Rice seed vigor is a life-cycle trait whose performance after sowing depends on physiological capacity established during seed development, preserved during storage, and reactivated during germination and seedling establishment. Rather than functioning as isolated stage-specific pathways, transcriptional networks coordinate a series of transitions between protection and growth. During seed development, transcription factors establish embryo competence, reserve organization, desiccation tolerance, and proteostasis, thereby creating the physiological capacity for subsequent performance. During storage, ABA- and auxin-associated bZIP networks, including the OsARF12–OsbZIP23 and OsbZIP23–PER1A modules and SAG9-associated regulation, maintain longevity through antioxidant and protective processes; emerging salicylic acid-associated signaling further extends this hormone–redox regulatory framework. After imbibition, ABA–GA balance, sugar and energy signaling, reserve mobilization, reactive oxygen species homeostasis, and cell expansion determine the timing and uniformity of germination, while related regulatory modules support establishment under salinity, chilling, water deficit, and oxygen limitation. Importantly, current evidence varies substantially in strength: some regulators are directly supported by germination, longevity, dormancy, or stress-vigor phenotypes, whereas others remain developmental candidates inferred mainly from grain composition or seed-development traits. Field-emergence validation and natural-storage evidence also remain limited. We therefore propose that rice seed-vigor improvement should prioritize stage-appropriate regulatory alleles and precise modulation of transcription-factor activity, while jointly considering storability, dormancy and pre-harvest sprouting resistance, field establishment, yield, and grain quality. Rice seed vigor emerges from stage-specific transcriptional regulation across seed development, storage, germination, and seedling establishment, providing a framework for identifying breeding targets that improve field performance.
The potential of bio inputs to enhance the organoleptic attributes of tomato, particularly, their nutraceutical benefits and export potential motivated us to develop stimulatory microbial formulations. Towards this endeavour, untargeted metabolic profiling and fruit volatile analysis in ‘Pusa Cherry 1’ tomatoes were undertaken, to analyse the differential elicitation of metabolites by microbial interventions. Treatment with cyanobacterium Anabaena laxa enhanced the fruit lycopene content by 1.13-fold while, a mesocarpic bacterium- Enterobacter cloacae enhanced the fruit lycopene, phenolics and flavonoids by 1.07, 1.5 and 2.54-fold respectively; combined inoculation led to 1.25 and 1.68-fold increase in phenolics and flavonoids, compared to control fruits. Untargeted metabolome analyses of fruits revealed A. laxa mediated enrichment of spermidine and benzoquinone and likely, induction of plant’s antioxidant defense system and hormonal modulation, towards enhanced lycopene content and accumulation of benzenoid derived floral volatiles. High lycopene, flavonoid and ascorbic acid content along with carotenoid and lipoxygenase derived fruity volatiles in the fruits of E. cloacae treatment can possibly be associated with the stimulation of sphingolipid metabolism, lipoxygenase mediated oxylipin synthesis and the accumulation of S-adenosyl methionine, both suggesting jasmonate/ethylene mediated induced systemic resistance. Enrichment of α-ketoglutarate, amines, purines and pyrimidines besides S-adenosyl methionine, sphingolipid and rutin accumulation in the fruits due to co-inoculation of A. laxa and E. cloacae was also supported by 20.4
Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), vital coenzymes for a wide array of plant metabolic processes, supporting photosynthesis, mitochondrial electron transport and fatty acid oxidation. While exogenous riboflavin application has been reported to improve plant responses to a range of abiotic and biotic stresses, the molecular responses associated with these protective effects remain largely unknown. Here, we present a comprehensive transcriptomic analysis of riboflavin-treated Arabidopsis seedlings, revealing significant changes in gene expression related to stress responses, signal transduction and secondary metabolism. Riboflavin treatment altered the expression of genes within specific cellular functional categories, suggesting a broad reprogramming of plant metabolism. Exogenous riboflavin caused pronounced changes in the expression of stress-responsive transcriptional regulators, including DREB19 and DREB2C, which are involved in stress-responsive signalling pathways. The transcriptional changes were consistent with a shift from growth-associated to stress-responsive functions, including repression of photosynthesis-related genes and activation of pathways associated with oxidative stress responses. These transcriptomic findings were accompanied by changes in cellular redox status, as riboflavin-treated seedlings exhibited reduced ROS accumulation, lower malondialdehyde levels, indicative of diminished lipid peroxidation and temporally regulated activities of CAT, SOD and APX. Furthermore, exogenous riboflavin altered the expression of genes involved in flavin metabolism, including FMN/FHY, which encodes a key bifunctional enzyme catalyzing the interconversion of riboflavin and FMN in the cytosol. Collectively, these results indicate that an acute increase in riboflavin availability triggers coordinated transcriptional and redox responses associated with stress-related pathways and flavin metabolism, highlighting the importance of tightly regulated riboflavin homeostasis in plants. Exogenous riboflavin reprograms stress-responsive transcriptional networks and modulates cellular redox homeostasis.
The biogenesis and function of plant mitochondria relies on the expression of the organellar genome, which involves extensive post-transcriptional processing of organellar transcripts in order to generate mature functional RNAs. This includes the removal of introns from many essential organellar transcripts through splicing, a process mediated by diverse nuclear-encoded RNA-processing factors, including numerous members of the pentatricopeptide repeat (PPR) protein family. Here, we report the analysis of PPR9 (At1g03560), a mitochondrial P-class PPR protein originally identified in genetic screens for essential protein cofactors. Loss of PPR9 function results in embryonic arrest at early stages of seed development. In vitro rescued homozygous ppr9 mutant plants could be recovered and maintained using a modified in vitro embryo-rescue method. The mutants display delayed growth and development which are associated with altered mitochondrial functions. Molecular analyses reveal that PPR9 functions in the splicing of several mitochondrial transcripts encoding respiratory complex I (CI) subunits, including nad2 intron 3 and nad7 introns 1 and 2. Accordingly, CI assembly is disrupted in ppr9 plants, resulting in altered OXPHOS activity and broad physiological defects. Together, these findings identify PPR9 as a key regulator of mt-RNA maturation in Arabidopsis, enabling CI biogenesis and optimal respiratory functions, and further highlight the roles of nuclear-encoded factors in coordinating mitochondria functions and (early) plant growth and development. Our study identifies PPR9 as a key mitochondrial RNA-processing factor required for the splicing of multiple group II introns that reside within genes encoding subunits essential for respiratory complex I biogenesis in Arabidopsis. By linking nuclear control of RNA maturation to mitochondrial function and plant development, this work emphasizes a critical layer of coordination between organellar gene expression, mitochondria function and developmental regulation in land plants.
The ubiquitination/deubiquitination system is a key regulatory mechanism for maintaining proteome homeostasis in eukaryotic cells. Deubiquitinating enzymes (DUBs), which remove ubiquitin from substrate proteins, regulate plant development, stress responses, and other physiological processes. Although DUBs have emerged as important regulators of plant growth and stress responses, their systematic genomic characterization in white birch (Betula platyphylla) remains limited, restricting our understanding of their potential roles in the reproduction of woody plants. In this study, 56 BpDUB genes were identified in white birch (Betula platyphylla) and classified into six conserved subfamilies (UBP, OTU, UCH, MJD, JAMM, and MINDY). Comparative and synteny analyses revealed that DUB genes are evolutionarily conserved while exhibiting lineage-specific divergence across angiosperms. Promoter analysis showed that BpDUBs harbor diverse cis-acting elements associated with growth and development, stress responses, hormone signaling, and transcription factor binding. Treatment with the broad-spectrum DUB inhibitor PR-619 markedly impaired both pollen germination and pollen tube elongation, supporting the involvement of DUB activity in pollen development. RNA-seq analysis showed that BpUBP3 exhibited stage-specific induction during pollen germination, and AS-ODN-mediated downregulation of BpUBP3 reduced pollen germination and pollen tube growth. These findings provide preliminary evidence supporting a role for BpUBP3 in pollen germination and pollen tube growth and provide a basis for further investigation of DUB functions in reproductive development in white birch. The identified DUB family is associated with pollen development in Betula platyphylla, with BpUBP3 showing potential involvement in pollen germination and pollen tube growth.
