Distinct Activation of Defense-Related Gene Networks in Rosetted Versus Symptomless Shoots in Rose Rosette Virus-Infected Roses

Integrated transcriptome and hormone dynamics uncover biphasic defense responses in sugar beet infected by Cercospora beticola

This study links major defense transcriptional programs and phytohormone dynamics, providing a comprehensive view of sugar beet responses to CLS, and revealed that a susceptible sugar beet genotype mounts an early and transient defense response against C. beticola.

Genome-Wide Profiling of Cold-Responsive Genes in Zelkova schneideriana Under Chilling Stress

Zelkova schneideriana Hand.-Mazz. is an ecologically and economically valuable tree species in China, but its sensitivity to low temperature restricts its use in colder regions. To identify genes and pathways associated with chilling responses, we combined physiological screening, full-length transcriptome construction, Illumina RNA-seq, and time-ordered gene co-expression network analysis (TO-GCN). Fifty seedling lines were evaluated after 7 d at 4 °C, and the line with the lowest relative electrolyte leakage (REL) and malondialdehyde (MDA) content was selected for transcriptome profiling at 0, 3, and 6 d of chilling treatment. RNA-seq detected 5875 differentially expressed genes. Most expression changes occurred by day 3 and were largely maintained on day 6. Pathway reconstruction showed contrasting dynamics between antioxidant-related systems: Flavonoid and anthocyanin biosynthesis were progressively activated, whereas glutathione-related genes, particularly glutathione S-transferase family members, were broadly repressed. TO-GCN highlighted ZeF3H (Ze_transcript_14112) as a late-stage hub associated with anthocyanin biosynthesis and ZeDRT102 (Ze_transcript_44427) as an early-stage hub linked to DNA damage repair and glutathione-associated genes. These results indicate that the chilling response in Z. schneideriana involves activation of flavonoid-based protection together with weakened glutathione-mediated redox regulation, providing candidate genes for functional validation and cold-resistance breeding. These insights provide a critical foundation for molecular breeding strategies that will ultimately facilitate the successful introduction and stable cultivation of this valuable species in northern temperate climates.

Genome-Wide Identification of the PsatGST Gene Family and Expression Analysis Under Freezing Stress in Peas (Pisum sativum L.)

Background: Glutathione S-transferases (GSTs) play pivotal roles in plant growth, abiotic stress responses, detoxification of xenobiotics, and maintenance of redox homeostasis. Methods: In this study, transcriptomic analysis was employed to identify differentially expressed genes (DEGs) in the pea cultivar DX27 under freezing stress (−4 °C) at 3, 6, and 12 h. Results:GO and KEGG enrichment analyses of global transcriptomic data further reveal that DEGs are significantly enriched in the following functional categories: oxidation–reduction processes, stress responses, glutathione metabolism, and secondary metabolite biosynthesis. A total of 52 PsatGST genes were identified and classified into nine subfamilies based on phylogenetic relationships. Chromosomal localization revealed a non-random distribution across seven chromosomes. Promoter cis-element analysis indicated that PsatGST genes harbor diverse regulatory elements associated with light responsiveness, hormone signaling (auxin, abscisic acid, gibberellin, salicylic acid, and MeJA), and abiotic/biotic stress responses. PsatGSTF2 expression analysis showed pronounced up-regulation under freezing stress (−4 °C) at 3, 6, and 12 h. Conclusions: These findings provide a foundational framework for understanding the evolutionary history and functional diversification of the PsatGST gene family and offer valuable candidate genes for the breeding of stress-tolerant pea varieties.

Genome-Wide Exploration of SUPPRESSOR OF MAX2 1-LIKE Genes in Peanut (Arachis hypogaea) Reveals Developmental and Stress-responsive Expression Patterns

Disease-stage-associated transcriptional responses underlying bacterial wilt resistance in tobacco cultivar Yunyan 87 caused by Ralstonia solanacearum.

Bacterial wilt caused by Ralstonia solanacearum severely limits tobacco production, yet the molecular basis of resistance to vascular wilt diseases remains poorly understood. We integrated field phenotyping, pathogen isolation, and transcriptomic analyses across different disease stages to investigate root responses of the resistant tobacco cultivar Yunyan 87 at healthy, moderately infected, and severely infected stages. Disease progression was accompanied by marked root biomass loss, with fresh and dry weights reduced by approximately 60% and 70%, respectively. Transcriptomic analyses identified 994 up-regulated and 1,151 down-regulated genes at the moderate stage, and 2,158 up-regulated and 2,284 down-regulated genes at the severe stage. WGCNA identified a disease severity-associated regulatory module. Functional enrichment analyses showed that moderate infection activated stress perception and redox homeostasis, whereas severe infection strongly suppressed translation and ribosome biogenesis. Dynamic expression pattern analysis further revealed coordinated activation of phenylpropanoid metabolism and lignin biosynthesis, and synergistic induction of MAPK, salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) signaling pathways, followed by progressive metabolic repression. Key transcription factor families, including WRKY, MYC2, and ERF, exhibited distinct stage-dependent expression patterns. Collectively, our results demonstrate a disease-stage-associated transcriptional reprogramming strategy that balances defense activation and metabolic restraint during bacterial wilt progression, providing valuable regulatory networks and candidate genes for breeding tobacco cultivars with enhanced resistance.

Integrated Transcriptomic Profiling Reveals Distinct and Overlapping Transcriptional Responses and Regulatory Pathways Mediated by Salicylic Acid, Jasmonic Acid, and Abscisic Acid in Lotus (Nelumbo nucifera)

Sacred lotus (Nelumbo nucifera) is an important aquatic crop whose growth and productivity are severely constrained by environmental stresses. Salicylic Acid (SA), Jasmonic Acid (JA), and Abscisic Acid (ABA) are key plant growth regulators (PGRs) involved in stress responses, but their regulatory mechanisms in lotus remain unclear. In this study, transcriptome sequencing was performed in lotus seedlings treated with exogenous SA, JA, and ABA to characterize hormone-responsive regulatory networks. SA predominantly resulted in transcriptional repression, with responsive genes mainly associated with photosynthesis and ribosome-related pathways, whereas JA and ABA showed similar regulatory patterns with enrichment of hormone signaling and Mitogen-activated protein kinase (MAPK) pathways, but distinct roles in defense regulation and stress adaptation. A total of 607 genes were identified as commonly responsive to the three PGRs and were significantly enriched in cold response, defense response, secondary metabolism, and photosynthesis-related pathways. Protein–protein interaction analysis identified two hub genes encoding light-harvesting chlorophyll a/b-binding proteins, suggesting that the photosynthesis–antenna proteins pathway may represent a convergent regulatory node in hormone-mediated stress responses. This study provides new insights into SA-, JA-, and ABA-mediated stress responses and identifies potential candidate genes for improving stress tolerance in lotus.