Search Results (1,627)

Leaf senescence, the final developmental stage of a leaf, is a highly regulated process that is vital for the recycling of nutrients and the maintenance of plant fitness. Its control operates at multiple levels, including chromatin remodeling, transcription, post-transcriptional regulation, translation, and post-translational modifications. This review summarizes recent advances in understanding the roles of key transcription factor (TF) families—WRKY, NAC, and MYB—in modulating leaf senescence in Arabidopsis thaliana. We detail how these TFs integrate internal and external signals to regulate senescence-associated genes (SAGs). In addition, we explore the pivotal role of microRNAs (miRNAs) in post-transcriptional control of senescence, focusing on their regulation of these TF families. In conjunction with the transcriptome data of Arabidopsis miRNAs under conditions of dark-induced senescence, we also highlight several novel senescence-associated miRNAs. Integrating transcriptional and post-transcriptional perspectives, this review presents an updated regulatory network for leaf senescence and discusses potential applications for manipulating senescence in crops to improve yield and quality. Full article

At present, the characteristics of key enzyme genes in the upstream pathway for triterpenoid saponin biosynthesis in P. grandiflorum, as well as their expression patterns over the growth duration, have not been systematically analyzed. This study, at the whole-genome level, conducts the first bioinformatics and expression analyses of the SS and SE gene families in P. grandiflorum. Four PgSS and seven PgSE genes were identified and distributed across six chromosomes. Members within the same subfamily exhibited highly conserved sequences and structures, while distinct structural divergence was observed between different subfamilies. Phylogenetic analysis showed that PgSS and PgSE genes were closely related to those of dicotyledons such as Panax ginseng and Polygala tenuifolia, suggesting high evolutionary conservation. Promoter analysis revealed abundant light- and hormone-responsive elements and MYB/MYC binding sites, indicating regulation by multiple signals. Protein secondary structures were dominated by the Alpha helix and were structurally stable. Quantitative real-time polymerase chain reaction (qPCR) demonstrated that expression levels of PgSS and PgSE in one-year-old Platycodonis Radix were significantly higher than in perennial Platycodonis Radix, especially for the PgSE family. This study characterized the basic biological features and growth-stage-dependent expression patterns of the SS and SE gene families in P. grandiflorum. The results identify key candidate genes and molecular targets for regulating triterpenoid saponin biosynthesis, and provide data supporting quality improvement and active metabolite research in this medicinal plant. Full article

Secondary cell wall (SCW) formation and lignin biosynthesis are critical biological processes that determine wood properties. Masson pine (Pinus massoniana Lamb) is a fast-growing conifer species with significant economic value for the pulp and paper industry. While R2R3-MYB transcription factors are known as master regulators of SCW biosynthesis, the specific R2R3-MYB members regulating lignin formation in Masson pine remain largely uncharacterized. In this study, we identified 317 R2R3-MYB genes in the Masson pine genome. Phylogenetic analysis revealed that PmMYB289, a member of the P20 subgroup, is highly homologous to the Arabidopsis SCW regulators AtMYB52 and AtMYB54. Expression profiling demonstrated that PmMYB289 is predominantly expressed in highly lignified old stems. Transcriptional activation assays confirmed that PmMYB289 lacks autoactivation activity. Subcellular localization analysis revealed that PmMYB289 was localized to the nucleus. Ectopic overexpression of PmMYB289 in tobacco (Nicotiana benthamiana) resulted in dwarfed plant growth, reduced stem diameter, and curled leaves. Molecular analysis of these transgenic lines showed a significant downregulation of most key SCW biosynthetic genes, with the exception of NbPAL1. These findings indicate that PmMYB289 acts as a crucial transcriptional repressor in SCW biosynthesis, providing valuable genetic resources for the molecular breeding of superior Masson pine varieties. Full article

IQ67-domain (IQD) proteins are plant-specific calmodulin (CaM)/calmodulin-like (CML) targets implicated in the spatial organization of Ca²⁺ signaling, yet their roles in tartary buckwheat (Fagopyrum tataricum) remain largely unexplored. Here, we identified 24 FtIQD genes and classified them into six phylogenetic subfamilies. FtIQDs show uneven chromosomal distribution and mainly arise from segmental duplication under purifying selection. Promoter analysis revealed the enrichment of MYB-, light-, and ABA-related cis-elements. To link FtIQDs with rutin variation, we performed an FtIQD-focused association analysis using whole-genome resequencing data from altitude-stratified panels of up to 220 accessions. Under additive, dominant, and recessive models, multiple significant SNPs (p < 1 × 10⁻⁵) were detected near a subset of FtIQD loci, showing clear model- and environment-dependent patterns. Recurrent loci included FtIQD22, FtIQD02, FtIQD16, and FtIQD19. RNA-seq under PEG-induced drought stress, tissue expression patterns, pathway co-expression, and qRT–PCR further prioritized FtIQD19. FtIQD19–GFP showed predominant nuclear localization with additional filamentous/peripheral signals, and yeast two-hybrid assays identified FtCaM7.2 as the strongest interactor among representative CaMs. Structural modeling of the FtIQD19–FtCaM7.2 complex suggested testable residue-level interaction features. Collectively, this work provides a foundational FtIQD resource and highlights candidate Ca²⁺/CaM–IQD modules potentially associated with altitude-dependent rutin variation in tartary buckwheat. Full article

Background/Objectives: Ludisia discolor, an endangered medicinal orchid, is a vital source of bioactive flavonoids which requires in vitro tissue culture for propagation and metabolite production. While light quality influences metabolic processes, the mechanisms connecting light conditions, phytohormone signaling, and flavonoid biosynthesis remain unclear. This study investigates how specific light qualities trigger secondary metabolism to improve tissue culture and conservation strategies. Methods: L. discolor was cultivated under strictly regulated LED environments (blue, red, yellow, and green). An integrated multi-omics approach, combining transcriptomic sequencing and targeted metabolomic profiling, was employed to analyze leaves, correlating plant hormone changes with flavonoid metabolite levels. Results: LED light qualities significantly altered flavonoid and phytohormone profiles, yielding 80 unique flavonoids. Blue and red light effectively promoted flavonoid accumulation, whereas yellow light suppressed it. Transcriptomics, validated by qRT-PCR, revealed distinct expression patterns in key structural genes (e.g., 4CL, PAL, CYP73A, FLS, CCoAOMT, C12RT1). Ten transcription factors (including MYB93, bZIP36, bHLH4, and bZIP44) with hormone-responsive cis-elements were co-expressed with 16 structural genes. Notably, blue light induced reactive oxygen species (ROS) signaling, activating phytohormone production (IAA, GA, ABA). These hormones subsequently stimulated transcription factors, increasing the biosynthesis of compounds like neohesperidin and hesperetin. Conclusions: We propose a novel regulatory model where light-induced ROS and phytohormone cascades activate specific transcription factors, enhancing structural gene expression in the flavonoid pathway. These findings elucidate the molecular mechanisms of light-driven secondary metabolism, providing valuable insights for the sustainable agriculture and ex situ conservation of endangered medicinal orchids. Full article

Leaf senescence is a critically regulated developmental process that determines crop yield and quality. MYB and NAC transcription factors (TFs) are central regulators within this network, yet the crosstalk between these TF families and their connection to the gibberellin (GA) pathway remain poorly understood. This study revealed that overexpression of DIV1, a MYB-like TF, leads to significantly reduced chlorophyll content and precocious leaf senescence. Based on the public transcriptome profiling of DIV1-overexpression leaves, 37 senescence-associated differentially expressed genes (DEGs), including the highly upregulated NAC59 and NAC92, were identified. Molecular assays confirmed that DIV1 directly binds to the promoters of NAC59 and NAC92 and activates their transcription. Meanwhile, yeast two-hybrid and split-luciferase assays demonstrated that DIV1 physically interacts with the GA biosynthetic enzyme ent-kaurene oxidase (KO1) both in vitro and in vivo. The promoted senescence phenotype in DIV1-overexpression lines was rescued by treatment with paclobutrazol (PAC), a GA biosynthesis inhibitor. In summary, our findings reveal a dual mechanism whereby DIV1 integrates the GA pathway and NAC-mediated transcription to regulate leaf senescence. This work provides new insights into the coordination between MYB and NAC TFs during hormone-mediated senescence. Full article

Epimedium brevicornu is an important medicinal plant in China, whose main bioactive components are flavonoid glycosides. UDP-glycosyltransferases (UGTs) play key roles in flavonoid glycosylation and metabolic diversification. In this study, transcriptome data from four representative production regions in Gansu Province were used to systematically identify and analyze the UGT gene family in E. brevicornu. A total of 359 UGT members were identified, and 168 homologous genes with clear expression evidence were obtained from four geographical populations. Molecular evolutionary analysis showed that most UGT genes were under purifying selection, whereas UGT2, UGT52, UGT57, UGT241, UGT269, and UGT271 exhibited significant signals of positive selection in specific lineages (p < 0.05). Protein interaction analysis indicated that many UGT proteins were closely associated with key enzymes involved in flavonoid biosynthesis, including CHS (TT4), CHI (TT5), F3H, FLS, and DFR, suggesting their potential involvement in flavonoid metabolism. Promoter analysis further revealed a high enrichment of ERF (11,169 occurrences) and MYB (7673 occurrences) transcription factor binding sites in the upstream regions of UGT genes. In addition, UGT57 and UGT241 showed significantly higher expression levels in the QLH population. Molecular docking analysis indicated relatively strong binding affinities with quercetin, with binding energies of −7.23 kcal/mol and −4.62 kcal/mol, respectively. These results suggest that the sequence variation and differential expression of UGT genes may be associated with flavonoid glycosylation and ecological adaptation in Epimedium. This study provides a basis for understanding the evolutionary characteristics and expression patterns of the UGT gene family and offers candidate genes for future studies on flavonoid metabolism. Full article

Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, a key acyltransferase in the phenylpropanoid pathway and a canonical member of the BAHD acyltransferase family (BAHD), catalyzes the formation of pivotal intermediates in the biosynthesis of secondary metabolites such as lignin, chlorogenic acid, and flavonoids. These compounds serve indispensable protective functions in terrestrial plants, underpinning their adaptive responses to abiotic stresses such as drought, ultraviolet (UV) radiation, and oxidative damage. Although the role of HCT/HQT in the core phenylpropanoid pathway has been extensively characterized, its precise functional contributions to the flavonoid biosynthetic branch—particularly with respect to substrate selectivity, kinetic regulation, and metabolic channeling—remain incompletely understood. This review systematically analyzes the structural features, spatial conformation, catalytic mechanism, and substrate promiscuity of HCT/HQT to clarify its molecular determinants of activity and specificity. Furthermore, it highlights regulatory factors influencing HCT/HQT gene expression, such as transcription factors (MYB, bHLH, WRKY), phytohormones (GA₃, Eth, MeJA, 6-BA, MT), and abiotic/biotic stressors (temperature, blue light, nitric oxide, nano-selenium). Collectively, these insights illuminate how plants dynamically fine-tune phenylpropanoid metabolism in coordination with developmental programs and environmental challenges. This work provides a foundation for further research on HCT/HQT and supports efforts to develop improved crop varieties through targeted regulation of this central metabolic node. Full article

KNOTTED1-LIKE HOMEOBOX (KNOX) genes are conserved transcription factors that play crucial roles in plant growth, development, and stress responses. However, systematic characterization of the KNOX family in Malus sieversii, a valuable germplasm resource with outstanding stress tolerance and flavonoid accumulation, remains lacking. In this study, we performed a genome-wide identification of the KNOX gene family in M. sieversii and identified 21 MsiKNOX genes. Phylogenetic analysis classified these genes into three subfamilies (Class I, II, and M), with structural features and motif compositions consistent with those of their orthologs in Arabidopsis thaliana and cultivated apple. Chromosomal localization revealed an uneven distribution across 13 chromosomes, and synteny analysis indicated both conserved evolution and lineage-specific expansion of the KNOX family in M. sieversii. Promoter cis-element analysis suggested that MsiKNOX genes are potentially involved in responses to multiple abiotic stresses and hormone signaling. Expression profiling under ABA and GA treatments showed that most MsiKNOX genes responded differentially to these phytohormones. Notably, MsiKNOX09 was significantly upregulated by ABA and downregulated by GA, and was further shown to physically interact with the anthocyanin-associated MsiMYB1 in yeast two-hybrid and split-luciferase assays. These findings provide a comprehensive overview of the KNOX gene family in M. sieversii and suggest that MsiKNOX09 acts as a hormone-responsive regulator and may participate in MsiMYB1-mediated regulatory pathways. Full article

Erythropoiesis is tightly regulated by lineage-specific transcription factors that govern erythroid commitment, proliferation, and differentiation. A core erythroid transcriptional network, together with non-DNA-binding cofactors, occupies regulatory regions of genes essential for erythroid development. This process is further shaped by epigenetic mechanisms, including histone post-translational modifications and long-range chromatin interactions. CCCTC-binding factor (CTCF) is a multifunctional regulator with a central role in three-dimensional chromatin organization. Although CTCF has been implicated in hematopoietic differentiation and leukemogenesis, its specific function in erythropoiesis remains poorly defined. Here, we investigated the role of CTCF during erythroid differentiation using two complementary models: pluripotent K562 leukemia cells and primary human CD34⁺ hematopoietic stem/progenitor cells, each induced toward the erythroid lineage by distinct stimuli. In both systems, CTCF silencing impaired erythroid differentiation by repression of key erythroid transcription factor genes, including LMO2, KLF1, MYB, and ETS1. This repression was associated with enrichment of repressive histone marks at CTCF-binding sites within their regulatory regions. Moreover, CTCF cooperated with cohesin to establish and stabilize long-range chromatin interactions at these loci. These results provide new insight into how CTCF-dependent chromatin regulation contributes to normal erythroid development and suggest that perturbation of this regulatory axis may have implications for hematopoietic disorders and malignancies. Full article

To develop safe and effective preservatives for fresh-cut produce, this study elucidates the multi-pathway mechanisms through which Melatonin (MT) regulates postharvest senescence in fresh-cut potatoes. Treatment with 0.1 mmol/L exogenous MT effectively inhibited browning and softening during storage. In terms of browning control, MT suppressed PPO and POD activities by 46% and ~10% at the end of storage (day 12), while enhancing enzymatic and non-enzymatic antioxidant capacity by 1.1- to 1.6-fold on average throughout storage. This alleviated oxidative damage and membrane lipid peroxidation, thereby reducing tissue browning. Regarding texture maintenance, MT downregulated PME and cellulase activities by 23% and 19% at the end of storage, activated phenylpropanoid metabolism, and inhibited starch degradation (maintaining 19% higher starch content), thus preserving cell wall structure and firmness (9.2% higher at the end of storage). Further analysis revealed that MT antagonized ethylene biosynthesis, upregulated StMYB168 expression (5.8-fold higher than control on average), and activated endogenous MT biosynthesis, establishing a self-sustaining positive regulatory cycle. Correlation analysis confirmed close relationships among physiological processes, signaling responses, and quality traits, with significant associations between firmness and starch content (r = 0.72), color indices and PPO/POD (|r| > 0.65), and MT biosynthesis genes and metabolic pathways (r = 0.65–0.75) (p < 0.01). Full article

Sour cherry (Prunus cerasus L.) exhibits remarkable phenotypic and genetic diversity, historically classified into morello and amarelle groups based on fruit pigmentation. However, the genetic foundations of these categories remain unclear. Here, we combine 10 SSR loci with S-RNase genotyping to evaluate genetic diversity, phylogenetic relationships, and population structure across 27 Hungarian and internationally relevant sour cherry cultivars. The marker panel proved highly informative, yielding 78 SSR alleles and 17 S-alleles, with a multilocus probability of identity of 3.97 × 10⁻⁷. Phylogenetic reconstruction, minimum spanning networks, Bayesian clustering, and PCoA consistently resolved five genetically coherent groups that largely reflect known breeding histories and regional selection rather than fruit color classes. High- and low-anthocyanin cultivars frequently co-occurred within clades, demonstrating that pigmentation does not track genome-wide relatedness. To investigate proximate molecular mechanisms, we profiled flavonoid-pathway gene expression in contrasting accessions (VN-1 and ‘Pipacs 1’). VN-1 exhibited strong late-ripening induction of structural genes and MYB10, whereas ‘Pipacs 1’ showed attenuated late activation and higher early expression of ANR, LAR, and UFGT, suggesting divergent transcriptional regulation and pathway flux between the two genotypes. Together, these results indicate that fruit color variation is largely independent of the multilocus relatedness patterns captured by our marker set, and is likely influenced by lineage-specific regulatory differences. Full article

Phosphorus (P) deficiency severely limits the growth and yield of crop plants, and anthocyanin accumulation is a key adaptive physiological response to low-P stress. However, the role of MYB transcription factors in regulating anthocyanin biosynthesis under P-deficient conditions and the application of favorable haplotypes in foxtail millet low-P tolerance breeding remain unclear. Here, we performed genome-wide identification of SiMYB genes, elucidated their evolutionary characteristics, and identified key members regulating anthocyanin accumulation under P deficiency to provide genetic resources and a theoretical basis for foxtail millet molecular breeding aimed at improving nutrient use efficiency. Specifically, a total of 229 SiMYB genes were identified in the foxtail millet genome and classified into three subgroups, with the R2R3-MYB subfamily accounting for 59.8%. Phylogenetic and synteny analyses across 15 plant species revealed diverse divergence times and complex relationships, with 29 R2R3-MYB genes showing conserved collinearity with rice and maize orthologs. Association analysis using 196 foxtail millet accessions showed that 38 single nucleotide polymorphisms (SNPs) from 16 SiMYB genes were significantly associated with leaf anthocyanin content under P deficiency (p < 0.001). Notably, the SiMYB169 gene exhibited differential tissue expression and was highly upregulated in the leaves of a P-tolerant genotype after 24 h of P deficiency treatment. Furthermore, accessions carrying the favorable G allele of SiMYB169 showed significantly higher anthocyanin accumulation under P deficiency (p < 0.01). Network prediction analysis found that SiMYB169 interacted with key genes and multiple transcription factors in the biosynthesis pathway of anthocyanin. These findings highlight SiMYB169 as an evolutionarily conserved regulator that modulated anthocyanin biosynthesis under P-deficient conditions. Full article

High-temperature (HT) stress during flowering causes male sterility and yield loss in soybean. MYB transcription factors are key regulators under abiotic stress, yet their function and mechanism in regulating male fertility under HT stress in soybean are not fully understood. In this study, a MYB transcription factor GmMYB21a in soybean was identified. GmMYB21a was induced by HT stress in soybean restorer line and was specifically expressed in pollen. Through overexpression and knockout experiments, we demonstrated that GmMYB21a positively regulated pollen viability and germination under HT stress. Overexpression of GmMYB21a significantly enhanced these traits in restorer line, whereas knockout plants exhibited the opposite effect. Transcriptome sequencing revealed that GmMYB21a overexpression upregulated numerous stress-responsive genes, particularly those involved in flavonoid biosynthesis and sugar metabolism. In addition, molecular experiments confirmed that GmMYB21a bound to the promoter of flavonoid synthesis gene GmCHI2-A and promoted its expression. In summary, our research indicated GmMYB21a enhanced the HT-tolerance of male fertility in soybean restorer line through reactive oxygen species scavenging and flavonoid synthesis. This study aims to elucidate the thermotolerance mechanism in soybean male fertility and identify genetic resources for breeding HT-tolerant restorer lines. Full article

Premium coffee depends on high-quality beans, influenced by a combination of genetic, environmental, and postharvest factors. This review summarizes the mechanisms underlying coffee bean quality, with an emphasis on the genetic differences between Coffea arabica and Coffea canephora, as well as the integrated roles of environmental conditions, agronomic practices, including nutrient and shade management, and postharvest processing technologies. The allotetraploid genome of C. arabica is influenced by homoeologous exchanges and subgenome-biased expression (such as decreased DXMT activity that reduces caffeine), which contribute to its complex flavor profile. Key lipid metabolism genes, particularly FADS2, play a critical role in regulating lipid metabolism. The effects of altitude (1600–2000 m) and shade influence various metabolic pathways. Cooler temperatures promote sugar accumulation, while excessive shading hinders carbon assimilation and the development of flavor precursors. Postharvest processing significantly influences flavor, where microbial or enzymatic treatments enhance sensory attributes. In addition, methods like natural, washed, or honey processing modulate various nonvolatile compounds, impacting lipid emulsification and aroma retention. Multi-omics analyses suggest that MYB proteins play a key role in regulating pathways involved in caffeine, chlorogenic acids, and terpenes. Effective hermetic packaging prevents oxidation, thereby preserving freshness. Overall, superior coffee quality stems from synergistic interactions across genetic, ecological, agronomic, and processing factors, highlighting the need for the development of an integrated strategy to support the sustainable production of premium coffee. Full article