Biotic Stress Responses Research Articles

Identification and Characterization of VDAC Family in Maize.

The voltage-dependent anion channel (VDAC) is the most abundant protein in the outer mitochondrial membrane (OMM) of all eukaryotes, having an important role in the communication between mitochondria and cytosol. The plant VDAC family consists of a wide variety of members that may participate in cell responses to several environmental stresses. However, there is no experimental information about the members comprising the maize VDAC (ZmVDAC) family. In this study, the ZmVDAC family was identified, and described, and its gene transcription profile was explored during the first six days of germination and under different biotic stress stimuli. Nine members were proposed as bona fide VDAC genes with a high potential to code functional VDAC proteins. Each member of the ZmVDAC family was characterized in silico, and nomenclature was proposed according to phylogenetic relationships. Transcript levels in coleoptiles showed a different pattern of expression for each ZmVDAC gene, suggesting specific roles for each one during seedling development. This expression profile changed under Fusarium verticillioides infection and salicylic acid, methyl jasmonate, and gibberellic acid treatments, suggesting no redundancy for the nine ZmVDAC genes and, thus, probably specific and diverse functions according to plant needs and environmental conditions. Nevertheless, ZmVDAC4b was significantly upregulated upon biotic stress signals, suggesting this gene's potential role during the biotic stress response.

DNA methylation role in subgenome expression dominance of Juglans regia and its wild relative J. mandshurica.

Subgenome expression dominance plays a crucial role in the environmental adaptation of polyploids. However, the epigenetic molecular mechanism underlying this process has not been thoroughly investigated, particularly in perennial woody plants. Persian walnut (Juglans regia) and its wild relative, Manchurian walnut (Juglans mandshurica), are woody plants of great economic importance and are both paleopolyploids that have undergone whole-genome duplication events. In this study, we explored the characteristics of subgenome expression dominance in these 2 Juglans species and examined its epigenetic basis. We divided their genomes into dominant subgenome (DS) and submissive subgenome (SS) and found that the DS-specific genes might play critical roles in biotic stress response or pathogen defense. We comprehensively elucidated the characteristics of biased gene expression, asymmetric DNA methylation, transposable elements (TEs), and alternative splicing (AS) events of homoeologous gene pairs between subgenomes. The results showed that biased expression genes (BEGs) in 2 Juglans species were mainly related to external stimuli response, while non-BEGs were related to complexes that might be involved in signal transduction. DS genes had higher expression and more AS events while having less DNA methylation and TEs than homoeologous genes from the SS in the 2 Juglans species. Further studies showed that DNA methylation might contribute to the biased expression of gene pairs by modifying LTR/TIR/nonTIR TEs and improving the AS efficiency of corresponding precursor mRNAs in a particular context. Our study contributes to understanding the epigenetic basis of subgenome expression dominance and the environmental adaptation of perennial woody plants.

TETRASPANIN 8-1 from Phaseolus vulgaris plays a key role during mutualistic interactions.

Arbuscular mycorrhizal (AM) fungi and rhizobia form two of the most important plant-microbe associations for the assimilation of phosphorus (P) and nitrogen (N). Symbiont-derived signals are able to coordinate the infection process by triggering multiple responses in the plant root, such as calcium influxes and oscillations, increased reactive oxygen species (ROS), cytoskeletal rearrangements and altered gene expression. An examination was made of the role of tetraspanins, which are transmembrane proteins that self-organize into tetraspanin web regions, where they recruit specific proteins into platforms required for signal transduction, membrane fusion, cell trafficking, and ROS generation. In plant cells, tetraspanins are scaffolding proteins associated with root radial patterning, biotic and abiotic stress responses, cell fate determination, plasmodesmata and hormonal regulation. Some plant tetraspanins, such as Arabidopsis thaliana TETRASPANIN 8 and TETRASPANIN 9 (AtTET8 and AtTET9) are associated with exosomes during inter-kingdom communication. In this study, a homolog of AtTET8, PvTET8-1, in common bean (Phaseolus vulgaris L. var. Negro Jamapa) was examined in roots during interactions with Rhizobium tropici and Rhizophagus irregularis. The promoter of PvTET8-1 contained several cis-acting regulatory DNA elements potentially related to mutualistic interactions, and PvTET8-1 was transcriptionally activated during AM fungal and rhizobial associations. Silencing it decreased the size and number of nodules, nitrogen fixation, and mycorrhizal arbuscule formation, whereas overexpressing it increased the size and number of nodules, and mycorrhizal arbuscule formation but decreased nitrogen fixation. PvTET8-1 appears to be an important element in both of these mutualistic interactions, perhaps through its interaction with NADPH oxidase and the generation of ROS during the infection processes.

Identification, characterization, and expression analysis of PpCPK gene family in response to Alternaria-infected peach fruits collected from different geographical regions of China

Peach is a popular and economically important fruit tree highly susceptible to biotic and abiotic stresses, including diseases caused by fungi, bacteria and viruses, pests and insects that feed fruits and leaves. Alteranria is a deadly disease agent, a genus of fungi that can cause significant damage to plants and crops such as peaches. Here, we investigated the role of CPK genes against in Alternaria species. The calcium-dependent protein kinase (CPK) gene family plays a vital role in the biotic stress response of plants. In this study, we aimed to identify, characterize, and analyze the expression pattern of the PpCPK gene family in response to Alternaria-infected peach fruits collected from different geographical regions of China. Based on phylogenetic analysis, 17 PpCPK genes were identified and classified into seven groups. The physicochemical properties, gene structure, conserved domains, and motifs of the PpCPK genes were analyzed to understand their molecular characteristics further. The Ka/Ks ratio analysis revealed the evolutionary facets of duplication events of PpCPKs and predicted the divergence time between 23.5 and 43.6 million years ago. The promoter region analysis confirmed the presence of plant growth, light, stress, and hormone-related cis-elements in PpCPKs. Additionally, the expression pattern of PpCPKs was analyzed using real-time quantitative PCR in Alternaria-infected peach fruits from different regions of China. The results indicated a differential expression pattern of PpCPK genes responding to Alternaria infection, suggesting their potential role in defense against biotic stress. Overall, our study provides insights into the molecular mechanisms of PpCPK genes in response to biotic stress, which could aid in developing strategies for improving peach resistance to biotic stress.

Genome-Wide Identification, Evolution and Expression Profile Analysis of NAC Transcription Factor in Simmondsia chinensis.

NAC transcription factors (TFs) are one of the largest plant-specific gene families and play important roles in plant growth, development, and the biotic and abiotic stress response. Although the sequencing of Jojoba (Simmondsia chinensis) has been completed, the genome-wide identification and analysis of its NAC TFs has not been reported. In this study, a total of 57 genes were identified in Jojoba, which were divided into eight groups based on phylogenetic analysis. The genes clustered in the same groups have a similar gene structure and motif distribution. Based on the analysis of cis-elements in NAC TFs, nine cis-acting elements were identified in the promoter region that involved in light response, hormonal response, and stress response. Synteny analysis showed a greater collinearity between Jojoba and V. vinifera than Arabidopsis thaliana. The 24 genes in the Jojoba NAC TFs are derived from fragment replication, which may be the main source of NAC amplification. Gene expression analysis identified seven genes that were highly expressed in seeds. The differential expression analysis of NAC TFs in cotyledon and embryonic axis tissues showed that the expression of 10 genes was up-regulated and 1 gene was down-regulated. This study provides more information on the classification, gene structure, conserved motif, and evolution of NAC TFs in Jojoba, facilitating further exploration of their specific functional analysis in Jojoba seed development.

Genome-wide identification and expression analysis of the Glutamine synthetase family genes in Zea mays under drought stress

Glutamine synthetase (GS) enzyme is involved in nitrogen metabolism by the assimilation of NH4+ with glutamate and glutamine, and hence play their role in plant development, biotic and abiotic stress responses, secondary metabolite synthesis and crop yield. However, in maize, the expression levels of ZmGS genes under drought stress are not explored. Globally drought stress significantly affected maize production. Keeping in view the importance of GS genes in maize, we have checked their response under drought stress. The targeted 05 ZmGS genes in maize evolutionary analysis was performed for 81 GS protein sequences in different species, clustered into three clades based on their phylogenetic analysis. GS genes that were identified in maize are distributed on Chromosome 1, chrom4, chrom5, and chrom9. Conserved domain analysis, gene structure, motifs analysis, and alignment of ZmGSs demonstrated that all genes showed a conserved pattern. Analysis of cis-regulatory elements in promoter region revealed that almost all the ZmGS genes had stress responsive and plant hormonal related cis elements and their number are different in all genes. We also identified 55 putative miRNAs targeting 5 ZmGS genes. Furthermore, GS genes of maize were identified as drought-responsive genes by using qRT-PCR expression analysis. The high expression level of GS genes was detected in the roots and leaves of Haq Nawaz compared to CIMMYT PAK maize cultivars. The analysis of all identified ZmGS genes using qRT-PCR data showed that they expressed in roots and shoots under normal and drought stress. The expression analysis of drought-responsive GS genes was found more in H. Nawaz than in C. Pak maize cultivar under drought stress. Therefore, the H. Nawaz cultivar could have the potential to tolerate mild to moderate drought stress. Our study offers valuable data on the functioning of GS genes in maize under drought stress and provides a foundation for further analysis of the function of GS gene family under abiotic stresses.

The Role of TCA Cycle Enzymes in Plants.

As one of the iconic pathways in plant metabolism, the tricarboxylic acid (TCA) cycle is commonly thought to not only be responsible for the oxidization of respiratory substrate to drive ATP synthesis but also provide carbon skeletons to anabolic processes and contribute to carbon-nitrogen interaction and biotic stress responses. The functions of the TCA cycle enzymes are characterized by a saturation transgenesis approach, whereby the constituent expression of proteins is knocked out or reduced in order to investigate their functionin vivo. The alteration of TCA cycle enzyme expression results in changed plant growth and photosynthesis under controlled conditions. Moreover, improvements in plant performance and postharvest properties are reported by overexpression of either endogenous forms or heterologous genes of a number of the enzymes. Given the importance of the TCA cycle in plant metabolism regulation, here, the function of each enzyme and its roles in different tissues are discussed. This article additionally highlights the recent finding that the plant TCA cycle, like that of mammals and microbes, dynamically assembles functional substrate channels or metabolons and discusses the implications of this finding to the current understanding of the metabolic regulation of the plant TCA cycle.

Genome-wide characterization of the PLATZ gene family in watermelon (Citrullus lanatus L.) with putative functions in biotic and abiotic stress response

Plant AT-rich sequence and zinc-binding (PLATZ) proteins are plant-specific transcription factors involved in growth, development, and stress responses. Here, we conducted a genome-wide characterization of the watermelon ClPLATZ family and examined its expression responsiveness to defense hormones and pathogen infection along with putative functions in biotic and abiotic stress responses. The watermelon genome contains 12 putative ClPLATZ genes, encoding proteins with a characteristic PLATZ domain, and their promoters contain various cis-elements related to plant growth, development, phytohormones and stress response. The ClPLATZ genes, except ClPLATZ6, are differentially expressed in response to defense hormones (e.g., salicylic acid and methyl jasmonate) and fungal infections caused by Fusarium oxysporum f. sp. niveum and Stagonosporopsis cucurbitacearum. Most ClPLATZ proteins interact with other proteins (viz., ClDP, ClRPT2a, and ClRPC53). Among ClPLATZ proteins, ClPLATZ8, 9, 10, and 11 are predominately localized in the nucleus. ClPLATZ3 and 8 positively, but ClPLATZ11 negatively regulate resistance against Pseudomonas syringe pv. tomato DC3000 in transgenic Arabidopsis lines. ClPLATZ8 and 11 positively regulate stress tolerance to NaCl and mannitol during seed germination in transgenic Arabidopsis. In conclusion, the characterization of the ClPLATZ family provides insights into the biological functions of ClPLATZ genes in growth, development, and stress response in watermelon. Further, the involvement of certain ClPLATZ genes in biotic and abiotic stress response in transgenic Arabidopsis suggests their potential application in engineering stress-tolerant crops.

WRKY gene family of Licorice (Glycyrrhiza uralensis): identification and expression analysis in response to abiotic stress

WRKY transcription factors (TF) control a variety of biological processes in higher plants, including abiotic and biotic stress responses. WRKY genes have been identified and functionally characterized in many plant species during the past ten years, but despite this progress, few investigations have focused on this TF family in licorice (Glycyrrhiza uralensis Fisch.). This study identified 72 WRKY genes from the licorice genome and classified them into three groups. The gene structure analysis indicated that the GuWRKY genes contain from one to eight introns, with the majority having two introns and three exons. Conserved motif analysis identified the conserved WRKY domain in most GuWRKYs. Further analysis of the promoter region revealed that almost all GuWRKYs had plant hormone- or stress-responsive cis-regulatory elements, with differences in the number of elements among the groups. The role of 10 selected GuWRKYs in regulating abiotic stress responses was further explored via quantitative real-time PCR (qRT-PCR) after low-temperature (4 °C), salt (150 mmol·L−1 NaCl), drought (15% polyethylene glycol 6000) treatments at 3, 6, 12, and 24 h. Thus, our study of the WRKY gene family in licorice provides a basis for further research on the structure and function of WRKY genes.

Genome-Wide Identification and Characterization of the TLP Gene Family in Phyllostachys edulis and Association with Witches' Broom Disease Resistance in Bamboo.

Thaumatin-like proteins (TLPs) are pathogenesis-related proteins with pivotal roles in plant defense mechanisms. In this study, various bioinformatics and RNA-seq methods were used to analyze the biotic and abiotic stress responses of the TLP family in Phyllostachys edulis. Overall, 81 TLP genes were identified in P. edulis; 166 TLPs from four plant species were divided into three groups and ten subclasses, with genetic covariance observed between these species. Subcellular localization in silico studies indicated that TLPs were primarily distributed in the extracellular. Analysis of the upstream sequences of TLPs demonstrated the presence of cis-acting elements related to disease defense, environmental stress, and hormonal responses. Multiple sequence alignment demonstrated that most TLPs possessed five conserved REDDD amino acid sequences with only a few amino acid residue differences. RNA-seq analysis of P. edulis responses to Aciculosporium take, the pathogenic fungus that causes witches' broom disease, showed that P. edulis TLPs (PeTLPs) were expressed in different organs, with the highest expression in buds. PeTLPs responded to both abscisic acid and salicylic acid stress. These PeTLP expression patterns were consistent with their gene and protein structures. Collectively, our findings provide a basis for further comprehensive analyses of the genes related to witches' broom in P. edulis.

Transcriptome Sequencing and WGCNA Reveal Key Genes in Response to Leaf Blight in Poplar.

Leaf blight is a fungal disease that mainly affects the growth and development of leaves in plants. To investigate the molecular mechanisms of leaf blight defense in poplar, we performed RNA-Seq and enzyme activity assays on the Populus simonii × Populus nigra leaves inoculated with Alternaria alternate fungus. Through weighted gene co-expression network analysis (WGCNA), we obtained co-expression gene modules significantly associated with SOD and POD activities, containing 183 and 275 genes, respectively. We then constructed a co-expression network of poplar genes related to leaf blight resistance based on weight values. Additionally, we identified hub transcription factors (TFs) and structural genes in the network. The network was dominated by 15 TFs, and four out of them, including ATWRKY75, ANAC062, ATMYB23 and ATEBP, had high connectivity in the network, which might play important functions in leaf blight defense. In addition, GO enrichment analysis revealed a total of 44 structural genes involved in biotic stress, resistance, cell wall and immune-related biological processes in the network. Among them, there were 16 highly linked structural genes in the central part, which may be directly involved in poplar resistance to leaf blight. The study explores key genes associated with leaf blight defense in poplar, which further gains an understanding of the molecular mechanisms of biotic stress response in plants.

The dynamics of touch-responsive gene expression in cereals.

Wind, rain, herbivores, obstacles, neighbouring plants, etc. provide important mechanical cues to steer plant growth and survival. Mechanostimulation to stimulate yield and stress resistance of crops is of significant research interest, yet a molecular understanding of transcriptional responses to touch is largely absent in cereals. To address this, we performed whole-genome transcriptomics following mechanostimulation of wheat, barley, and the recent genome-sequenced oat. The largest transcriptome changes occurred ±25 min after touching, with most of the genes being upregulated. While most genes returned to basal expression level by 1-2 h in oat, many genes retained high expression even 4 h post-treatment in barley and wheat. Functional categories such as transcription factors, kinases, phytohormones, and Ca2+ regulation were affected. In addition, cell wall-related genes involved in (hemi)cellulose, lignin, suberin, and callose biosynthesis were touch-responsive, providing molecular insight into mechanically induced changes in cell wall composition. Furthermore, several cereal-specific transcriptomic footprints were identified that were not observed in Arabidopsis. In oat and barley, we found evidence for systemic spreading of touch-induced signalling. Finally, we provide evidence that both the jasmonic acid-dependent and the jasmonic acid-independent pathways underlie touch-signalling in cereals, providing a detailed framework and marker genes for further study of (a)biotic stress responses in cereals.

Genome-wide survey of glutaredoxin gene family in four Solanaceae species and exploitation of duplicated CC-type following different environmental stimuli in tomato (Solanum lycopersicum)

Glutaredoxins (GRXs) are ubiquitous oxidoreductases involved in cell signaling, development and plant defense response against oxidative stress. Despite this gene family has been characterized in several species, clues about their evolution, diversification and function in Solanaceae are still in infancy. By exploring genomes of cultivated tomato (Solanum lycopersicum), potato (S. tuberosum) and their wild relatives (S. pennellii, S. commersonii), a total of 237 GRX genes were identified and grouped in CPYC-, CGFS-, GRL- and CC-types. Focusing on cultivated tomato, we highlighted that a higher diversity within CC-type resulted from tandem duplication events, indicating that this latter might be the force driving GRXs evolution. The presence of a rich repertoire of cis-regulatory elements suggested specialized functions of SlGRXs in plant development, hormonal and (a)biotic stress responses, as also confirmed by their different expression patterns observed in various tissues and during fruit development through an in silico approach. qRT-PCR analysis revealed a divergent profile of tandem and segmental duplicated CC-type members in tomato response to abiotic stresses, pathogenic or beneficial microorganisms. This study reported the first insights on the GRX gene family in four Solanaceae species and provided a comprehensive and detailed analysis of their gene structure and role in tomato. The divergent profile of selected duplicated CC-type members against various environmental constraints, highlighted candidate genes that will be used as a reference for functional analysis and genetic improvement not only in tomato but also in related species.

Non-specific LIPID TRANSFER PROTEIN 1 enhances immunity against tobacco mosaic virus in Nicotiana benthamiana.

Plant non-specific lipid transfer proteins (nsLTPs) are small, cysteine-rich proteins that play significant roles in biotic and abiotic stress responses; however, the molecular mechanism of their functions against viral infections remains unclear. In this study, we employed virus-induced gene-silencing and transgenic overexpression to functionally analyse a type-I nsLTP in Nicotiana benthamiana, NbLTP1, in the immunity response against tobacco mosaic virus (TMV). NbLTP1 was inducible by TMV infection, and its silencing increased TMV-induced oxidative damage and the production of reactive oxygen species (ROS), compromised local and systemic resistance to TMV, and inactivated the biosynthesis of salicylic acid (SA) and its downstream signaling pathway. The effects of NbLTP1-silencing were partially restored by application of exogenous SA. Overexpressing NbLTP1 activated genes related to ROS scavenging to increase cell membrane stability and maintain redox homeostasis, confirming that an early ROS burst followed by ROS suppression at the later phases of pathogenesis is essential for resistance to TMV infection. The cell-wall localization of NbLTP1 was beneficial to viral resistance. Overall, our results showed that NbLTP1 positively regulates plant immunity against viral infection through up-regulating SA biosynthesis and its downstream signaling component, NONEXPRESSOR OF PATHOGENESIS-RELATED 1 (NPR1), which in turn activates pathogenesis-related genes, and by suppressing ROS accumulation at the later phases of viral pathogenesis.

Soybean Root Transcriptomics: Insights into Sucrose Signaling at the Crossroads of Nutrient Deficiency and Biotic Stress Responses.

Soybean (Glycine max) is an important agricultural crop, but nutrient deficiencies frequently limit soybean production. While research has advanced our understanding of plant responses to long-term nutrient deficiencies, less is known about the signaling pathways and immediate responses to certain nutrient deficiencies, such as Pi and Fe deficiencies. Recent studies have shown that sucrose acts as a long-distance signal that is sent in increased concentrations from the shoot to the root in response to various nutrient deficiencies. Here, we mimicked nutrient deficiency-induced sucrose signaling by adding sucrose directly to the roots. To unravel transcriptomic responses to sucrose acting as a signal, we performed Illumina RNA-sequencing of soybean roots treated with sucrose for 20 min and 40 min, compared to non-sucrose-treated controls. We obtained a total of 260 million paired-end reads, mapping to 61,675 soybean genes, some of which are novel (not yet annotated) transcripts. Of these, 358 genes were upregulated after 20 min, and 2416 were upregulated after 40 min of sucrose exposure. GO (gene ontology) analysis revealed a high proportion of sucrose-induced genes involved in signal transduction, particularly hormone, ROS (reactive oxygen species), and calcium signaling, in addition to regulation of transcription. In addition, GO enrichment analysis indicates that sucrose triggers crosstalk between biotic and abiotic stress responses.

Image-Based High-Throughput Phenotyping in Horticultural Crops.

Plant phenotyping is the primary task of any plant breeding program, and accurate measurement of plant traits is essential to select genotypes with better quality, high yield, and climate resilience. The majority of currently used phenotyping techniques are destructive and time-consuming. Recently, the development of various sensors and imaging platforms for rapid and efficient quantitative measurement of plant traits has become the mainstream approach in plant phenotyping studies. Here, we reviewed the trends of image-based high-throughput phenotyping methods applied to horticultural crops. High-throughput phenotyping is carried out using various types of imaging platforms developed for indoor or field conditions. We highlighted the applications of different imaging platforms in the horticulture sector with their advantages and limitations. Furthermore, the principles and applications of commonly used imaging techniques, visible light (RGB) imaging, thermal imaging, chlorophyll fluorescence, hyperspectral imaging, and tomographic imaging for high-throughput plant phenotyping, are discussed. High-throughput phenotyping has been widely used for phenotyping various horticultural traits, which can be morphological, physiological, biochemical, yield, biotic, and abiotic stress responses. Moreover, the ability of high-throughput phenotyping with the help of various optical sensors will lead to the discovery of new phenotypic traits which need to be explored in the future. We summarized the applications of image analysis for the quantitative evaluation of various traits with several examples of horticultural crops in the literature. Finally, we summarized the current trend of high-throughput phenotyping in horticultural crops and highlighted future perspectives.

NPR1 Translocation from Chloroplast to Nucleus Activates Plant Tolerance to Salt Stress.

Chloroplasts play crucial roles in biotic and abiotic stress responses, regulated by nuclear gene expression through changes in the cellular redox state. Despite lacking the N-terminal chloroplast transit peptide (cTP), nonexpressor of pathogenesis-related genes 1 (NPR1), a redox-sensitive transcriptional coactivator was consistently found in the tobacco chloroplasts. Under salt stress and after exogenous application of H2O2 or aminocyclopropane-1-carboxylic acid, an ethylene precursor, transgenic tobacco plants expressing green fluorescent protein (GFP)-tagged NPR1 (NPR1-GFP) showed significant accumulation of monomeric nuclear NPR1, irrespective of the presence of cTP. Immunoblotting and fluorescence image analyses indicated that NPR1-GFP, with and without cTP, had similar molecular weights, suggesting that the chloroplast-targeted NPR1-GFP is likely translocated from the chloroplasts to the nucleus after processing in the stroma. Translation in the chloroplast is essential for nuclear NPR1 accumulation and stress-related expression of nuclear genes. An overexpression of chloroplast-targeted NPR1 enhanced stress tolerance and photosynthetic capacity. In addition, compared to the wild-type lines, several genes encoding retrograde signaling-related proteins were severely impaired in the Arabidopsis npr1-1 mutant, but were enhanced in NPR1 overexpression (NPR1-Ox) transgenic tobacco line. Taken together, chloroplast NPR1 acts as a retrograding signal that enhances the adaptability of plants to adverse environments.

Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth.

Studying intraspecific variation in multistress responses is central for predicting and managing the population dynamics of wild plant species under rapid global change. Yet, it remains a challenging goal in this field to integrate knowledge on the complex biochemical underpinnings for the targeted 'non-model' species. Here, we studied divergence in combined drought and heat responses among Northern and Southern European populations of the dune plant Cakile maritima, by combining comprehensive plant phenotyping with metabolic profiling via FT-ICR-MS and UPLC-TQ-MS/MS. We observed pronounced constitutive divergence in growth phenology, leaf functional traits, and defence chemistry (glucosinolates and alkaloids) among population origins. Most importantly, the magnitude of growth reduction under drought was partly weaker in southern plants and associated with divergence in plastic growth responses (leaf abscission) and the modulation of primary and specialized metabolites with known central functions not only in plant abiotic but also in biotic stress responses. Our study indicates that divergent selection has shaped the constitutive and drought-/heat-induced expression of numerous morphological and biochemical functional traits to mediate higher abiotic stress resistance in southern Cakile populations, and highlights that metabolomics can be a powerful tool to explore the underlying mechanisms of local adaptation in 'non-model' species.

Genome-wide identification and expression analysis of glycogen synthase kinase encoding genes in foxtail millet (Setaria italica L.) under salinity, dehydration, and oxidative stress

Glycogen Synthase Kinase 3 (GSK3)/SHAGGY-like Kinase (SK) proteins in plants govern growth, development, and several abiotic and biotic stress responses. GSK3 proteins are cytoplasmic serine/threonine kinases that control glycogen metabolism in eukaryotes. However, nothing is known about the discovery and characterization of glycogen synthase kinase (GSK) genes in foxtail millet (Setaria italica). In the present study, eight Setaria italica GSK (SiGSKs) genes were identified and divided into four groups based on their phylogenetic affinities with rice and Arabidopsis. The gene structure and motif organizations were examined to delve deeper into SiGSKs function and its evolution. The SiGSKs encode active protein kinases, according to conserved motif and kinase domain analysis. Many growth hormones and stress-responsive elements were found in the SiGSK promoter regions, which is compatible with their expression in diverse organs and their changed expression in response to abiotic stress such as salt, drought, and oxidative damage. qRT-PCR expression analysis of SiGSKs under three different abiotic stresses suggests its role in signaling and regulating the mechanism under the mentioned abiotic stresses. The current research opens up new opportunities for SiGSK functional validation in S. italica (L.) by genetic engineering.

ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses.

Participating in both biotic and abiotic stress responses, plant-specific class III peroxidases (PERs) show promise as candidates for crop improvement. The multigenic PER family is known to take part in diverse functions, such as lignin formation and defense against pathogens. Traditionally linked to hydrogen peroxide (H2O2) consumption, PERs can also produce reactive oxygen species (ROS), essential in tissue development, pathogen defense and stress signaling. The amino acid sequences of both orthologues and paralogues of PERs are highly conserved, but discovering correlations between sequence differences and their functional diversity has proven difficult. By combining meta-analysis of transcriptomic data and sequence alignments, we discovered a correlation between three key amino acid positions and gene expression in response to biotic and abiotic stresses. Phylogenetic analysis revealed evolutionary pressure on these amino acids toward stress responsiveness. Using AlphaFold modeling, we found unique interdomain and protein-heme interactions involving those key amino acids in stress-induced PERs. Plausibly, these structural interactions may act as "gate keepers" by preventing larger substrates from accessing the heme and thereby shifting PER function from consumption to the production of ROS.