High temperature (HT) is a critical abiotic factor that restricts plant growth and development. The role of abscisic acid (ABA) in stress tolerance is well established, and ABA 8'-hydroxylase (ABA8ox), a key enzyme in ABA degradation, is crucial for plant responses to abiotic stress. In this study, a CsABA8ox1-deficient mutant, yf-343, and its wild-type counterpart, BY, were subjected to continuous HT treatment to assess phenotypic, physiological, and transcriptomic changes. Under HT, ABA accumulation increased in BY and yf-343, with significantly higher levels in the yf-343 mutant. Exogenous ABA application accelerated leaf yellowing in BY and triggered pronounced leaf senescence and cell death in yf-343. HT treatment also increased the activities of superoxide dismutase and peroxidase, elevated ABA and malondialdehyde content, and simultaneously inhibited catalase activity and photosynthetic rate. Comparative RNA sequencing (RNA-seq) revealed that genes associated with plant hormone signaling, secondary metabolite biosynthesis, starch and sucrose metabolism, phenylalanine metabolism, and the mitogen-activated protein kinase signaling pathway were differentially expressed between yf-343 and BY under 42 °C HT treatment. Among these, two genes, heat shock proteins 70 (CsHSP70) and wall-associated receptor kinase 2 (CsWAKL2), were validated through virus-induced gene silencing. Knockdown of CsHSP70 and CsWAKL2 enhanced susceptibility to HT, confirming the reliability and significance of the candidate genes involved in HT stress response identified by RNA-seq. These findings establish a strong foundation for elucidating the role of ABA8ox in cucumber resistance to abiotic stress.

Legumes are the second most important food crop after cereals for the world population. It is a significant protein source for developing countries and integral to global food security. However, various agroecological constraints and biotic and abiotic factors often compromise the production of pulses. Legumes are long-term neglected crops worldwide and follow traditional breeding, leading to a time-consuming, labor-intensive, less economically feasible program associated with linkage drag. Recent sequencing attempts in the twenty-first century, with the development of an enormous repertoire of genetic and genomic resources, allowed scientists to accelerate the improvement of legumes with modern genome editing tools. One such promising tool is CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), which has revolutionized and transformed the landscape of genetic engineering. The emergence of CRISPR/Cas systems has redefined precision breeding, offering unprecedented control over genome manipulation in legume crops. It has tremendous potential for crop improvement and can precisely make changes at genomic locations with incredible accuracy. Therefore, identifying the desired genes and their precise manipulation has enormous implications for legume crop improvement. This review will give an overview of the genome editing tools available for crop improvement and the efficiency of different transformation methods in legume crops. It will also discuss the current status of genome editing in legume crops, including challenges and future perspectives.

Tiller and spikelet numbers are important agronomic traits affecting wheat grain yield, but the molecular mechanisms controlling these traits are largely unknown. We have identified a gene (Wheat Tiller-1, WT-1) that regulates numbers of these two very important agronomic traits. While trying to understand the early events of tiller development in wheat, cross section analysis of the crown region showed that differentiation of the tiller buds and apical meristem into spikelets occurs during early seedling stages. The gene was identified by VIGS silencing using sequence around the VHIID motif of the LS gene of tomato that controls branching. VIGS gene silencing, first using the tomato sequence and then from the gene identified from wheat resulted in uniculm and reduce tiller number phenotype. Overall, the WT-1 showed only 37.6% predicted protein similarity to the LS gene although the VHIID motif was conserved. The gene has three structural copies one each on the three wheat homoeologous group 7 chromosomes. Although share > 98% sequence similarity, the three gene copies showed different expression pattern in various tissues and growth stages. Silencing of the gene via stable RNAi showed reduction in both tiller and spikelet number. SEM analysis of the RNAi plants showed that silencing of WT-1 reduced the tiller bud initiation. Among the progeny of independent RNAi events, variation in both spikelet and tiller numbers correlated with the level of reduction in the gene expression, showing role of the gene in controlling tiller number and spikelet number per spike.

Sugarcane holds significant economic importance in sugar and biofuel production. Despite extensive research, understanding highly quantitative traits remains challenging due to its complex genomic landscape. We conducted a multiomic investigation to elucidate the genetic architecture and molecular mechanisms governing sugarcane sucrose accumulation. Using a biparental cross and a genetically diverse collection of sugarcane genotypes, we evaluated the soluble solids (Brix) and sucrose content (POL) across various years. Both populations were genotyped using a genotyping-by-sequencing approach. Genotype‒phenotype associations were established using a combination of traditional linear mixed-effect models and machine learning algorithms. Furthermore, we conducted an RNA sequencing experiment on genotypes exhibiting distinct Brix and POL profiles across different developmental stages. Differentially expressed genes (DEGs) potentially associated with variations in sucrose accumulation were identified. All findings were integrated through gene coexpression network analyses. Strong correlations among the evaluated characteristics were observed, with estimates of modest to high heritabilities. By leveraging a broad set of single-nucleotide polymorphisms (SNPs) identified for both populations, we identified several SNPs potentially linked to phenotypic variance. Our examination of genes close to these markers facilitated the association of such SNPs with DEGs for contrasting sucrose levels. Through the integration of these results with a gene coexpression network, we delineated a set of genes potentially involved in the regulatory mechanisms of sucrose accumulation. Our findings constitute a significant resource for biotechnology and plant breeding initiatives. Furthermore, our genotype‒phenotype association models hold promise for application in genomic selection, offering valuable insights into the molecular underpinnings governing sucrose accumulation in sugarcane.

Perilla frutescens (L.) Britt., a traditional Chinese herb used for both medicinal and culinary purposes, contained various bioactive compounds such as volatile oils, flavonoids, and phenolic acids, which contribute to its diverse pharmacological activities. BBXs (B-box zinc finger genes), a subfamily of zinc finger proteins, play critical regulatory roles in plant growth and development, abiotic stress responses, and pigment accumulation. However, research on the PfBBXs in P. frutescens remains limited. In this study, 31 PfBBXs were identified from the P. frutescens genome. Their protein physicochemical properties, phylogeny, conserved domains, motifs, cis-acting elements, and expression patterns were systematically analyzed. Phylogenetic analysis classified PfBBXs into five subfamilies, with similar conserved motifs and gene structures within each subfamily but notable divergence among them. Promoter regions of PfBBXs were enriched in cis-regulatory elements related to light responsiveness, stress responses, and phytohormone signaling. Different light intensities significantly affected the leaf area and the accumulation of anthocyanins and flavonoids. Integrated metabolomic and transcriptomic analyses revealed that light intensity modulated the biosynthesis of flavonoids and anthocyanins. Transcriptomic screening identified five highly light-responsive PfBBXs (PfBBX10, 12, 13, 17, and 18), whose light-induced expression patterns were further validated by qRT-PCR. Among them, PfBBX10, 12, and 17 exhibited significant positive correlations with anthocyanin and flavonoid contents, suggesting their pivotal roles in light signaling and secondary metabolism regulation. This study lays a foundation for functional characterization of PfBBXs in P. frutescens particularly in light signal transduction and anthocyanin accumulation.

Highly specific, second-generation RNA interference tools are based on artificial small RNAs (art-sRNAs), such as artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs). Recent progress includes the use of minimal-length precursors to express art-sRNAs in plants. These minimal precursors retain the minimal structural elements for recognition and efficient processing by host enzymes. They yield high amounts of art-sRNAs and remain stable when incorporated into potato virus X-based viral vectors for art-sRNA-mediated virus-induced gene silencing (art-sRNA-VIGS). However, further adaptation to new viral vector systems with reduced symptomatology is needed to improve the versatility of art-sRNA-VIGS. Here, we developed a novel platform based on tobacco rattle virus (TRV)-a widely used viral vector inducing minimal or no symptoms-for the delivery of art-sRNAs into plants. TRV was engineered to express authentic amiRNAs and syn-tasiRNAs from minimal precursors in Nicotiana benthamiana, resulting in robust and highly specific silencing of endogenous genes. Notably, the expression of syn-tasiRNAs through TRV conferred strong resistance against tomato spotted wilt virus, an economically important pathogen. Furthermore, we established a transgene-free approach by applying TRV-containing crude extracts through foliar spraying, eliminating the need for stable genetic transformation. In summary, our results highlight the unique advantages of minimal precursors and extend the application of art-sRNA-VIGS beyond previously established viral vector systems, providing a scalable, rapid and highly specific tool for gene silencing.

Glyoxalase I (GLYI) constitute the first enzyme of the glyoxalase pathway which is a two-step reaction to convert methylglyoxal (MG), an inherent cytotoxin to D-lactate. In plants, multiple members of the glyoxalase pathway genes have been reported. However, not all exhibit glyoxalase activity. OsGLYI-10 is one such member from rice GLYI family which we report here, to lack GLYI enzymatic activity. Instead, OsGLYI-10 shows high structural homology to glutathione-S-transferase (GST) proteins and exhibits GST activity. Further, we found OsGLYI-10 to be highly expressed in seeds, its expression starting at the milk stage, reaching its maximum in the mature seed and finally disappearing after four days of imbibition. Importantly, through molecular docking and site-directed mutagenesis studies, we showed that GLYI activity can be reinstated to some extent via the introduction of a 10 amino acid stretch as well as substitution of certain amino acids in OsGLYI-10. Further increase in GLYI activity could be achieved through the substitution of Met with Tyr at 55th position, restoring 35% activity in OsGLYI-10 relative to a functionally active and highly efficient GLYI, OsGLYI-8 enzyme from rice. Our findings therefore, suggest OsGLYI-10 to be a reminiscent of GLYI enzyme that has diverged in its catalytic function over the course of evolution to adopt newer activities and roles in cellular physiology.

Sugar metabolism in plants is highly dynamic throughout their life cycle, driven by the continuous production, accumulation, and distribution of these molecules along the plant body. To cope with fluctuating sugar levels during their life cycle, plants have developed mechanisms to sense and respond to these changes accordingly. Noteworthy, sugars not only fulfill metabolic roles, but also act as signaling molecules that regulate plant growth and development. Of the array of sugar responses, their influence on gene expression is particularly significant, as it impacts a wide range of physiological processes, including key economic traits of plants. However, despite the broad regulatory role of sugars in gene expression, the transcriptional mechanisms behind their regulation remain largely unknown. Among the many sugar-regulated genes in plants, efforts have been focused on identifying cis-regulatory elements (CREs) and trans-regulatory factors (transcription factors, TFs) involved in gene sugar responsiveness at transcriptional level, but only some have been experimentally confirmed. Therefore, this review outlines those approaches used for identifying sugar CREs and TFs, along with an updated compilation of the elements associated with glucose and sucrose signaling transcriptional responses. In addition, the evolutionary conservation of these regulatory elements in different plant species is addressed, highlighting those with potential biotechnological applications. In summary, the gathering of this information has the purpose of updating our current knowledge regarding the mechanism of how sugars exert its effect on gene expression. This understanding is essential for advancing in the manipulation of these regulatory elements to improve key traits in economically valuable plants, such as oil and sugar accumulation, crop yield, and fruit quality.

Plants, constantly exposed to dynamic environmental conditions, encounter various abiotic stresses that significantly affect their growth and development. In response, plants initiate complex physiological and molecular adjustments, including altered gene expression. One of the most influential factors in mitigating stress impacts is the plant-microbe interaction. Among these, plant growth-promoting rhizobacteria (PGPR) are well-studied for their ability to enhance plant resilience. More recently, microalgae have emerged as potential members of the plant microbiome, although their roles remain comparatively underexplored. This study investigates the transcriptomic responses of Arabidopsis thaliana to inoculation with the PGPR strain Stutzerimonas stutzeri, the green microalgae Chlorella vulgaris, and a consortium of both microorganisms under salt stress conditions. Through RNA-seq analysis, we identified a set of core genes commonly regulated across all inoculation treatments, including SALT OVERLY SENSITIVE 3 (SOS3), the potassium channel AKT2, and CBL-INTERACTING PROTEIN KINASE 5 (CIPK5), suggesting a shared stress-mitigation mechanism. Additionally, we identified genes uniquely regulated in response to the S. stutzeri-C. vulgaris consortium. These included components of the ethylene signaling pathway (EIN3/EIL1), detoxification-associated genes such as β-GLUCOSIDASE (BGLU22), and transcription factors linked to stress response, notably NAC6 and MYB12. Together, these findings provide insight into the specific and overlapping transcriptomic changes induced by bacterial, algal, and combined inoculations, contributing to our understanding of plant-microbe interactions under salt stress.

The redox-dependent modulation of redox-sensitive proteins and transcription factors serves as a central mechanism to regulate plant defense responses against necrotrophic fungal pathogens. This process is interconnected with hormone signaling pathways involving salicylic acid (SA) or jasmonic acid (JA)/ethylene (ET), resulting in a coordinated holistic defense response to combat pathogen infection. In response to infection, additional reactive oxygen species (ROS) production triggers an appropriate response to the invasive hyphae, acting as a primary defense mechanism in Brassicaceae. This ROS signaling pathway, involving receptors, kinases, transcriptional activators, and downstream genes such as and / among others, is critical for the well-coordinated plant response to disease These pathways can lead to either tolerance or programmed cell death (PCD), depending on the balance of signaling events. Despite the significant contribution of redox-mediated pathways, blight continues to infect crops in the Brassicaceae family, leading to yield losses in Brassica species, especially oilseed crops, exerting a substantial economic impact. Given the importance of this pathogen, the current review provides an in-depth understanding of the oxidative stress and associated signaling networks triggered by blight. Special emphasis is given to the interaction of with oilseed Brassica crops, highlighting key molecular pathways involved in disease progression and plant response. Understanding these complex interactions provides valuable clues into the plant’s adaptations to stress. Thus, opening avenues for identifying novel solutions in producing resilience against the pathogen, ensuring sustainable productivity in Brassica crops.

Drought is a major natural disaster that affects plant growth. Agropyron mongolicum possesses a wide range of drought tolerance genes acquired during its long evolution and adaptation to harsh environments. However, the regulatory mechanisms for drought resistance in A. mongolicum are complex, limiting the development and utilization of gene resources in response to drought stress. In this study, we examined differences in morphological, physiological, metabolite and transcript levels between the drought-tolerant (T) and drought-sensitive (S) genotypes of A. mongolicum to identify key metabolites and genes associated with the drought response. The morphological and physiological results suggest that the S genotype is suppressed by drought stress to a greater extent than the T genotype. Based on the metabolome and transcriptome data, we identified that serine/threonine-protein kinase SRK2 (SRK2), peptide chain release factor subunit 1 (eRF1), glutamine synthetase (GS), polyphenol oxidase (PPO), and aspartyl protease family protein (ASP) were highly correlated with key metabolites such as L-γ-glutamyl-L-leucine and γ-glutamylphenylalanine in leaves by co-expression network analysis, and alcohol-forming fatty acyl-CoA reductase (FAR), DNA oxidative demethylase (ALKBH), GDSL esterase/lipase (GELP), beta-fructofuranosidase (INV), and glutamine synthetase (GS) were highly correlated with key metabolites such as Trp-Glu-Ile and citric acid diglucoside in roots. Moreover, we identified the potential involvement of fatty acid degradation and glycolysis/glucogenesis pathways in the enhancement of drought tolerance in A. mongolicum. This study provides a foundation for genetic engineering studies of drought resistance in Poaceae plants.

Wheat, an important staple crop providing food and nutrition worldwide, is aptly called the "King of Cereals". Salinization is a process when soil is tainted with salt that consequently impacts the growth and development of plants, which leads to a decline in the yield of many food crops. The present study provides a brief impression about salinity stress on physiological and molecular processes, which affects the plants' growth and development. Salinity stress in crop plants is responsible for various metabolic and physiological changes. In this study we summarize the genes and molecular mechanism involved in ion transport like Sodium/hydrogen antiporter exchanger (NHXs), High-affinity potassium transporters (HKTs) and osmolytes that causes nutritional disturbance and inhibits the process of uptake of water by roots, seed germination, photosynthesis, and declines the growth of plants. Salinity in wheat inhibits the spike development and yield potential of crop plants, lower yield production is particularly related to a decrease in tiller numbers and by sterile spikelets in some cultivars. Future studies should focus on crop tolerance to salinity to gain better understanding of crop tolerance in saline field conditions. Global cereal production is hampered by soil salinity and sodicity, but tolerance breeding has also been sluggish. Narrow gene pools, an overemphasis on the sodium exclusion mechanism, a lack of awareness against stress tissue tolerance mechanisms in which aggregation of inorganic ions such as Na is involved, and the lack of appropriate screening tools, which leads to slowed development. This review summarizes current knowledge and emphasizes the need for integrative strategies to enhance wheat resilience under saline conditions.

Environmental challenges such as drought, salinity, heavy metal contamination, and nutrient deficiencies threaten global agricultural productivity and food security. These stressors drastically reduce crop yields, necessitating innovative solutions. Recent advancements in omics-based research-spanning genomics, metabolomics, proteomics, transcriptomics, epigenomics, and phenomics-have transformed our understanding of plant stress responses at the molecular level. High-throughput sequencing, mass spectrometry, and computational biology have facilitated the identification of stress-responsive genes, proteins, and metabolites critical for enhancing plant resilience. This review evaluates omics-driven strategies for improving crop performance under environmental stress. It emphasizes multi-omics data integration, precision breeding, artificial intelligence (AI) in crop modeling, and genome-editing technologies. Notably, breakthroughs in machine learning and AI have refined predictive modeling, enabling precise selection of stress-tolerant traits and optimizing breeding strategies. Despite these advancements, challenges remain, including the complexity of multi-omics data analysis, high technology costs, and regulatory barriers. Bridging the gap between research and practical applications requires developing cost-effective platforms, enhancing AI-driven models, and conducting large-scale field validations. This review highlights the transformative potential of omics technologies to develop climate-resilient crops. By integrating these advanced methodologies, agriculture can achieve sustainable food production and bolster global food security in the face of climate change and environmental stressors.

To address the problem of lower anthocyanin contents in blood oranges at the ripening stage in local orchards, we compared the effects of postharvest storage at different temperatures on anthocyanin production in the pulps of fruit. Transcriptome sequencing and non-targeted metabolomics methods were used to analyze the dynamic changes in differentially expressed genes and differentially accumulated metabolites, respectively, during storage at 8 ℃ or room temperature (15 ℃). The results indicated that anthocyanin and citrate contents in fruit were higher at 8 ℃ than at other storage temperatures. The mRNA levels of TT8, a bHLH transcription factor, were higher in fruits stored at 8 ℃ than at room temperature throughout the entire storage period. Conversely, alternative splicing transcripts of TT8△, lacking a partial coding sequence, exhibited lower expression levels in fruit stored at 8 ℃. During postharvest storage, the genes involved in flavonoid biosynthesis and proton pumping were activated by TT8 and its partners. So that the increasing anthocyanin contents in juice sac tissues were attributed partially to TT8 expression changes caused by the alternative splicing during postharvest storage at a moderate temperature.

Convergent evolution, where unrelated species independently evolve similar traits, provides valuable insights into the genetic and developmental adaptation. In plants, physical defenses like spines, thorns, and prickles exemplifies this phenomenon. These structures, collectively termed "spinescence," arise from distinct developmental origins-spines from leaves, thorns from stems or branches, and prickles as epidermal outgrowths-but converge in function to deter herbivory and enhance survival. Among these, prickles are particularly interesting due to their morphological diversity and repeated gain or loss across various plant lineages. The genus Solanum serve as model for studying prickle genetics. In "Spiny Solanums," prickles evolved approximately six million years ago, with prickle loss occurring multiple times as seen in domesticated eggplant (Solanum melongena). Recent studies identify the LONELY GUY (LOG) gene family, crucial for cytokinin biosynthesis, as a key regulator of prickle development. Loss-of-function mutations in LOG homologs associated with prickleless phenotypes in various plants, including roses, chinese dates, and alfalfa, suggesting a conserved role in prickle suppression. This review explores the evolutionary, genetic, and molecular mechanisms underlying prickle development, emphasizing the LOG gene family. It discusses phenotypic convergence and agriculture applications, such as breeding prickle-free crops, offering broader insights into plant adaptation and the evolution of physical defenses.