plants, mosses have evolved distinct chemical and physical defense mechanisms. Notably, they exhibit resistance to many pathogens that typically affect vascular plants. Their evolutionary significance, relatively simple morphology, and well-conserved defense mechanisms make mosses excellent model organisms for studying plant-pathogen interactions. This article reviews current research on moss-pathogen interactions, examining host-pathogen specificity, characterizing infection phenotypes and physiological responses, and comparing pathogen susceptibility and defense mechanisms between mosses and angiosperms. Through this analysis, we aim to deepen our understanding of plant immune system evolution and potentially inform innovative approaches to enhancing crop disease resistance.

Identification of a central regulator of ginkgolide biosynthesis in Ginkgo biloba that integrates jasmonate and light signaling

Ginkgolides are secondary metabolites unique to Ginkgo biloba with the potential to prevent and treat cardiovascular and cerebrovascular diseases. Although the biosynthetic pathways of ginkgolides have been partly uncovered, the mechanism regulating their biosynthesis is still largely unknown. Here, using multiomic and genetic analyses, we report the identification of a transcription factor, named ETHYLENE RESPONSE FACTOR ASSOCIATED WITH GINKGOLIDE BIOSYNTHESIS (GbEAG), as a critical regulator of ginkgolide biosynthesis. GbEAG is highly expressed in the roots of G. biloba, and its expression is significantly induced by methyl jasmonate (MeJA). Ginkgolide content was significantly increased in roots by overexpressing GbEAG using a "cut-dip-regeneration" system. GbEAG positively regulates ginkgolide biosynthesis by directly binding to the GCC-boxes in the promoter regions of genes involved in the biosynthesis of ginkgolides, such as ISOPENTENYL DIPHOSPHATE ISOMERASE (GbIDI) and CYTOCHROME P450 7005C3 (GbCYP7005C3). GbEAG mediates the jasmonic acid (JA)-activated ginkgolide synthesis through its direct interaction with the JASMONATE ZINC-FINGER INFLORESCENCE MERISTEM DOMAIN 3 (GbJAZ3) repressor. Importantly, we also found that the central light-response regulator ELONGATED HYPOCOTYL 5 (GbHY5) mediates light induction of ginkgolide biosynthesis by binding to the G-box in the GbEAG promoter. Our findings provide mechanistic insights into the coordinated regulation of ginkgolide biosynthesis via JA and light signals, with GbEAG as a central regulator in G. biloba, and shed light on the potential to develop ginkgolide-rich varieties through molecular breeding and gene editing.

Genome-wide identification of CAMTA gene family in teak (Tectona grandis) and functional characterization of TgCAMTA1 and TgCAMTA3 in cold tolerance

BACKGROUND

Calmodulin-binding transcription activator (CAMTA) proteins play significant roles in signal transduction, growth and development, as well as abiotic stress responses, in plants. Understanding their involvement in the low-temperature stress response of teak is vital for revealing cold resistance mechanisms.

RESULTS

Through bioinformatics analysis, the CAMTA gene family in teak was examined, and six CAMTA genes were identified in teak. The encoded proteins were predicted to be located in the nucleus and exhibited hydrophilic properties, with molecular weights ranging from 103.4 to 123.3 kDa and isoelectric points ranging from 5.49 to 7.55. On the basis of protein sequence homology, the CAMTA family could be divided into three subgroups. Domain and 3D structure analyses demonstrated that all the TgCAMTA proteins contained the typical CAMTA domain with the CaMBD binding domain, which was exposed on the surface. Expression analysis of different tissues revealed the expression of TgCAMTA genes in teak roots, stems, leaves, flowers, fruits, and branches. Furthermore, the promoter region contained various cis-acting elements related to light, hormone, and abiotic stress responses. After low-temperature stress treatment, different expression patterns of TgCAMTAs were observed in teak roots, stems, and leaves, with TgCAMTA1 showing the highest expression level in leaves compared with stems. Transgenic lines carrying the TgCAMTA1/3 promoter::GUS construct cold stress induction of TgCAMTA1/3 genes revealed the presence of multiple low-temperature responsive cis-acting elements in the TgCAMTA1/3 promoter region. Subcellular localization analysis indicated that these genes were functional predominantly in the nucleus. Compared with wild-type Arabidopsis, TgCAMTA1/3-overexpressing Arabidopsis presented increased tolerance to freezing stress, with increased expression of AtCOR genes. Moreover, under low-temperature conditions, TgCAMTA3-overexpressing Arabidopsis presented significantly elevated expression levels of genes related to the CBF signaling pathway, including AtCBF1/2/3.

CONCLUSIONS

Our findings add significantly to the existing knowledge regarding cold stress tolerance and help elucidate cold response mechanisms in teak.

The transcription factor TaFDL2-1A functions in auxin metabolism mediated by abscisic acid to regulate shoot growth in wheat

Genetic strategies can be effective in improving wheat (Triticum aestivum L.) drought stress tolerance, but accumulating evidence suggests that overexpressing drought-resistance genes, especially genes related to the abscisic acid (ABA) signaling pathway, can retard plant growth. We previously characterized the positive roles of the wheat bZIP transcription factor TaFD-Like2-1A (TaFDL2-1A) in drought stress tolerance and ABA biosynthesis and response, whereas a dwarfing shoot exhibited under normal conditions. This study determined the underlying mechanisms that allow TaFDL2-1A to affect shoot growth. Overexpressing TaFDL2-1A decreased cell length, cell width, leaf size, shoot length, and biomass in wheat. The results of RNA-seq showed that multiple differently expressed transcripts are enriched in the auxin signaling pathway. Further analysis indicated higher expression levels of Gretchen Hagen3 (GH3) genes and lower indole-3-acetic acid (IAA) concentrations in the TaFDL2-1A overexpression lines. Exogenous IAA treatment restored the phenotypes of the TaFDL2-1A overexpression lines to wild-type levels. Transcriptional regulation analysis suggested that TaFDL2-1A enhances the expression of auxin metabolism genes, such as TaGH3.2-3A, TaGH3.2-3B, TaGH3.8-2A, and TaGH3.8-2D, by directly binding to ACGT core cis-elements. Furthermore, tafdl2 knockout plants had lower expression levels of these GH3 genes and higher IAA levels than Fielder wheat. These GH3 gene expression and IAA levels were induced and reduced in Fielder wheat and tafdl2 knockout plants treated with exogenous ABA. Our findings elucidate mechanisms underlying the functional redundancy of TaFDL2-1A in the crosstalk between ABA and IAA to affect shoot growth and provide insights into the balance between drought resistance and yield in wheat.

Genome-wide identification, characterization and expression profiles of FORMIN gene family in cotton (Gossypium Raimondii L.)

BACKGROUND

Gossypium raimondii serves as a widely used genomic model cotton species. Its genetic influence to enhance fiber quality and ability to adapt to challenging environments both contribute to increasing cotton production. The formins are a large protein family that predominately consists of FH1 and FH2 domains. The presence of the formin domains highly regulates the actin and microtubule filament in the cytoskeleton dynamics confronting various abiotic stresses such as drought, salinity, and cold temperatures.

RESULTS

In this study, 26 formin genes were analyzed and characterized in G. raimondii and mostly were found in the nucleus and chloroplast. According to the evolutionary phylogenetic relationship, GrFH were dispersed and classified into seven different groups and shared an ancestry relationship with MtFH. The GrFH gene structure prediction revealed diverse intron-exon arrangements between groups. The FH2 conserved domain was found in all the GrFH distributed on 12 different chromosomes. Moreover, 11 pairs of GrFH transpired segmental duplication. Among them, GrFH4-GrFH7 evolved 35 million years ago (MYA) according to the evolutionary divergence time. Besides, 57 cis-acting regulatory elements (CAREs) motifs were found to play a potential role in plant growth, development, and in response to various abiotic stresses, including cold stress. The GrFH genes mostly exhibited biological processes resulting in the regulation of actin polymerization. The ERF, GATA, MYB, and LBD, major transcription factors (TFs) families in GrFH, regulated expression in abiotic stress specifically salt as well as defense against certain pathogens. The microRNA of GrFH unveiled the regulatory mechanism to regulate their gene expression in abiotic stresses such as salt and cold. One of the most economic aspects of cotton (G.raimondii) is the production of lint due to its use in manufacturing fabrics and other industrial applications. The expression profiles of GrFH in different tissues particularly during the conversion from ovule to fiber (lint), and the increased levels (up-regulation) of GrFH4, GrFH6, GrFH12, GrFH14, and GrFH26 under cold conditions, along with GrFH19 and GrFH26 in response to salt stress, indicated their potential involvement in combating these environmental challenges. Moreover, these stress-tolerant GrFH linked to cytoskeleton dynamics are essential in producing high-quality lint.

CONCLUSIONS

The findings from this study can contribute to elucidating the evolutionary and functional characterizations of formin genes and deciphering their potential role in abiotic stress such as cold and salt as well as in the future implications in wet lab.

APETALA2/ethylene-responsive factors in higher plant and their roles in regulation of plant stress response

Plants, anchored throughout their life cycles, face a unique set of challenges from fluctuating environments and pathogenic assaults. Central to their adaptative mechanisms are transcription factors (TFs), particularly the AP2/ERF superfamily-one of the most extensive TF families unique to plants. This family plays instrumental roles in orchestrating diverse biological processes ranging from growth and development to secondary metabolism, and notably, responses to both biotic and abiotic stresses. Distinguished by the presence of the signature AP2 domain or its responsiveness to ethylene signals, the AP2/ERF superfamily has become a nexus of research focus, with increasing literature elucidating its multifaceted roles. This review provides a synoptic overview of the latest research advancements on the AP2/ERF family, spanning its taxonomy, structural nuances, prevalence in higher plants, transcriptional and post-transcriptional dynamics, and the intricate interplay in DNA-binding and target gene regulation. Special attention is accorded to the ethylene response factor B3 subgroup protein Pti5 and its role in stress response, with speculative insights into its functionalities and interaction matrix in tomatoes. The overarching goal is to pave the way for harnessing these TFs in the realms of plant genetic enhancement and novel germplasm development.

Genome-wide identification, structural characterization and expression profiling of AP2/ERF gene family in bayberry (Myrica rubra)

BACKGROUND

Bayberry is the most economically significant fruit within the Myricaceae family, having high nutritional and medicinal value. The AP2/ERF family is a class of transcription factors found mainly in plants. However, the bayberry AP2/ERF gene family has not previously been studied.

RESULTS

In this study, 113 members of the bayberry AP2/ERF gene family were identified. According to the phylogenetic tree, the members of this group are divided into three subfamilies, namely AP2, ERF, and DREB. The gene structure and conserved motifs were analyzed. Chromosome localization showed that 95 genes were unevenly distributed on 8 chromosomes and 18 genes were located on the skeleton. Gene collinearity analysis of the bayberry AP2/ERF gene family showed 12 segmental duplication events, involving 21 AP2/ERFs. In addition, we further investigated the evolutionary relationship of the AP2/ERF gene family between bayberry and six other species. It was found that bayberry was most closely related to Populus trichocarpa and Malus pumila, with 153 and 141 homologous gene pairs, respectively. Cis-acting elements indicated that AP2/ERFs were related to phytohormone responses, light response, abiotic and biotic stress tolerance. Transcriptomic data showed that the expression pattern of AP2/ERF gene was different in bayberry space electric field treatment and at different stages of fruit development. The results of GO annotation revealed the biological processes, cellular component and molecular function that the AP2/ERF genes were involved. And KEGG enrichment analysis indicated that these genes were mainly clustered in genetic information processing and metabolism pathways.

CONCLUSIONS

The AP2/ERF gene was identified in the genome of bayberry, and its structure, conserved motif, and phylogenetic relationship were analyzed. These findings of this study serve as a reference for the genome-wide identification of the AP2/ERF gene family in other species and groundwork for future research on the function of AP2/ERF genes in bayberry.

Identification and characterization of the Quinoa AP2/ERF gene family and their expression patterns in response to salt stress

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play crucial roles in plant growth, development, and responses to biotic and abiotic stresses. This study was performed to comprehensively identify and characterize the AP2/ERF gene family in quinoa (Chenopodium quinoa Willd.), a highly resilient pseudocereal crop known for its salinity tolerance. A total of 150 CqAP2/ERF genes were identified in the quinoa genome; these genes were unevenly distributed across the chromosomes. Phylogenetic analysis divided the CqAP2/ERFs into five subfamilies: 71 ERF, 49 DREB, 23 AP2, 3 RAV, and 4 Soloist. Additionally, the DREB and ERF subfamilies were subdivided into four and seven subgroups, respectively. The exon-intron structure of the putative CqAP2/ERF genes and the conserved motifs of their encoded proteins were also identified, showing general conservation within the phylogenetic subgroups. Promoter analysis revealed many cis-regulatory elements associated with light, hormones, and response mechanisms within the promoter regions of CqAP2/ERF genes. Synteny analysis revealed that segmental duplication under purifying selection pressure was the major evolutionary driver behind the expansion of the CqAP2/ERF gene family. The protein-protein interaction network predicted the pivotal CqAP2/ERF proteins and their interactions involved in the regulation of various biological processes including stress response mechanisms. The expression profiles obtained from RNA-seq and qRT-PCR data detected several salt-responsive CqAP2/ERF genes, particularly from the ERF, DREB, and RAV subfamilies, with varying up- and downregulation patterns, indicating their potential roles in salt stress responses in quinoa. Overall, this study provides insights into the structural and evolutionary features of the AP2/ERF gene family in quinoa, offering candidate genes for further analysis of their roles in salt tolerance and molecular breeding.

GmBSK1-GmGSK1-GmBES1.5 regulatory module controls heat tolerance in soybean

INTRODUCTION

Heat stress poses a severe threat to the growth and production of soybean (Glycine max). Brassinosteroids (BRs) actively participate in plant responses to abiotic stresses, however, the role of BR signaling pathway genes in response to heat stress in soybean remains poorly understood.

OBJECTIVES

In this study, we investigate the regulatory mechanisms of GmBSK1 and GmBES1.5 in response to heat stress and the physiological characteristics and yield performance under heat stress conditions.

METHODS

Transgenic technology and CRISPR/Cas9 technology were used to generated GmBSK1-OE, GmBES1.5-OE and gmbsk1 transgenic soybean plants, and transcriptome analysis, LUC activity assay and EMSA assay were carried out to elucidate the potential molecular mechanism underlying GmBSK1-GmBES1.5-mediated heat stress tolerance in soybean.

RESULTS

CRISPR/Cas9-generated gmbsk1 knockout mutants exhibited increased sensitivity to heat stress due to a reduction in their ability to scavenge reactive oxygen species (ROS). The expression of GmBES1.5 was up-regulated in GmBSK1-OE plants under heat stress conditions, and it directly binds to the E-box motif present in the promoters of abiotic stress-related genes, thereby enhancing heat stress tolerance in soybean plants. Furthermore, we identified an interaction between GmGSK1 and GmBES1.5, while GmGSK1 inhibits the transcriptional activity of GmBES1.5. Interestingly, the interaction between GmBSK1 and GmGSK1 promotes the localization of GmGSK1 to the plasma membrane and releases the transcriptional activity of GmBES1.5.

CONCLUSION

Our findings suggest that both GmBSK1 and GmBES1.5 play crucial roles in conferring heat stress tolerance, highlighting a potential strategy for breeding heat-tolerant soybean crops involving the regulatory module consisting of GmBSK1-GmGSK1-GmBES1.5.

Synergistic Interaction Between PbbZIP88 and PbSRK2E Enhances Drought Resistance in Pear Through Regulation of PbATL18 Expression and Stomatal Closure

Drought poses significant challenges to agricultural production, ecological stability and global food security. While wild pear trees exhibit strong drought resistance, cultivated varieties show weaker drought tolerance. This study aims to elucidate the molecular mechanisms underlying pear trees' response to drought stress. We identified a drought resistance-related transcription factor, PbbZIP88, which binds to and activates the expression of the drought-responsive gene PbATL18. Overexpression of PbbZIP88 in Arabidopsis and pear seedlings resulted in enhanced drought resistance and significantly improved physiological parameters under drought stress. We discovered that PbbZIP88 interacts with the key protein PbSRK2E in the ABA signalling pathway. This interaction enhances PbbZIP88's ability to activate PbATL18 expression, leading to higher levels of PbATL18. Furthermore, the PbbZIP88 and PbSRK2E interaction accelerates the regulation of stomatal closure under ABA treatment conditions, reducing water loss more effectively. Experimental evidence showed that silencing PbbZIP88 and PbSRK2E genes significantly decreased drought resistance in pear seedlings. In conclusion, this study reveals the synergistic role of PbbZIP88 and PbSRK2E in enhancing drought resistance in pear trees, particularly in the upregulation of PbATL18 expression, and the accelerated promotion of stomatal closure. These findings provide new candidate genes for breeding drought-resistant varieties and offer a theoretical foundation and technical support for achieving sustainable agriculture.

Master Regulatory Transcription Factors in β-Aminobutyric Acid-Induced Resistance (BABA-IR): A Perspective on Phytohormone Biosynthesis and Signaling in Arabidopsis thaliana and Hordeum vulgare

The endogenous stress metabolite β-aminobutyric acid (BABA) primes plants for enhanced resistance against abiotic and biotic stress by activating a complex phytohormone signaling network that includes abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and ethylene (ET). In this study, through stringent filtering, we identify 14 master regulatory transcription factors (TFs) from the DOF, AHL, and ERF families that potentially regulate the biosynthesis and signaling of these phytohormones. Transcriptional analysis of BABA-treated Arabidopsis thaliana and Hordeum vulgare suggests that DOF family TFs play a crucial role in stress response regulation in both species. BABA treatment in A. thaliana upregulates the TFs MNB1A and PBF and enhances the expression of the genes ICS1, EDS5, and WIN3 in the SA biosynthesis pathway, potentially boosting NPR1 and PR1 in the SA signaling pathway. Conversely, in H. vulgare, the BABA-induced upregulation of TF DOF5.8 may negatively regulate SA biosynthesis by downregulating ICS1, EDS5, and PR1. Additionally, in A. thaliana, BABA triggers the expression of TF PBF, which may result in the decreased expression of MYC2, a key gene in JA signaling. In contrast, H. vulgare exhibits increased expression of ERF2 TF, which could positively regulate the JA biosynthesis genes LOX and Tify9, along with the COI1 and JAZ genes involved in the JA signaling pathway. These findings offer new perspectives on the transcriptional regulation of phytohormones during plant priming.

Enhancing Photosynthesis and Plant Productivity through Genetic Modification

Enhancing crop photosynthesis through genetic engineering technologies offers numerous opportunities to increase plant productivity. Key approaches include optimizing light utilization, increasing cytochrome b6f complex levels, and improving carbon fixation. Modifications to Rubisco and the photosynthetic electron transport chain are central to these strategies. Introducing alternative photorespiratory pathways and enhancing carbonic anhydrase activity can further increase the internal CO2 concentration, thereby improving photosynthetic efficiency. The efficient translocation of photosynthetically produced sugars, which are managed by sucrose transporters, is also critical for plant growth. Additionally, incorporating genes from C4 plants, such as phosphoenolpyruvate carboxylase and NADP-malic enzymes, enhances the CO2 concentration around Rubisco, reducing photorespiration. Targeting microRNAs and transcription factors is vital for increasing photosynthesis and plant productivity, especially under stress conditions. This review highlights potential biological targets, the genetic modifications of which are aimed at improving photosynthesis and increasing plant productivity, thereby determining key areas for future research and development.

Identification of DREB Family Genes in Banana and Their Function under Drought and Cold Stress

Bananas are one of the most important cash crops in the tropics and subtropics. Drought and low-temperature stress affect the growth of banana. The DREB (dehydration responsive element binding protein) gene family, as one of the major transcription factor families, plays crucial roles in defense against abiotic stress. Currently, systematic analyses of the banana DREB (MaDREB) gene family have not yet been reported. In this study, 103 members of the MaDREB gene family were identified in the banana genome. In addition, transcriptomic analysis results revealed that MaDREBs responded to drought and cold stress. The expression of MaDREB14/22/51 was induced by drought and cold stress; these geneswere selected for further analysis. The qRT-PCR validation results confirmed the transcriptome results. Additionally, transgenic Arabidopsis plants overexpressing MaDREB14/22/51 exhibited enhanced resistance to drought and cold stress by reducing MDA content and increasing PRO and soluble sugar content. This study enhances our understanding of the function of the MaDREB gene family, provides new insights into their regulatory role under abiotic stress, and lays a good foundation for improving drought and cold stress-tolerant banana verities.

The transcription factor MdERF023 negatively regulates salt tolerance by modulating ABA signaling and Na+/H+ transport in apple

KEY MESSAGE

MdERF023 is a transcription factor that can reduce salt tolerance by inhibiting ABA signaling and Na+/H+ homeostasis. Salt stress is one of the principal environmental stresses limiting the growth and productivity of apple (Malus × domestica). The APETALA2/ethylene response factor (AP2/ERF) family plays key roles in plant growth and various stress responses; however, the regulatory mechanism involved has not been fully elucidated. In the present study, we identified an AP2/ERF transcription factor (TF), MdERF023, which plays a negative role in apple salt tolerance. Stable overexpression of MdERF023 in apple plants and calli significantly decreased salt tolerance. Biochemical and molecular analyses revealed that MdERF023 directly binds to the promoter of MdMYB44-like, a positive modulator of ABA signaling-mediated salt tolerance, and suppresses its transcription. In addition, MdERF023 downregulated the transcription of MdSOS2 and MdAKT1, thereby reducing the Na+ expulsion, K+ absorption, and salt tolerance of apple plants. Taken together, these results suggest that MdERF023 reduces apple salt tolerance by inhibiting ABA signaling and ion transport, and that it could be used as a potential target for breeding new varieties of salt-tolerant apple plants via genetic engineering.

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.

Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the "sprout tumble" phenomenon because of high temperatures, resulting in a significant yield reduction. However, the molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat-response genes, microRNAs (miRNAs), and key miRNA-target pairs in P. ternata that differed between heat-stress and room-temperature conditions. Transcriptome analysis revealed extensive reprogramming of 4,960 genes across various categories, predominantly associated with cellular and metabolic processes, responses to stimuli, biological regulation, cell parts, organelles, membranes, and catalytic and binding activities. miRNAome sequencing identified 1,597 known/conserved miRNAs that were differentially expressed between the two test conditions. According to the analysis, genes and miRNAs associated with the regulation of transcription, DNA template, transcription factor activity, and sequence-specific DNA binding pathways may play a major role in the resistance to heat stress in P. ternata. Integrated analysis of the transcriptome and miRNAome expression data revealed 41 high-confidence miRNA-mRNA pairs, forming 25 modules. MYB-like proteins and calcium-responsive transcription coactivators may play an integral role in heat-stress resistance in P. ternata. Additionally, the candidate genes and miRNAs were subjected to quantitative real-time polymerase chain reaction to validate their expression patterns. These results offer a foundation for future studies exploring the mechanisms and critical genes involved in heat-stress resistance in P. ternata.

Transcriptome Analysis Reveals Key Genes Involved in Trichome Formation in Pepper (Capsicum annuum L.)

Trichomes are specialized organs located in the plant epidermis that play important defense roles against biotic and abiotic stresses. However, the mechanisms regulating the development of pepper epidermal trichomes and the related regulatory genes at the molecular level are not clear. Therefore, we performed transcriptome analyses of A114 (less trichome) and A115 (more trichome) to dig deeper into the genes involved in the regulatory mechanisms of epidermal trichome development in peppers. In this study, the epidermal trichome density of A115 was found to be higher by phenotypic observation and was highest in the leaves at the flowering stage. A total of 39,261 genes were quantified by RNA-Seq, including 11,939 genes not annotated in the previous genome analysis and 18,833 differentially expressed genes. Based on KEGG functional enrichment, it was found that DEGs were mainly concentrated in three pathways: plant-pathogen interaction, MAPK signaling pathway-plant, and plant hormone signal transduction. We further screened the DEGs associated with the development of epidermal trichomes in peppers, and the expression of the plant signaling genes GID1B-like (Capana03g003488) and PR-6 (Capana09g001847), the transcription factors MYB108 (Capana05g002225) and ABR1-like (Capana04g001261), and the plant resistance genes PGIP-like (Capana09g002077) and At5g49770 (Capana08g001721) in the DEGs were higher at A115 compared to A114, and were highly expressed in leaves at the flowering stage. In addition, based on the WGCNA results and the establishment of co-expression networks showed that the above genes were highly positively correlated with each other. The transcriptomic data and analysis of this study provide a basis for the study of the regulatory mechanisms of pepper epidermal trichomes.

Comparative Transcriptome Analysis Reveals Inhibitory Roles of Strigolactone in Axillary Bud Outgrowth in Ratoon Rice

Axillary bud outgrowth, a key factor in ratoon rice yield formation, is regulated by several phytohormone signals. The regulatory mechanism of key genes underlying ratoon buds in response to phytohormones in ratoon rice has been less reported. In this study, GR24 (a strigolactone analogue) was used to analyze the ratooning characteristics in rice cultivar Huanghuazhan (HHZ). Results show that the elongation of the axillary buds in the first seasonal rice was significantly inhibited and the ratoon rate was reduced at most by up to 40% with GR24 treatment. Compared with the control, a significant reduction in the content of auxin and cytokinin in the second bud from the upper spike could be detected after GR24 treatment, especially 3 days after treatment. Transcriptome analysis suggested that there were at least 742 and 2877 differentially expressed genes (DEGs) within 6 h of GR24 treatment and 12 h of GR24 treatment, respectively. Further bioinformatics analysis revealed that GR24 treatment had a significant effect on the homeostasis and signal transduction of cytokinin and auxin. It is noteworthy that the gene expression levels of OsCKX1, OsCKX2, OsGH3.6, and OsGH3.8, which are involved in cytokinin or auxin metabolism, were enhanced by the 12 h GR24 treatment. Taken overall, this study showed the gene regulatory network of auxin and cytokinin homeostasis to be regulated by strigolactone in the axillary bud outgrowth of ratoon rice, which highlights the importance of these biological pathways in the regulation of axillary bud outgrowth in ratoon rice and would provide theoretical support for the molecular breeding of ratoon rice.

Genome-Wide Identification and Transcriptional Analysis of AP2/ERF Gene Family in Pearl Millet (Pennisetum glaucum)

The apetala2/ethylene response factor (AP2/ERF) gene family plays a crucial role in regulating plant growth and development and responding to different abiotic stresses (e.g., drought, heat, cold, and salinity). However, the knowledge of the ERF family in pearl millet remains limited. Here, a total of 167 high-confidence PgERF genes are identified and divided into five subgroups based on gene-conserved structure and phylogenetic analysis. Forty-one pairs of segmental duplication are found using collinear analysis. Nucleotide substitution analysis reveals these duplicated pairs are under positive purification, indicating they are actively responding to natural selection. Comprehensive transcriptomic analysis reveals that PgERF genesare preferentially expressed in the imbibed seeds and stem (tilling stage) and respond to heat, drought, and salt stress. Prediction of the cis-regulatory element by the PlantCARE program indicates that PgERF genes are involved in responses to environmental stimuli. Using reverse transcription quantitative real-time PCR (RT-qPCR), expression profiles of eleven selected PgERF genes are monitored in various tissues and during different abiotic stresses. Transcript levels of each PgERF gene exhibit significant changes during stress treatments. Notably, the PgERF7 gene is the only candidate that can be induced by all adverse conditions. Furthermore, four PgERF genes (i.e., PgERF22, PgERF37, PgERF88, and PgERF155) are shown to be involved in the ABA-dependent signaling pathway. These results provide useful bioinformatic and transcriptional information for understanding the roles of the pearl millet ERF gene family in adaptation to climate change.

A Cerasus humilis transcription factor, ChDREB2C, enhances salt tolerance in transgenic Arabidopsis

DREB transcription factors play important roles in plant responses to various abiotic and biotic stresses. We conducted bioinformatics analysis of ChDREB2C, explored subcellular localization, transcription activation activity, and heterologous expression in Arabidopsis, and measured expression of related physiological indicators and genes under salt stress. A transcription factor of the DREB family was cloned and named ChDREB2C. ChDREB2C protein was localized in the nucleus, and its C-terminal domain exhibited transcriptional activation activity. ChDREB2C formed a homologous dimer in yeast. Arabidopsis plants overexpressing ChDREB2C were more tolerant to salt stress than WT plants, through increased scavenging capacity of ROS and accumulation of proline. Overexpression of ChDREB2C resulted in increased expression of AtSOS1, AtNHX1, AtRD29A, AtRD29B, AtKIN1, AtABA4, and AtABF2 genes. The interaction between ChABF2 (ABA response element binding factor 2) and ChDREB2C was verified using yeast two-hybrid and firefly luciferase assays. The results suggest that ChDREB2C could have a positive role in mediating the abiotic response.

Uncovering the transcriptional responses of tobacco (Nicotiana tabacum L.) roots to Ralstonia solanacearum infection: a comparative study of resistant and susceptible cultivars

BACKGROUND

Tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum is the most serious soil-borne disease of tobacco that significantly reduces crop yield. However, the limited availability of resistance in tobacco hinders breeding efforts for this disease.

RESULTS

In this study, we conducted hydroponic experiments for the root expression profiles of D101 (resistant) and Honghuadajinyuan (susceptible) cultivars in response to BW infection at 0 h, 6 h, 1 d, 3 d, and 7d to explore the defense mechanisms of BW resistance in tobacco. As a result, 20,711 and 16,663 (total: 23,568) differentially expressed genes (DEGs) were identified in the resistant and susceptible cultivars, respectively. In brief, at 6 h, 1 d, 3 d, and 7 d, the resistant cultivar showed upregulation of 1553, 1124, 2583, and 7512 genes, while the susceptible cultivar showed downregulation of 1213, 1295, 813, and 7735 genes. Similarly, across these time points, the resistant cultivar had downregulation of 1034, 749, 1686, and 11,086 genes, whereas the susceptible cultivar had upregulation of 1953, 1790, 2334, and 6380 genes. The resistant cultivar had more up-regulated genes at 3 d and 7 d than the susceptible cultivar, indicating that the resistant cultivar has a more robust defense response against the pathogen. The GO and KEGG enrichment analysis showed that these genes are involved in responses to oxidative stress, plant-pathogen interactions, cell walls, glutathione and phenylalanine metabolism, and plant hormone signal transduction. Among the DEGs, 239 potential candidate genes were detected, including 49 phenylpropane/flavonoids pathway-associated, 45 glutathione metabolic pathway-associated, 47 WRKY, 48 ERFs, eight ARFs, 26 pathogenesis-related genes (PRs), and 14 short-chain dehydrogenase/reductase genes. In addition, two highly expressed novel genes (MSTRG.61386-R1B-17 and MSTRG.61568) encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins were identified in both cultivars at 7 d.

CONCLUSIONS

This study revealed significant enrichment of DEGs in GO and KEGG terms linked to glutathione, flavonoids, and phenylpropane pathways, indicating the potential role of glutathione and flavonoids in early BW resistance in tobacco roots. These findings offer fundamental insight for further exploration of the genetic architecture and molecular mechanisms of BW resistance in tobacco and solanaceous plants at the molecular level.

PoWRKY71 is involved in Paeonia ostii resistance to drought stress by directly regulating light-harvesting chlorophyll a/b-binding 151 gene

Although the functions of WRKY transcription factors in drought resistance are well known, their regulatory mechanisms in response to drought by stabilising photosynthesis remain unclear. Here, a differentially expressed PoWRKY71 gene that was highly expressed in drought-treated Paeonia ostii leaves was identified through transcriptome analysis. PoWRKY71 positively responded to drought stress with significantly enhanced expression patterns and overexpressing PoWRKY71 in tobacco greatly improved plant tolerance to drought stress, whereas silencing PoWRKY71 in P. ostii resulted in a drought-intolerant phenotype. Furthermore, lower chlorophyll contents, photosynthesis, and inhibited expression of photosynthesis-related light-harvesting chlorophyll a/b-binding 151 (CAB151) gene were found in PoWRKY71-silenced P. ostii. Meanwhile, a homologous system indicated that drought treatment increased PoCAB151 promoter activity. Interactive assays revealed that PoWRKY71 directly bound on the W-box element of PoCAB151 promoter and activated its transcription. In addition, PoCAB151 overexpressing plants demonstrated increased drought tolerance, together with significantly higher chlorophyll contents and photosynthesis, whereas these indices were dramatically lower in PoCAB151-silenced P. ostii. The above results indicated that PoWRKY71 activated the expression of PoCAB151, thus stabilising photosynthesis via regulating chloroplast homeostasis and chlorophyll content in P. ostii under drought stress. This study reveals a novel drought-resistance mechanism in plants and provides a feasible strategy for improving plant drought resistance via stabilising photosynthesis.

Crosstalk and trade-offs: Plant responses to climate change-associated abiotic and biotic stresses

As sessile organisms, plants are constantly challenged by a dynamic growing environment. This includes fluctuations in temperature, water availability, light levels, and changes in atmospheric constituents such as carbon dioxide (CO2 ) and ozone (O3 ). In concert with changes in abiotic conditions, plants experience changes in biotic stress pressures, including plant pathogens and herbivores. Human-induced increases in atmospheric CO2 levels have led to alterations in plant growth environments that impact their productivity and nutritional quality. Additionally, it is predicted that climate change will alter the prevalence and virulence of plant pathogens, further challenging plant growth. A knowledge gap exists in the complex interplay between plant responses to biotic and abiotic stress conditions. Closing this gap is crucial for developing climate resilient crops in the future. Here, we briefly review the physiological responses of plants to elevated CO2 , temperature, tropospheric O3 , and drought conditions, as well as the interaction of these abiotic stress factors with plant pathogen pressure. Additionally, we describe the crosstalk and trade-offs involved in plant responses to both abiotic and biotic stress, and outline targets for future work to develop a more sustainable future food supply considering future climate change.

TaAP2-10, an AP2/ERF transcription factor, contributes to wheat resistance against stripe rust

The AP2/ERF TF (transcription factor) family is involved in regulating plant responses to various biotic and abiotic stresses. Nevertheless, understanding of the function of AP2/ERF TFs in wheat (Triticum aestivum L.) resistance against the obligate biotrophic stripe rust fungus (Puccinia striiformis f. sp tritici, Pst) remains limited. From a wheat-Pst incompatible interaction cDNA library, the transcript of TaAP2-10 was identified to be significantly induced during Pst infection. TaAP2-10, encodes an AP2 TF with two typical AP2-binding domains. There are three homologues of TaAP2-10 in the wheat genome, located on chromosome 6A, 6B and 6D. TaAP2-10 is localized in the nucleus of wheat protoplasts. A transactivation assay in yeast revealed that TaAP2-10 had transcriptional activation activity that was dependent on its C-terminal region. Quantitative real-time PCR (qRT-PCR) analyses verified that the expression of TaAP2-10 was specifically upregulated by avirulent Pst infection but not by virulent Pst, suggesting its role in wheat resistance to Pst. Furthermore, TaAP2-10 is also induced by abiotic stresses and hormone treatments, particularly under PEG4000 and abscisic acid (ABA) treatments, indicating its potential role in facilitating wheat adaptation to environmental stresses. Silencing TaAP2-10 by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) significantly reduced wheat resistance against Pst, resulting in a decreased reactive oxygen species (ROS) burst, and promoted Pst growth and development. These findings suggest that TaAP2-10, as a nuclear-localized transcription factor, positively regulates wheat resistance to Pst.

Comprehensive Transcriptome and Metabolome Analyses Reveal Primary Molecular Regulation Pathways Involved in Peanut under Water and Nitrogen Co-Limitation

The yield and quality of peanut (Arachis hypogaea L.), an oil crop planted worldwide, are often limited by drought stress (DS) and nitrogen (N) deficiency. To investigate the molecular mechanism by which peanut counteracts DS and N deficiency, we conducted comprehensive transcriptomic and metabolomic analyses of peanut leaves. Herein, 829 known differentially accumulated metabolites, 324 differentially expressed transcription factors, and 5294 differentially expressed genes (DEGs) were identified under different water and N conditions. The transcriptome analysis demonstrated that drought-related DEGs were predominantly expressed in "glycolysis/gluconeogenesis" and "glycerolipid metabolism", while N-deficiency-related DEGs were mainly expressed in starch and sucrose metabolism, as well as in the biosynthesis of amino acid pathways. The biosynthesis, transport, and catabolism of secondary metabolites accounted for a large proportion of the 1317 DEGs present in water and N co-limitation. Metabolomic analysis showed that the metabolic accumulation of these pathways was significantly dependent on the stress conditions. Additionally, the roles of metabolites and genes in these pathways, such as the biosynthesis of amino acids and phenylpropanoid biosynthesis under different stress conditions, were discussed. The results demonstrated that different genes, metabolic pathways, and metabolites were related to DS and N deficiency. Thus, this study elucidates the metabolic pathways and functional genes that can be used for the improvement of peanut resistance to abiotic stress.

An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life

The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.

ZmEREB57 regulates OPDA synthesis and enhances salt stress tolerance through two distinct signalling pathways in Zea mays

In plant, APETALA2/ethylene-responsive factor (AP2/ERF)-domain transcription factors are important in regulating abiotic stress tolerance. In this study, ZmEREB57 encoding a AP2/ERF transcription factor was identified and its function was investigated in maize. ZmEREB57 is a nuclear protein with transactivation activity induced by several abiotic stress types. Furthermore, two CRISPR/Cas9 knockout lines of ZmEREB57 showed enhanced sensitivity to saline conditions, whereas the overexpression of ZmEREB57 increased salt tolerance in maize and Arabidopsis. DNA affinity purification sequencing (DAP-Seq) analysis revealed that ZmEREB57 notably regulates target genes by binding to promoters containing an O-box-like motif (CCGGCC). ZmEREB57 directly binds to the promoter of ZmAOC2 involved in the synthesis of 12-oxo-phytodienoic acid (OPDA) and jasmonic acid (JA). Transcriptome analysis revealed that several genes involved in regulating stress and redox homeostasis showed differential expression patterns in OPDA- and JA-treated maize seedlings exposed to salt stress compared to those treated with salt stress alone. Analysis of mutants deficient in the biosynthesis of OPDA and JA revealed that OPDA functions as a signalling molecule in the salt response. Our results indicate that ZmEREB57 involves in salt tolerance by regulating OPDA and JA signalling and confirm early observations that OPDA signalling functions independently of JA signalling.

The DREB transcription factor, a biomacromolecule, responds to abiotic stress by regulating the expression of stress-related genes

Abiotic stress is a crucial factor that affects plant survival and growth and even leads to plant death in severe cases. Transcription factors can enhance the ability of plants to fight against various stresses by controlling the expression of downstream genes. The dehydration response element binding protein (DREB) is the most extensive subfamily of AP2/ERF transcription factors involved in abiotic stress. However, insufficient research on the signal network of DREB transcription factors has limited plant growth and reproduction. Furthermore, field planting of DREB transcription factors and their roles under multiple stress also require extensive research. Previous reports on DREB transcription factors have focused on the regulation of DREB expression and its roles in plant abiotic stress. In recent years, there has been new progress in DREB transcription factors. Here, the structure and classification, evolution and regulation, role in abiotic stress, and application in crops of DREB transcription factors were reviewed. And this paper highlighted the evolution of DREB1/CBF, as well as the regulation of DREB transcription factors under the participation of plant hormone signals and the roles of subgroups in abiotic stress. In the future, it will lay a solid foundation for further study of DREB transcription factors and pave the way for the cultivation of resistant plants.

Comprehensive analysis and expression profiles of the AP2/ERF gene family during spring bud break in tea plant (Camellia sinensis)

BACKGROUND

AP2/ERF transcription factors (AP2/ERFs) are important regulators of plant physiological and biochemical metabolism. Evidence suggests that AP2/ERFs may be involved in the regulation of bud break in woody perennials. Green tea is economically vital in China, and its production value is significantly affected by the time of spring bud break of tea plant. However, the relationship between AP2/ERFs in tea plant and spring bud break remains largely unknown.

RESULTS

A total of 178 AP2/ERF genes (CsAP2/ERFs) were identified in the genome of tea plant. Based on the phylogenetic analysis, these genes could be classified into five subfamilies. The analysis of gene duplication events demonstrated that whole genome duplication (WGD) or segmental duplication was the primary way of CsAP2/ERFs amplification. According to the result of the Ka/Ks value calculation, purification selection dominated the evolution of CsAP2/ERFs. Furthermore, gene composition and structure analyses of CsAP2/ERFs indicated that different subfamilies contained a variety of gene structures and conserved motifs, potentially resulting in functional differences among five subfamilies. The promoters of CsAP2/ERFs also contained various signal-sensing elements, such as abscisic acid responsive elements, light responsive elements and low temperature responsive elements. The evidence presented here offers a theoretical foundation for the diverse functions of CsAP2/ERFs. Additionally, the expressions of CsAP2/ERFs during spring bud break of tea plant were analyzed by RNA-seq and grouped into clusters A-F according to their expression patterns. The gene expression changes in clusters A and B were more synchronized with the spring bud break of tea plant. Moreover, several potential correlation genes, such as D-type cyclin genes, were screened out through weighted correlation network analysis (WGCNA). Temperature and light treatment experiments individually identified nine candidate CsAP2/ERFs that may be related to the spring bud break of tea plant.

CONCLUSIONS

This study provides new evidence for role of the CsAP2/ERFs in the spring bud break of tea plant, establishes a theoretical foundation for analyzing the molecular mechanism of the spring bud break of tea plant, and contributes to the improvement of tea cultivars.

Regulatory roles of miRNAs associated with the aging pathway in tree vegetative phase changes

The transition from the vegetative juvenile phase to the adult phase is a crucial event in the life cycle of flowering plants, with flowering being the most important milestone. While the regulatory pathways of flowering have been well established in model plants such as Arabidopsis and a few crops, the flowering regulation pathways in perennial forest trees remain poorly understood. This paper summarizes the regulation of flowering time by miR156 and miR172, which are the main members of the aging pathway, and also presents new information on the role of miR159 and miR169. These two microRNAs interact with miR156 and miR172 to jointly regulate flowering time in forest trees. Overall, this review sheds light on the complex regulatory mechanisms underlying flowering time in forest trees and provides insights into potential targets for manipulating the flowering time of these economically and ecologically important species.

Genome-Wide Analysis of DREB Family Genes and Characterization of Cold Stress Responses in the Woody Plant Prunus nana

Dehydration response element binding factor (DREB) is a family of plant-specific transcription factors, whose members participate in the regulation of plant responses to various abiotic stresses. Prunus nana, also known as the wild almond, is a member of the Rosaceae family that is rare and found to grow in the wild in China. These wild almond trees are found in hilly regions in northern Xinjiang, and exhibit greater drought and cold stress resistance than cultivated almond varieties. However, the response of P. nana DREBs (PnaDREBs) under low temperature stress is still unclear. In this study, 46 DREB genes were identified in the wild almond genome, with this number being slightly lower than that in the sweet almond (Prunus dulcis cultivar ‘Nonpareil’). These DREB genes in wild almond were separated into two classes. All PnaDREB genes were located on six chromosomes. PnaDREB proteins that were classified in the same groups contained specific shared motifs, and promoter analyses revealed that PnaDREB genes harbored a range of stress-responsive elements associated with drought, low-temperature stress, light responsivity, and hormone-responsive cis-regulatory elements within their promoter regions. MicroRNA target site prediction analyses also suggested that 79 miRNAs may regulate the expression of 40 of these PnaDREB genes, with PnaDREB2. To examine if these identified PnaDREB genes responded to low temperature stress, 15 of these genes were selected including seven homologous to Arabidopsis C-repeat binding factor (CBFs), and their expression was assessed following incubation for 2 h at 25 °C, 5 °C, 0 °C, −5 °C, or −10 °C. In summary, this analysis provides an overview of the P. nana PnaDREB gene family and provides a foundation for further studies of the ability of different PnaDREB genes to regulate cold stress responses in almond plants.

Heterologous VvDREB2c Expression Improves Heat Tolerance in Arabidopsis by Inducing Photoprotective Responses

Extreme temperatures limit grape production and sustainability. Dehydration-responsive element-binding (DREB) transcription factors affect plant responses to temperature related stresses. Therefore, we investigated the role of VvDREB2c, a DREB-coding gene, found in grapes (Vitis vinifera L.). Protein characterization revealed that VvDREB2c is localized to the nucleus and that its AP2/ERF domain contains three β-sheets and one α-helix sheet. Analysis of the VvDREB2c promoter region revealed the presence of light-, hormone-, and stress-related cis-acting elements. Furthermore, we observed that the heterologous expression of VvDREB2c in Arabidopsis improved growth, drought tolerance, and heat tolerance. Furthermore, it improved the leaf quantum yield of regulated energy dissipation [Y(NPQ)], elevated the activities of RuBisCO, and phosphoenolpyruvate carboxylase and reduced the quantum yield of non-regulated energy dissipation [Y(NO)] in plants exposed to high temperatures. VvDREB2c-overexpressing lines also specifically upregulated several photosynthesis-related genes (CSD2, HSP21, and MYB102). In addition, VvDREB2c-overexpressing lines reduced light damage and enhanced photoprotective ability by dissipating excess light energy and converting it into heat, which eventually improves tolerance to high temperature. The contents of abscisic acid, jasmonic acid, and salicylic acid and differentially expressed genes (DEGs) in the mitogen-activated protein kinase (MAPK) signaling pathway were affected by heat stress in VvDREB2c-overexpressing lines, which indicated that VvDREB2c positively regulates heat tolerance via a hormonal pathway in Arabidopsis. VvDREB2c promotes heat tolerance in Arabidopsis by exerting effects on photosynthesis, hormones, and growth conditions. This study may provide useful insights into the enrichment of the heat-tolerance pathways in plants.

GmDof41 regulated by the DREB1-type protein improves drought and salt tolerance by regulating the DREB2-type protein in soybean

Despite their essential and multiple roles in biological processes, the molecular mechanism of Dof transcription factors (TFs) for responding to abiotic stresses is rarely reported in plants. We identified a soybean Dof gene GmDof41 which was involved in the responses to drought, salt, and exogenous ABA stresses. Overexpression of GmDof41 in soybean transgenic hairy roots attenuated H2O2 accumulation and regulated proline homeostasis, resulting in the drought and salt tolerance. Yeast one-hybrid and electrophoretic mobility shift assay (EMSA) illustrated that GmDof41 was regulated by the DREB1-type protein GmDREB1B;1 that could improve drought and salt tolerance in plants. Further studies illustrated GmDof41 can directly bind to the promoter of GmDREB2A which encodes a DREB2-type protein and affects abiotic stress tolerance in plants. Collectively, our results suggested that GmDof41 positively regulated drought and salt tolerance by correlating with GmDREB1B;1 and GmDREB2A. This study provides an important basis for further exploring the abiotic stress-tolerance mechanism of Dof TFs in soybean.

Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia)

BACKGROUND

'Whangkeumbae' (Pyrus pyrifolia) is a typical climacteric fruit variety of sand pear with excellent taste. However, the rapid postharvest ethylene production limits the shelf life of 'Whangkeumbae' fruit. AP2/ERF superfamily is a large family of transcription factors involved in plant growth and development, including fruit ripening and senescence through the ethylene signaling pathway. The numbers and functions of AP2/ERF superfamily members in sand pear remain largely unknown.

RESULTS

In this study, a total of 234 AP2/ERF family members were identified through the transcriptome of Pyrus pyrifolia 'Whangkeumbae' (17 genes) and Pyrus pyrifolia genome (223 genes) analyses. Six genes (Accession: EVM0023062.1, EVM0034833.1, EVM0027049.1, EVM0034047.1, EVM0028755.1, EVM0015862.1) identified via genome analysis shared 100% identity with PpERF14-L, PpERF5-L, PpERF3a, PpERF3, PpERF017 and PpERF098, respectively, which were identified from transcriptome sequencing. Further, the AP2/ERF superfamily members were divided into AP2, ERF, and RAV subfamilies, each comprising 38, 188, and 8 members, respectively. Tissue-specific expression analysis showed that PpERF061, PpERF113, PpERF51L-B, PpERF5-L, and PpERF017 were predominantly expressed in fruits than in other tissues. Additionally, PpERF5-L and PpERF017 showed higher expressions at the early stage of fruit development. While, PpERF51B-L exhibited higher expression during the fruit ripening stage. Besides, PpERF061 and PpERF113 had pronounced expressions during fruit senescence.

CONCLUSION

These results indicate that PpERF061, PpERF113, PpERF51L-B, PpERF5-L, and PpERF017 could play crucial roles in sand pear fruit development, ripening, and senescence. Overall, this study provides valuable information for further functional analysis of the AP2/ERF genes during fruit ripening and senescence in sand pear.

Overexpression of SmMYC2 enhances salt resistance in Arabidopsis thaliana and Salvia miltiorrhiza hairy roots

Soil salinity significantly affects both Salvia miltiorrhiza growth and development as well as seed germination throughout field cultivation and production. The basic helix-loop-helix (bHLH) transcription factor (TF) MYC2 contributes significantly to plant stress resistance as a key regulator of the jasmonic acid signaling pathway. In transgenic S. miltiorrhiza hairy roots, SmMYC2 has been shown to promote the accumulation of tanshinone and salvianolic acid, but its role in S. miltiorrhiza of resistance to abiotic stress is unclear. Herein, we found methyl jasmonate (MeJA), NaCl, and PEG treatment all significantly increased SmMYC2 expression. In response to salt stress, SmMYC2 overexpression in yeast increased its rate of growth. Additionally, overexpression of SmMYC2 transgenic Arabidopsis thaliana and S. miltiorrhiza hairy root showed that it might improve salt resistance in transgenic plant. In particular, compared to WT, overexpression of SmMYC2 transgenic Arabidopsis had higher levels of three antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), proline (Pro) content, and ABA-dependent and ABA-independent genes expression. They also had lower levels of malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation. What's more, overexpression of SmMYC2 increases the expression of flavonoid synthesis genes and the accumulation of related components in Arabidopsis. These findings imply that SmMYC2 functions as a positive regulator that regulates plant tolerance to salt through ABA-dependent and independent signaling pathways.

PpERF1b-like enhances lignin synthesis in pear (Pyrus pyrifolia) 'hard-end' fruit

The hard-end is a disorder of pear fruit, however, the mechanisms underlying its development remain unknown. In this study, we found that the hard-end fruit contained a higher transcript abundance level of ethylene-response factor 1b-like (PpERF1b-like) and released more ethylene compared to normal pear. In the ethephon treated normal fruit, flesh tissues accumulated more lignin together with elevated expression of PpERF1b-like. Overexpressing PpERF1b-like transiently in fruit and stably in callus increased lignin accumulation and the expression of lignin biosynthesis genes; the opposite results were observed in fruit showing repressed expression of PpERF1b-like. These results confirmed the role of PpERF1b-like in promoting hard-end formation through promoting lignin synthesis. This study provided valuable information for further clarifying the regulation of hard-end formation in pear.

Pinpointing genomic loci for drought-induced proline and hydrogen peroxide accumulation in bread wheat under field conditions

BACKGROUND

Proline (Pro) and hydrogen peroxide (H₂O₂) play a critical role in plants during drought adaptation. Genetic mapping for drought-induced Pro and H₂O₂ production under field conditions is very limited in crop plants since their phenotyping with large populations is labor-intensive. A genome-wide association study (GWAS) of a diversity panel comprised of 184 bread wheat cultivars grown in natural field (control) and rain-out shelter (drought) environments was performed to identify candidate loci and genes regulating Pro and H₂O₂ accumulation induced by drought.

RESULTS

The GWAS identified top significant marker-trait associations (MTAs) on 1A and 2A chromosomes, respectively for Pro and H₂O₂ in response to drought. Similarly, MTAs for stress tolerance index (STI) of Pro and H₂O₂ were identified on 5B and 1B chromosomes, respectively. Total 143 significant MTAs were identified including 36 and 71 were linked to drought and 2 and 34 were linked to STI for Pro and H₂O_2, respectively. Next, linkage disequilibrium analysis revealed minor alleles of significant single-markers and haplotypes were associated with higher Pro and H₂O₂ accumulation under drought. Several putative candidate genes for Pro and H₂O₂ content encode proteins with kinase, transporter or protein-binding activities.

CONCLUSIONS

The identified genetic factors associated with Pro and H₂O₂ biosynthesis underlying drought adaptation lay a fundamental basis for functional studies and future marker-assisted breeding programs.

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

AP2/ERF transcription factors (TFs) are one of the largest superfamilies in plants, and play vital roles in growth and response to biotic/abiotic stresses. Although the AP2/ERF family has been extensively characterized in many species, very little is known about this family in ramie (Boehmeria nivea L.). In this study, 138 AP2/ERF TFs were identified from the ramie genome and were grouped into five subfamilies, including the AP2 (19), RAV (5), Soloist (1), ERF (77), and DREB (36). Unique motifs were found in the DREB/ERF subfamily members, implying significance to the AP2/ERF TF functions in these evolutionary branches. Segmental duplication events were found to play predominant roles in the BnAP2/ERF TF family expansion. Light-, stress-, and phytohormone-responsive elements were identified in the promoter region of BnAP2/ERF genes, with abscisic acid response elements (ABRE), methyl jasmonate response elements, and the dehydration response element (DRE) being dominant. The integrated transcriptome and quantitative real-time PCR (qPCR) revealed 12 key BnAP2/ERF genes positively responding to waterlogging. Five of the genes are also involved in ramet development, with two (BnERF-30 and BnERF-32) further showing multifunctional roles. The protein interaction prediction analysis further verified their crosstalk mechanism in coordinating waterlogging resistance and ramet development. Our study provides new insights into the presence of AP2/ERF TFs in ramie, and provides candidate AP2/ERF TFs for further studies on breeding varieties with coupling between water stress tolerance and high yield.

Flooding and herbivory: the effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties

BACKGROUND

In nature and in cultivated fields, plants encounter multiple stress factors. Nonetheless, our understanding of how plants actively respond to combinatorial stress remains limited. Among the least studied stress combination is that of flooding and herbivory, despite the growing importance of these stressors in the context of climate change. We investigated plant chemistry and gene expression changes in two heirloom tomato varieties: Cherokee Purple (CP) and Striped German (SG) in response to flooding, herbivory by Spodoptera exigua, and their combination.

RESULTS

Volatile organic compounds (VOCs) identified in tomato plants subjected to flooding and/or herbivory included several mono- and sesquiterpenes. Flooding was the main factor altering VOCs emission rates, and impacting plant biomass accumulation, while different varieties had quantitative differences in their VOC emissions. At the gene expression levels, there were 335 differentially expressed genes between the two tomato plant varieties, these included genes encoding for phenylalanine ammonia-lyase (PAL), cinnamoyl-CoA-reductase-like, and phytoene synthase (Psy1). Flooding and variety effects together influenced abscisic acid (ABA) signaling genes with the SG variety showing higher levels of ABA production and ABA-dependent signaling upon flooding. Flooding downregulated genes associated with cytokinin catabolism and general defense response and upregulated genes associated with ethylene biosynthesis, anthocyanin biosynthesis, and gibberellin biosynthesis. Combining flooding and herbivory induced the upregulation of genes including chalcone synthase (CHS), PAL, and genes encoding BAHD acyltransferase and UDP-glucose iridoid glucosyltransferase-like genes in one of the tomato varieties (CP) and a disproportionate number of heat-shock proteins in SG. Only the SG variety had measurable changes in gene expression due to herbivory alone, upregulating zeatin, and O-glucosyltransferase and thioredoxin among others.

CONCLUSION

Our results suggest that both heirloom tomato plant varieties differ in their production of secondary metabolites including phenylpropanoids and terpenoids and their regulation and activation of ABA signaling upon stress associated with flooding. Herbivory and flooding together had interacting effects that were evident at the level of plant chemistry (VOCs production), gene expression and biomass markers. Results from our study highlight the complex nature of plant responses to combinatorial stresses and point at specific genes and pathways that are affected by flooding and herbivory combined.

Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress

Simple Summary

The ethylene-responsive element (AP2/ERF) is one of the key and conserved transcription factors (TFs) in plants, and it plays a crucial role in regulating plant growth, development, and stress response. The cultivated almond in Xinjiang is often affected by short-term ultralow temperature freezing stress during the winter dormancy period, resulting in the death of large-scale almond plants. In this study, we conducted the first genome-wide analysis of the PdAP2/ERF family in almond, including protein physicochemical properties, phylogenetic relationships, motif types, gene structures, gene replication types, collinearity relationships, and cis-element types in promoter regions. We further analyzed the expression patterns of the PdAP2/ERF gene in different tissues of almond and under freezing stress at different temperatures in annual dormant branches using transcriptome data. In addition, we also analyzed the expression levels of 13 PdAP2/ERF genes in four tissues of almond and in annual dormant branches treated with freezing stress at different temperatures using fluorescence quantitative technology. This study laid the foundation for further exploring the function of the PdAP2/ERF gene in almond.

Abstract

The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene family in almond (Prunus dulcis). In this study, a total of 136 PdAP2/ERF genes were identified from the almond genome, and their protein physicochemical properties were analyzed. The PdAP2/ERF members were divided into five subgroups: AP2, RAV, ERF, DREB, and Soloist. The PdAP2/ERF members in each subgroup had conserved motif types and exon/intron numbers. PdAP2/ERFS members are distributed on eight chromosomes, with 22 pairs of segmental duplications and 28 pairs of tandem duplications. We further explored the colinear relationship between almond and Arabidopsis thaliana, Oryza sativa, Malus domestica, and Prunus persicaAP2/ERF genes and their evolution. The results of cis-acting elements showed that PdAP2/ERF members are widely involved in various processes, such as growth and development, hormone regulation, and stress response. The results based on transcriptome expression patterns showed that PdAP2/ERF genes had significant tissue-specific expression characteristics and were involved in the response of annual dormant branches of almond to low-temperature freezing stress. In addition, the fluorescence quantitative relative expression results of 13 representative PdAP2/ERF genes in four tissues of ‘Wanfeng’ almond and under six low-temperature freezing treatments of annual dormant branches were consistent with the transcriptome results. It is worth noting that the fluorescence quantitative expression level showed that the PdERF24 gene was extremely significant at −30 °C, suggesting that this gene may play an important role in the response of almond dormancy to ultralow temperature freezing stress. Finally, we identified 7424 and 6971 target genes based on AP2 and ERF/DREB DNA-binding sites, respectively. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on PdAP2/ERF genes, including 13 PdAP2/ERF genes, and performed fluorescence quantitative analysis of annual dormant shoots under different low-temperature freezing stress treatments to understand the tolerance of almond dormancy to freezing stress and suggest future improvements.

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 moss-specific transcription factor PpERF24 positively modulates immunity against fungal pathogens in Physcomitrium patens

APETALA2/ethylene response factors (AP2/ERFs) transcription factors (TFs) have greatly expanded in land plants compared to algae. In angiosperms, AP2/ERFs play important regulatory functions in plant defenses against pathogens and abiotic stress by controlling the expression of target genes. In the moss Physcomitrium patens, a high number of members of the ERF family are induced during pathogen infection, suggesting that they are important regulators in bryophyte immunity. In the current study, we analyzed a P. patens pathogen-inducible ERF family member designated as PpERF24. Orthologs of PpERF24 were only found in other mosses, while they were absent in the bryophytes Marchantia polymorpha and Anthoceros agrestis, the vascular plant Selaginella moellendorffii, and angiosperms. We show that PpERF24 belongs to a moss-specific clade with distinctive amino acids features in the AP2 domain that binds to the DNA. Interestingly, all P. patens members of the PpERF24 subclade are induced by fungal pathogens. The function of PpERF24 during plant immunity was assessed by an overexpression approach and transcriptomic analysis. Overexpressing lines showed increased defenses to infection by the fungal pathogens Botrytis cinerea and Colletotrichum gloeosporioides evidenced by reduced cellular damage and fungal biomass compared to wild-type plants. Transcriptomic and RT-qPCR analysis revealed that PpERF24 positively regulates the expression levels of defense genes involved in transcriptional regulation, phenylpropanoid and jasmonate pathways, oxidative burst and pathogenesis-related (PR) genes. These findings give novel insights into potential mechanism by which PpERF24 increases plant defenses against several pathogens by regulating important players in plant immunity.

Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes

Flooding is a frequent environmental stress that reduces soybean (Glycine max) growth and grain yield in many producing areas in the world, such as, e.g., in the United States, Southeast Asia and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas by rotating with rice (Oryza sativa), which provides numerous technical, economic and environmental benefits. Given these realities, this work aimed to characterize physiological responses, identify genes differentially expressed under flooding stress in Brazilian soybean genotypes with contrasting flooding tolerance, and select SNPs with potential use for marker-assisted selection. Soybean cultivars TECIRGA 6070 (flooding tolerant) and FUNDACEP 62 (flooding sensitive) were grown up to the V6 growth stage and then flooding stress was imposed. Total RNA was extracted from leaves 24 h after the stress was imposed and sequenced. In total, 421 induced and 291 repressed genes were identified in both genotypes. TECIRGA 6070 presented 284 and 460 genes up- and down-regulated, respectively, under flooding conditions. Of those, 100 and 148 genes were exclusively up- and down-regulated, respectively, in the tolerant genotype. Based on the RNA sequencing data, SNPs in differentially expressed genes in response to flooding stress were identified. Finally, 38 SNPs, located in genes with functional annotation for response to abiotic stresses, were found in TECIRGA 6070 and absent in FUNDACEP 62. To validate them, 22 SNPs were selected for designing KASP assays that were used to genotype a panel of 11 contrasting genotypes with known phenotypes. In addition, the phenotypic and grain yield impacts were analyzed in four field experiments using a panel of 166 Brazilian soybean genotypes. Five SNPs possibly related to flooding tolerance in Brazilian soybean genotypes were identified. The information generated from this research will be useful to develop soybean genotypes adapted to poorly drained soils or areas subject to flooding.

RNA-seq reveals transcriptional differences in anthocyanin and vitamin biosynthetic pathways between black and white rice

Anthocyanins and vitamins in black rice are the micronutrients vital to human health, both of which predominantly accumulate in the bran fraction. Some studies have demonstrated that black rice contains more vitamins compared with common white rice, indicating potential association between anthocyanin and vitamin accumulation. In this study, transcriptomes of pericarps collected from 27 black rice accessions and 49 white rice accessions at 10 days after flowering (DAF) were sequenced and analyzed. We identified 830 differentially expressed genes (DEGs) including 58 transcription factors (TFs) between black and white rice. Among 58 differentially expressed transcription factors, OsTTG1 was confirmed to be the one and only WD40 repeat protein regulating anthocyanin biosynthesis in the pericarp. Moreover, we identified 53 differentially expressed synthetic-related genes among 42 main synthesis enzymes in the biosynthesis pathway of seven vitamins including β-carotene, vitamin B1, vitamin B2, vitamin B5, vitamin B7, vitamin B9 and vitamin E. Collectively, our results provide valuable insights into the molecular mechanism of biosynthesis of anthocyanins and vitamins and the potential effect of anthocyanin biosynthesis on vitamin biosynthesis in black rice.