Cultivated grapevine (Vitis) is a highly valued horticultural crop, and cold stress affects its growth and productivity. Wild Amur grape (Vitis amurensis) PAT1 (Phytochrome A signal transduction 1, VaPAT1) is induced by low temperature, and ectopic expression of VaPAT1 enhances cold tolerance in Arabidopsis (Arabidopsis thaliana). However, little is known about the molecular mechanism of VaPAT1 during the cold stress response in grapevine. Here, we confirmed the overexpression of VaPAT1 in transformed grape calli enhanced cold tolerance. Yeast two-hybrid and bimolecular fluorescence complementation assays highlighted an interaction between VaPAT1 with INDETERMINATE-DOMAIN 3 (VaIDD3). A role of VaIDD3 in cold tolerance was also indicated. Transcriptome analysis revealed VaPAT1 and VaIDD3 overexpression and cold treatment coordinately modulate the expression of stress-related genes including lipoxygenase 3 (LOX3), a gene encoding a key jasmonate biosynthesis enzyme. Co-expression network analysis indicated LOX3 might be a downstream target of VaPAT1. Both electrophoretic mobility shift and dual luciferase reporter assays showed the VaPAT1-IDD3 complex binds to the IDD-box (AGACAAA) in the VaLOX3 promoter to activate its expression. Overexpression of both VaPAT1 and VaIDD3 increased the transcription of VaLOX3 and JA levels in transgenic grape calli. Conversely, VaPAT1-SRDX (dominant repression) and CRISPR/Cas9-mediated mutagenesis of PAT1-ED causing the loss of the C-terminus in grape calli dramatically prohibited the accumulation of VaLOX3 and JA levels during cold treatment. Together, these findings point to a pivotal role of VaPAT1 in the cold stress response in grape by regulating JA biosynthesis.

Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. Nine TFs, including CBF4, RAV1 and ERF104, were identified after cold treatment. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) analysis revealed that these TFs may regulate cold response through different pathways. As a prime candidate TF, overexpression of VaRAV1 in grape cells improved its cold tolerance. The transgenic cells exhibited low electrolyte leakage and malondialdehyde content and high peroxidase activity. Moreover, the TF gene TCP8 and a gene involving in homogalacturonan biosynthesis were found to be regulated by VaRAV1, suggesting that the contribution of VaRAV1 to cold tolerance may be achieved by enhancing the stability of cell membrane and regulating the expression of target genes involved in plant cell wall composition. Our work provides novel insights into plant response to cold stress and demonstrates the utility of ATAC-seq and RNA-seq for the rapid identification of TFs in response to cold stress in grapevine. VaRAV1 may play an important role in adaption to cold stress.

DNA-binding with one finger (Dof) proteins comprise a large family that play central roles in stress tolerance by regulating the expression of stress-responsive genes via the DOFCORE element or by interacting with other regulatory proteins. Although the Dof TF has been identified in a variety of species, its systemic analysis in potato (Solanum tuberosum L.) is lacking and its potential role in abiotic stress responses remains unclear. A total of 36 potential Dof genes in potato were examined at the genomic and transcriptomic levels in this work. Five phylogenetic groups can be formed from these 36 Dof proteins. An analysis of cis-acting elements revealed the potential roles of Dofs in potato development, including under numerous abiotic stress conditions. The cycling Dof factors (CDFs) might be the initial step in the abiotic stress response signaling cascade. In potato, five CDFs (StCDF1/StDof19, StCDF2/StDof4, StCDF3/StDof11, StCDF4/StDof24, and StCDF5/StDof15) were identified, which are homologs of Arabidopsis CDFs. The results revealed that these genes were engaged in a variety of abiotic reactions. Moreover, an expression analysis of StDof genes in two potato cultivars (‘Long10′ (drought tolerant) and ‘DXY’ (drought susceptible)) of contrasting tolerances under drought stress was carried out. Further, a regulatory network mediated by lncRNA and its target Dofs was established. The present study provides fundamental knowledge for further investigation of the roles of Dofs in the adaptation of potato to drought stress, aiming to provide insights into a viable strategy for crop improvement and stress-resistance breeding.

Coordinated transcriptional regulation of stress-responsive genes orchestrated by a complex network of transcription factors (TFs) and the reprogramming of metabolism ensure a plant’s continued growth and survival under adverse environmental conditions (e.g., abiotic stress). DNA-binding with one finger (Dof) proteins, a group of plant-specific TF, were identified as one of several key components of the transcriptional regulatory network involved in abiotic stress responses. In many plant species, Dofs are often activated in response to a wide range of adverse environmental conditions. Dofs play central roles in stress tolerance by regulating the expression of stress-responsive genes via the DOFCORE element or by interacting with other regulatory proteins. Moreover, Dofs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid, jasmonate, SA and redox signaling in response to many abiotic stresses. Taken together, we highlight a unique role of Dofs in hormone and stress signaling that integrates plant response to adverse environmental conditions with different aspects of plant growth and development.

Revealed 12, 6, and 6 BRX candidate genes in Gossypium hirsutum, G. raimondii and G. arboreum, respectively (Wei et al., 2024). Chromosomal localization and collinearity analysis suggest that segmental duplications were the primary driver of BRX gene amplification. Silencing of abioticstress responsive GhBRX.1, GhBRX.2, and GhBRXL4.3 further confirmed their pivotal roles in plant tolerance to salt and low-temperature stress, extending their function beyond root and shoot growth (Beuchat et al., 2010).Plant-specific TIFY transcription factors (TFs), characterized by a conserved TIFY domain, are known to regulate growth, development, and stress tolerance (Vanholme et al., 2007). In this issue, Wang et al. identified 16 TIFY plant transcription family candidate genes dispersed across seven subgroups in pepper (Capsicum annuum L.). In particular, CaTIFY7 and CaTIFY10b were highly induced in leaves during cold stress. Knockdown of CaTIFY7 and CaTIFY10b compromised cold tolerance, while their overexpression enhanced it, by influencing many cold-responsive and reactive oxygen species (ROS)-related genes (Wang et al., 2023).Ding et al investigated the impact of five physiologically relevant day/night temperature regimes in two thermotolerant and thermosensitive genotypes (Ding et al., 2024). A comprehensive evaluation of physiological, biochemical, and genetic analyses revealed that 35/27°C (T4) was the optimal regime for growth and yield in their study system. At this temperature, plants showed enhanced photosynthesis, antioxidant activity, and upregulation of key heat stress-responsive genes.Singh et al. ( 2024) performed a multi-tissue comparative transcriptomic analysis and revealed distinct genotype (tolerant vs sensitive)-and tissue (root vs leaf)-specific heat-responsive expression. Enrichment of heat shock proteins (HSPs), ROS scavenging, diverse TF families, and secondary metabolism pathways were observed. Interestingly, foxtail millet shared a high degree of collinearity with pearl millet in specific heat-responsive HSP and TF genes, compared to other cereal grains (Singh et al. 2024).Fábián et al. used cutting-edge histochemical and transcriptomic methods to compare the responses of heat-tolerant and heat-sensitive wheat cultivars to heat stress during male meiosis. Their study revealed pivotal structural and temporal alterations of wheat male meiocytes and tapetal cells and their transcriptional responses triggered by meiosis-timed heat stress. Notably, the heattolerant cultivar maintained cytoskeletal integrity and upregulated genes involved in stress response and meiosis, whereas the heat-sensitive cultivar displayed cytoskeletal disruption, impaired meiotic division, and aberrant tapetum development (Fábián et al., 2024).Growth-regulating factors (GRFs) are a plant-specific TF family with diverse roles including regulation of plant growth under stress conditions (Omidbakhshfard et al., 2015). In this issue, 12 candidate GRF genes were identified in potatoes (Cui et al., 2024) A systematic analysis of StGRF promoter regions identified numerous cis-acting elements associated with plant growth, development, abiotic stress, and hormone responses. Transcriptomic data supported the tissuespecific expression (e.g. stamens, roots, and young tubers) and differential expression of StGRFs under abiotic/biotic stress (e.g. heat and Phytophthora infestans infection) and hormone treatment.In plants, mitogen-activated protein kinase (MAPK) modules (MAPKKK-MAPKK-MAPK) are activated by various environmental cues, including heat and cold stress, triggering a cascade of cellular signaling events (Bigeard and Hirt, 2018;Manna et al., 2023) In this special topic, Zhu et al. (2023b); Zhu et al. (2024b) screened MAPK and MAPKK gene expression in potato (Solanum tuberosum) plants cultivated under mild (30°C) and/or acute (35°C) heat stress conditions, revealing that StMAPK1 and StMAPKK5 exhibited highly induced and sustained expression profiles. Overexpression of StMAPK1 modified photosynthesis and preserves membrane stability in response to heat stress by inducing the expression of heat stress genes (StHSP90, StHSP70, StHSP20, and StHSFA3) and regulating multiple redox balance and turgor maintenance pathways. Similarly, StMAPKK5 overexpression/silencing significantly affected both morphological (plant weight/height) and physiological (photosynthesis, transpiration) traits under heat stress by modulating various stress-responsive and antioxidant enzyme genes and associated biochemical defenses.Plant GATA (TFs) regulate diverse developmental processes and organ development (e.g. photomorphogenesis, chlorophyll biosynthesis, stomata formation), however, their role in abiotic stress remains relatively unexplored in plants (Schwechheimer et al., 2022). Zhu et al. (2023a) screened over 50 potato GATA transcription factor (TF) genes for heat stress response and found that StGATA2 was among the few exhibiting strong and prolonged induction. A deeper understanding of autophagy-related genes (ATG) in potatoes were also gained in this special issue (Zhu et al., 2024a). A systematic analysis of phylogenetic relationships, chromosome distribution, gene structure, interspecific collinearity, and organ-(e.g. leaf, flower, stem, root, stolon, petiole, and tuber) and stress-(i.e. heat) responsive expression was performed on six putative ATG18 subfamily members identified in the potato genome. StATG18a emerged to be highly induced by heat stress in several organs. StGATA2and StATG18a-overexpression also elicited comparable phenotypic, biochemical, and genetic responses to heat stress atypical to transgenic potato lines overexpressing StMAPK1 and StMAPKK5 (Zhu et al., 2023a;Zhu et al., 2024a) .