The papain-like cysteine proteases (PLCP) in tomato: Identification, expression analysis, and functional characterization of SlRD19B under salt stress.

Functional characterization of sorghum aquaporin SbTIP2;1 for enhanced salt, drought and heat tolerance in transgenic tobacco.

Mycorrhiza, water stress, and rootstock–scion combinations shape plant physiological traits and gene expression in grapevine

Evolution of plant gene delivery: From biolistic to next-generation nanocarriers

Kelps are ecologically and economically important organisms. Kelp biomass generates habitat structure and carbon flux and is increasingly harvested as a sustainable resource. Kelp blades grow through cell proliferation at the proximal meristem and erode from the distal end, resulting in a spatiotemporal map reflecting tissue development. Diel physiology, such as photosynthesis, respiration, and carbohydrate metabolism, changes across the growing blade, yet the interaction of the circadian clock with age / blade structure has not been explicitly tested. Here, we sampled the proximal and distal ends of giant kelp (Macrocystis pyrifera) blades over 48 h under constant lab conditions to compare differential transcriptomic and circadian regulation across the blade. Gene function was differentially enriched across the blade, with proliferative and protective pathways upregulated in the younger proximal tissue and carbon acquisition and metabolic pathways upregulated in older distal tissue. We identified candidate aging-related genes based on similarities to plant, animal, and fungal senescence-associated genes, which were enriched in the older, distal tissue. While ~13% of analyzed genes displayed consistent circadian regulation across the blade, ~2% displayed altered rhythmic parameters, with consistently lower amplitudes and longer periods in older distal tissue. This is evidence of variable circadian physiology across giant kelp anatomy. The interacting developmental and circadian influences on the giant kelp transcriptome evoked here are integral for understanding the coordination of physiology important to kelp growth and health.

Alternative splicing (AS) represents a crucial post-transcriptional regulatory mechanism that enhances protein diversity by generating distinct transcripts from the same mRNA precursors. It is estimated that 60-70% of plant genes containing introns undergo AS events. The splicing complex, which comprises RNA-protein components such as the spliceosome, small nuclear RNAs, and ribonucleoproteins, is responsible for the excision of introns, the joining of exons, and the modulation of alternative 3' or 5' splicing sites. These splicing components play a vital role in fine-tuning mRNA processing, thereby ensuring normal plant growth and development, as well as facilitating rapid responses to environmental changes. This review aims to summarize recent advancements in the understanding of AS in plants and to discuss the research challenges associated with the dynamic regulation of AS in the near future.

ABSTRACT Drought events can have a devastating impact on agriculture, and due to climate change, such extreme events are expected to become more frequent. Sugarcane plays a critical role in the Brazilian economy by producing sugar and bioethanol, contributing positively to the reduction of CO2 emissions. Although sugarcane is considered resilient to drought, this stress remains the primary abiotic factor reducing sugar and biomass yields. Here, we describe the role of a sugarcane gene, ScTpx2, which is induced by drought in sugarcane leaves under field conditions. When overexpressed in Arabidopsis, ScTpx2 enhanced plant survival under extreme water deficit and improved performance under mild stress conditions, which better represent field scenarios. We subsequently overexpressed the ScTpx2 gene in sugarcane plants. After 10 days of water deficit at 30% field capacity in a greenhouse, net photosynthesis in ScTpx2-overexpressing lines (ScTpx2OE) was 12–23% higher than in wild-type plants. While malondialdehyde (MDA) content, a marker of oxidative stress, increased by 129% in wild-type plants under water deficit, in ScTpx2OE plants, the increase ranged from 20% to 107%. Additionally, the vascular bundles and xylem areas were larger in ScTpx2OE compared to WT. These findings suggest that the ScTpx2 protein influences the development of the vascular system, thereby improving water transport efficiency. Our results demonstrate that overexpression of the ScTpx2 gene mitigates the effects of water deficit in sugarcane, offering promising opportunities for biotechnological applications in developing drought-tolerant commercial cultivars.

Poplar is severely damaged byHyphantria cunea (fall webworm), which significantly reduces tree productivity. However, conventional pest management methods are largely ineffective against fall webworm infestation. In this study, we demonstrated that the Vip3A protein possesses high insecticidal activity againstH. cunea by overexpressing a syntheticTHI1-Vip3A gene in poplar plants. A dicot codon-optimizedVip3A gene, fused with theTHI1 chloroplast signal peptide sequence, was chemically synthesized and introduced into the poplar cv. '741' genome viaAgrobacterium-mediated transformation. PCR, RT-PCR, and ELISA analyses confirmed the integration and successful expression of the transgene at both the mRNA and protein levels. The Vip3A protein concentration in chloroplasts was approximately 4.8-fold higher than in the whole leaf extract, indicating that the Vip3A protein was successfully targeted to and accumulated within the chloroplasts by the THI1 signal peptide. Subsequently, four transgenic lines with high Vip3A expression were subjected to H. cunea infestation. Compared to wild-type plants, these four transgenic lines exhibited significantly higher resistance, resulting in pest mortality rates exceeding 95% and significantly reduced leaf damage. Together, these results indicate that Vip3A possesses high insecticidal activity againstH. cunea. Therefore, transgenicTHI1-Vip3A poplar plants can serve as valuable germplasm for breeding poplar cultivars with high resistance toH. cunea infestation.

Climate change is a critical global issue fueled by greenhouse gas (GHG) emissions. Rice cultivation, especially under anaerobic conditions, significantly contributes to methane (CH4) emissions, a potent GHG. In this study, we investigated CH4 emissions in rice using a custom chamber with a sensitive methane sensor and a graphical user interface (GUI) for tracking emissions. Here, we examined the 120 Cheongcheong/Nagdong double haploid (CNDH) population, with methane measurements conducted at the fourth leaf stage. Using Windows QTL Cartographer 2.5 and a genetic map, we identified QTLs associated with CH4 emission on chromosome 1, 3, and 6. Gene expression analysis highlighted significant differences in the expression of LOC_Os03g07480 (OsSUT1q3), a sucrose transporter, and LOC_Os03g13274 (OsNRTq3), a nitrate transporter on chromosome 3 between RM14330-RM7197. In rice plants, sucrose transporter genes release sugars, including sucrose, which are becoming a carbon source for methanogens in the soil. Nitrate transporter genes in rice plants influence nitrogen availability in paddy soil. Gene variations directly affect microbial nitrogen metabolism, enhanced carbon release and modified nitrogen availability in the rhizosphere, potentially changing methane emissions from rice paddies. Validation across 65 Korean rice cultivars confirmed a strong association between methane emission levels and the expression patterns of these two genes. Our findings shed light on the genetic factors influencing methane production in rice and offer hope for creating climate-resilient rice varieties that reduce methane emissions.

Heterologous expression of MfERF053 enhances alfalfa drought resistance by regulating ABA signaling, antioxidant defense, and photosynthetic protection.

Genome-wide identification of CsREMs and their roles in tea plant overwintering bud dormancy and sprouting.

The transcription factor SlPLATZ22 negatively regulates salinity tolerance in tomato plants.

Roles of the Mediator complex and transcriptional activators/repressors in regulating plant gene expression under salt stress

Despite the rapid expansion of information on eukaryotic genomes, data on ribosomal DNA (rDNA) loci encoding ribosomal RNAs, crucial for the biogenesis of ribosomes, are absent in almost all cases due to difficulties in assembling the long regions of tandemly repeated DNA units. Taking advantage of the uniquely low rDNA copy number in the aquatic plant Spirodela polyrhiza, we resolved the species' complete 5S rDNA architecture at a nucleotide level. A combination of in situ hybridization, extra-long DNA reads, and conventional DNA sequencing allowed the assembly of near-complete loci sequences of 40,878 bp, specific for one haplotype of chromosome ChrSp6, and of 110,911 bp specific for a haplotype of ChrSp13. The completely resolved 5S rDNA locus of ChrSp6 contains 40 copies of tandemly repeated gene units with an intergenic spacer (NTS) of 400 bp for one haplotype, and more than 60 highly homogenized gene copies for the second haplotype. The ChrSp13 locus contains 5S rDNA clusters with NTSs of 1,056 or 1,069 bp arranged in two sub-clusters. The G/C-rich 5S rDNA arrays in both loci are embedded in A/T-enriched chromosome regions. This work advances our understanding of the basic principles of rDNA organization and evolution of rRNA genes in plants by revealing the molecular architecture and evolutionary dynamics of 5S rDNA loci.

IntroductionRoot- and leaf-associated microbiomes are crucial for plant health and influence the yield and quality of the products. The composition of microbes and their association with the host depend on different factors that must be continuously investigated.ResultsWe examined the composition and structure of bacterial and fungal communities in four compartments (root, rhizoplane, rhizosphere, and leaf endosphere) of two grapevine varieties (‘Alachua’ and ‘Noble’) targeting the 16S rRNA V5–V7 and ITS regions.Results and discussionA comparison of the effects of the varieties and compartments showed that they were the major factors contributing to variations in the microbial structures. Bacterial alpha diversity significantly decreased from the rhizosphere to leaf endosphere, while the fungal alpha diversity did not show linear variations. According to normalized stochastic ratio analysis, deterministic processes dominated the bacterial and fungal assemblies of the leaf endosphere while stochastic processes in the rhizosphere and rhizoplane dominated the microbial assemblies. Assembly processes in bacterial and fungal roots differed (stochastic processes in bacteria and deterministic processes in fungi). Twenty shared core operational taxonomic units (OTUs) (bacteria, 13; fungi, 7) were identified across all compartments. Various stilbene compounds in leaf were significantly correlated with these shared core microbes, and weighted gene co-expression network analysis revealed that some hub genes were correlated with these metabolites. Thus, their role as regulators of grapevine microbiome interactions needs to be further evaluated. This study provided new profiles of the microbiota in different grapevines compartments, which suggested their association with grape metabolites and plant genes, representing a major development for further studies focused in understanding the role of these microorganisms for grapevine production.

As a core regulatory component of photomorphogenic signaling, phytochrome interacting factor 4 (PIF4) participates in multiple developmental processes in plants. To analyze the function and mechanism of this gene in ornamental plants, this study elucidated the role of PhPIF4 in the branching development of Petunia hybrida and its downstream regulatory pathways through genetic transformation and RNA sequencing (RNA-seq). The results showed that Arabidopsis transgenic lines overexpressing PhPIF4 exhibited reduced branches, whereas PhPIF4-RNAi transgenic lines of P. hybrida displayed significantly increased branches. RNA-seq results revealed that 591 differentially expressed genes in PhPIF4-overexpressing lines were significantly enriched in phytohormone metabolic pathways, and the expression levels of cytokinin biosynthesis-related genes IPT3/5, CYP735A1, and LOG2 were markedly downregulated. Further verification demonstrated that PhPIF4 affected branching by activating the branching inhibitor genes BRC1 and SPL9 and the far-red light chaperone gene FHL. This study provides a theoretical basis for further elucidating the molecular mechanisms by which PhPIF4 regulates the branching of P. hybrida.

Pathogens significantly impair plant growth and developmental processes. Emerging evidence has highlighted the pivotal roles of MYB transcription factors (TFs) and histone H3K36me3 transferase in orchestrating regulatory networks that govern plant defense responses against pathogen stress. However, the potential for synergistic interactions among these genes in woody plants, particularly within poplar subjected to biotic stress, remains largely unexplored. Functional analysis showed that PopMYB4 overexpression (OE) reduced pathogen tolerance, whereas RNA interference (RNAi)-mediated suppression enhanced host resistance to pathogens. This phenotypic change was linked to modified reactive oxygen species (ROS) dynamics and the coordinated regulation of defense genes, notably PopGSTU7. Y1H, EMSA, and dual-luciferase assays indicated that PopMYB4 directly binds to the PopGSTU7 promoter and represses its transcription. We further established that PopSDG36 physically interacts with PopMYB4, thereby alleviating PopMYB4's inhibitory effects on PopGSTU7 expression. Functional analysis using overexpression demonstrated that PopSDG36 positively regulates resistance to Colletotrichum gloeosporioides in poplars. Moreover, the PopSDG36 transgenic plants led to increased H3K36me3 levels at PopGSTU7, thus increasing PopGSTU7 expression. The PopMYB4-PopSDG36 represents a dual-function regulatory hub in poplars, integrating transcriptional regulation and H3K36me3-mediated epigenetic regulation to fine-tune immune signaling networks, thereby providing mechanistic insights into plant-pathogen coevolution.

Abstract Dof (DNA-binding with one finger) transcription factors play key roles in regulating plant gene expression, thereby influencing developmental regulation, stress response, and metabolic network construction. However, their involvement in plant pathogen defense has been less studied, particularly in the resistance mechanism to Botryosphaeria dothidea . This study reveals the apple ( Malus × domestica ) transcription factor MdCDof3L positively regulates resistance against B. dothidea . Overexpression of MdCDof3L in apple calli and fruits significantly enhanced disease resistance to B. dothidea . Jasmonic acid (JA) and salicylic acid (SA) contents, as well as the expression of JA and SA synthesis-related and signaling-related genes, were higher in MdCDof3L -overexpressing apple calli and fruits than those in the control after inoculation. In addition, MdCDof3L plays a crucial role in apple responses to JA and SA signaling. Furthermore, exogenous application of methyl jasmonate (MeJA) and SA significantly induced MdCDof3L expression and enhanced apple resistance to B. dothidea . Overall, these findings suggest that MdCDof3L enhances apple resistance to B. dothidea through the JA and SA pathways, providing new insights into the role of Dof transcription factors in regulating plant disease resistance.

Herbicide-resistant (HR) oilseed rape (Brassica napus, AACC, 2n = 38) is the potential for transgenes to spread to its wild relative, Brassica juncea (AABB, 2n = 36). Previous research identified gene silencing in these progenies, observing plants that carried the HR gene PAT but did not express it normally (silenced, or r-s plants). We found that r-s plants exhibited more stable inheritance compared to plants normally expressing PAT (expressed, or r-e, plants). Chromosome numbers in backcross progenies of r-s plants were consistently around 2n = 36. Specifically, r-s plants self-pollinated by r-e plants also showed chromosome numbers concentrated around 2n = 36, whereas in the r-e plants self-pollinated by r-e plants displayed numbers concentrated around 2n = 37. The meiotic indices of r-s plants exceeded 90%, further indicating their superior genetic stability compared with r-e plants. Despite these differences in genetic stability, r-s plants and r-e plants showed similar fitness. As the number of self-pollinated generations increased, the fitness of succeeding progeny gradually approached that of wild B. juncea. Integrating the transgene onto the C-chromosome, which exhibits low genetic stability, holds significant promise for reducing the gene flow risk associated with HR crops. © 2026 Society of Chemical Industry.

Deciphering adaptation to habitat shifts across the salinity boundary necessitates investigation of "lost" and "acquired" saline genes. By assembling a telomere-to-telomere genome, we propose that the euryhaline Chlorophyta Chlorella sp. MEM25 represents an early-diverging saltwater species that has evolved numerous genes essential for saltwater-freshwater transitions. By comparison with Viridiplantae genomes, we identify ancestral genes and lineage-specific genes related to salinity adaptation. Loss-of-function mutants of the proposed salt-sensitive genes in algae and plants exhibit increased salt resistance, highlighting the potential of the MEM25 genome as a breeding resource. Notably, the gene RMI1 plays an important role in salinity tolerance across species, from microalgae to higher plants.