5-Aminolevulinic acid (ALA) is an emerging plant growth regulator, yet its mechanisms in fruit development remain unclear. Here, we show that ALA promotes early growth and ultimate size in peach (Prunus persica) fruits. ALA treatment significantly enhanced the mesocarp area and the cell number, accompanied by elevated levels of indole-3-acetic acid (IAA) and trans-zeatin riboside. Transcriptomic analysis identified PpARF9 as a key transcriptional factor, regulating auxin homeostasis and responsive to ALA treatment. Functional studies with yeast-one-hybrid (Y1H), dual-luciferase (DLR), electrophoretic mobility shift assay (EMSA) and homogenous genetic transformation revealed that PpARF9 directly transcriptionally activates PpGH3.1, a crucial gene which encodes chloroplastic auxin amide synthetase to conjugate free IAA and repress cell division. Overexpression of PpGH3.1 reduced free IAA with more IAA conjugate accumulation, thereby suppressing cell cycle. Conversely, silencing PpGH3.1 with RNA interference had opposite effects. Notably, exogenous ALA alleviated the inhibitory effects of PpARF9 and PpGH3.1 on cell proliferation. These findings indicate that ALA promotes cell division by downregulating the PpARF9–PpGH3.1 module to maintain higher levels of active IAA, facilitating cell division, increasing cell number and fruit size. These provide a mechanistic insight into ALA-regulated fruit development and support its application in improving fruit production.
Flower size is a key ornamental trait in roses (Rosa spp.), determined by coordinated regulation of cell proliferation and expansion. Although jasmonic acid (JA) influences plant growth, its role in flower size control remains unclear. Here, we showed that methyl jasmonate (MeJA) treatment reduces flower size in Rosa chinensis, accompanied by elevated expression of the JA-responsive transcription factor RcMYC2. Silencing RcMYC2 resulted in larger flowers due to enhanced petal cell expansion and upregulation of cell expansion-related genes. Mechanistically, RcMYC2 directly bound to the promoter of the expansin gene RcEXPA8 and repressed its transcription via its interaction with the Mediator subunit RcMED25. Consistently, MeJA failed to reduce flower size in RcMED25-silenced plants. Upon JA signal activation, RcMYC2 recruited RcMED25 and the histone deacetylase RcHDA8 to the RcEXPA8 promoter, leading to transcriptional repression via histone deacetylation and restriction of petal cell expansion. These findings demonstrate that histone deacetylation links JA signaling to flower size control, providing new insights into hormone-mediated regulation of organ growth in ornamental plants.
Cold stress severely limits the yield and quality of fruit crops, yet its regulatory mechanisms in pitaya remain poorly understood. Here, we identified a cold-inducible bZIP transcription factor, HubZIP6, that plays a central role in enhancing cold tolerance in pitaya. HubZIP6 is a nuclear-localized protein with transcriptional activation activity, and its overexpression in Arabidopsis and tomato significantly improved cold tolerance, as reflected by higher survival rates, reduced ion leakage, and lower reactive oxygen species accumulation. Mechanistically, HubZIP6 directly binds to ACGT motifs in the promoters of HuCBF1 and HuCBF3, thereby activating their expression under cold stress. In addition, HubZIP6 physically interacts with the salicylic acid-binding protein HuSABP2, which synergistically enhances the transcriptional activation of HuCBF genes. Notably, HubZIP6 also directly activates HuSABP2, forming a regulatory loop that connects CBF transcriptional control with salicylic acid signaling. Consistently, overexpression of HuSABP2 further enhances cold tolerance in transgenic plants. Collectively, these findings demonstrate that cold tolerance is enhanced through HubZIP6-mediated integration of CBF activation and salicylic acid signaling, providing a promising genetic target for improving stress resilience in fruit crops.
Lychee (Litchi chinensis Sonn.) is a commercially important subtropical fruit. Lychee downy blight (LDB), caused by Peronophythora litchii, poses a major threat to lychee production. Here, we identified the LDB-resistant cultivar Yurong (YR) and the susceptible cultivar Guiwei (GW) from 288 global lychee germplasms. Widely targeted metabolomics analysis revealed a striking accumulation of podophyllotoxin (PTOX) in YR. Both in vitro and in vivo assays demonstrated that PTOX effectively inhibited the growth of P. litchii. Further investigation identified LcOMT1 as a key gene encoding an O-methyltransferase (OMT) in the phenylpropanoid pathway. In resistant cultivars, a 773-bp insertion mutation (Hap3 haplotype) in the LcOMT1 promoter enhanced its transcriptional activity. Transgenic approaches using hairy roots in lychee showed that the overexpression of either LcOMT1 or the Hap3 haplotype led to increased PTOX biosynthesis and enhanced resistance to P. litchii. These results demonstrate that the Hap3-mediated upregulation of LcOMT1 drives PTOX accumulation, establishing a crucial defense mechanism against LDB. This study provides new insights into the genetic and metabolic regulatory network underlying lychee resistance to LDB. This study may also lay a theoretical foundation for the development of PTOX-based biopesticides and offer valuable genetic resources for breeding LDB-resistant lychee cultivars.
Red-fleshed peach exhibits attractive anthocyanin (AN) pigmentation but is often accompanied by undesirable proanthocyanidin (PA)-derived astringency and high fruit acidity (FA), limiting its commercial value. The genetic mechanisms underlying this co-occurrence remain unclear. Using an F1 population derived from ‘wen30’ and ‘wen48’, we identified co-localized QTLs for AN, PA, and FA within a 0.32–4.74 Mb region on chromosome 5. Integrating transcriptomics with Y1H, EMSA, and dual-luciferase assays, we demonstrated that PpBL functions as a key regulator of both AN and PA accumulation. PpBL directly activates PpUGT73C3, independently of PpMYB10.1, to promote AN biosynthesis, and enhances PA accumulation by directly upregulating PpLAR and PpANR; PpUGT73C3 also contributes to PA accumulation via an unclear mechanism. In contrast, FA is not directly regulated by PpBL but is associated with a high-acidity PpTST1 allele tightly linked to a blood-TE insertion in the PpBL promoter. The haplotype carrying both the insertion and PpUGT73C3 coding variants confers elevated AN and PA but also increased FA due to linkage drag. These findings reveal pleiotropic control of color and astringency and a linkage-based association with acidity, providing insights for peach breeding.
Root-knot nematodes (RKNs; Meloidogyne spp.) are destructive agricultural parasites, but although giant cell formation is required for establishing parasitism, the mechanism of action has not been fully elucidated. Spatial transcriptomics enables precise spatiotemporal analyses of gene expression, facilitating studies of cell heterogeneity. We performed spatial transcriptomic sequencing on Moneymaker tomato root galls caused by M. incognita infection at 3, 5, and 7 days post-inoculation to investigate RKN-induced giant cell formation. Five major cell types were identified; of these, giant cell clusters were localized predominantly in the xylem, stele, and meristem. Four novel giant cell-specific marker genes were confirmed through RNA in situ hybridization. Pseudotime analysis revealed genes potentially associated with giant cell formation. Virus-induced gene silencing (VIGS) of four genes encoding a cyclin-dependent kinase, two cell division cycle-associated proteins, and a MYB3R-1-like transcription factor—hypothesized to maintain the cell cycle or gene expression during mitosis—resulted in significantly fewer galls and significantly smaller giant cells. This study established the first spatiotemporal atlas of RKN-infected tomato roots and identified genes associated with giant cell formation, laying a foundation for further research on the establishment of RKN feeding sites, providing novel insights into RKN pathogenic mechanisms, and potentially guiding novel control strategies.
To defend against pathogen invasion, plants deploy a variety of strategies, among which salicylic acid (SA), a key plant defense hormone, plays crucial roles in enhancing host resistance to biotrophic and semibiotrophic microbes. Although numerous studies elucidated mechanisms of the SA signaling pathway, many questions remain. In this study, we show that the group IIc WRKY transcription factor VvWRKY8 is involved in grape (Vitis vinifera) defense responses to the oomycete pathogen Plasmopara viticola, as indicated by transcriptome analyses. VvWRKY8 increases the expression of defense-related genes and SA accumulation, thereby promoting grape resistance to P. viticola. Further analyses reveal that VvWRKY8 is recruited to the promoters of VvCBP60g and VvSARD1, which encode two key regulators of SA biosynthesis, and upregulates their transcription. Moreover, VvWRKY8 transcription is induced by SA and by two bZIP transcription factors, VvTGA2a and VvTGA2b, which cooperate with the SA receptors VvNPR1 and VvNPR3 to modulate the expression of SA-responsive genes. Collectively, our results indicate that a positive feedback loop involving VvWRKY8 and the SA pathway components VvCBP60g, VvSARD1, and VvTGA2a/2b functions in response to P. viticola attack in grapevine.
Improving glucosinolate (GSL) profiles in rapeseed (Brassica napus)—high in leaves for pathogen resistance but low in seeds for meal quality—is a key breeding goal, yet its genetic basis remains unclear. Here, we present a chromosome-level genome assembly for ZY821, an elite high-GSL variety, generated using long-read sequencing and Hi-C scaffolding. Comparative analysis with the low-GSL variety ZS11 identified three major homoeologous exchange (HE) events and extensive structural variation. Notably, an A09–C09 HE event replaced the low-expression BnaC09.MYB28 allele with the high-expression BnaA09.MYB28 allele, resulting in elevated MYB28s expression and thereby increased GSL accumulation in ZY821, whereas a deletion of BnaA09.MYB28 in ZS11 significantly reduced the expression of multiple putative downstream targets in the GSL biosynthesis pathway, leading to a reduction in GSL content. This mechanism was supported by population-level HE analysis and time-course transcriptomes across 116 RNA-Seq samples. Furthermore, joint differential expression and co-expression network analyses uncovered several novel candidate genes implicated in GSL metabolism. Collectively, our study provides new mechanistic insights into the genetic control of GSL accumulation, with significant implications for breeding optimized GSL profiles.
Aromatic esters are key determinants of apple fruit aroma and consumer preference. Here, we investigated the molecular mechanisms underlying ester biosynthesis by characterizing MdAAT2-like, a critical ester-synthesizing gene in apple. MdAAT2-like expressions were significantly upregulated during fruit ripening and positively correlated with ester accumulation. Functional validation in apple and tomato demonstrated that MdAAT2-like overexpression enhanced ester contents, while silencing or knockout reduced ester production. Enzymatic assays revealed that MdAAT2-like exhibits higher catalytic efficiency for medium- and short-chain acyl-CoAs compared to other AAT family members. Two transcription factors, MdMYB98-like and MdWRKY21, were identified as direct activators of MdAAT2-like. Both factors bind its promoter and synergistically enhance transcription through protein interaction. Notably, we uncovered a positive feedback model wherein MdMYB98-like and MdWRKY21 reciprocally activate each other's expression, reinforcing rapid ester synthesis during ripening. This study reveals a MYB-WRKY regulatory module controlling ester biosynthesis in apple.
Medicinal plants are a valuable reservoir of diverse secondary metabolites (SMs), which serve as essential sources for natural drug development. However, the natural production of these bioactive compounds is generally low. Moreover, the biosynthetic processes of these SMs are regulated by a sophisticated network involving transcription factors, post-translational modifications, as well as plant hormones and environmental factors. Recent studies have identified an increasing number of non-coding RNAs (ncRNAs) and confirmed their roles in regulating SM biosynthesis. In this review, we systematically summarize the research progress on the regulation of SM biosynthesis by ncRNAs in medicinal plants, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and phased secondary siRNAs (phasiRNAs). Additionally, we summarize ncRNA‑mediated studies in staple crops, horticultural plants, and woody species to provide references for medicinal plant research. Finally, we discuss future research directions for ncRNAs in medicinal plants, including the construction of spatiotemporal regulatory networks, the application of artificial intelligence (AI)-assisted approaches, the elucidation of molecular regulatory mechanisms, and potential applications of ncRNAs in the standardized production of medicinal plants.
The lifecycle of tomato fruit mainly comprises two distinct phases: the initial growth and development phase, followed by the ripening and senescence phase. However, the mechanism initially triggering the transition from an energy-intensive growth phase to the ripening phase remains unclear. First, we found that the fruit energy charge was significantly reduced before this transition, which might be caused by elevated levels of adenosine monophosphate (AMP) and histidine (His). Second, we constructed transgenic tomato plants for the key enzymes in the AMP salvage pathway (SlAPRT1) and His biosynthesis pathway (SlATP-PRT) via genome editing and overexpression. All transgenic plants caused a severe inhibition of fruit ripening, which was consistent with exogenous AMP treatment on wild-type plants, primarily due to the increased energy charge. Particularly, Slatp-prt mutant fruits could hardly produce ethylene or initiate ripening, but exogenous His treatment could restore their energy charge and ripening initiation. Finally, reducing the energy charge via exogenous His treatment also effectively accelerated the growth-to-ripening transition of wild-type fruits both on the plant and post-harvest. In conclusion, this study reveals that low energy charge and high His levels co-trigger the growth-to-ripening transition of tomato fruits, providing novel and valuable insights into the mechanisms underlying ripening initiation.
In plant, lycopene β-cyclase is a crucial enzyme in carotenoid metabolic pathway, which can induce color alteration. Carrots (Daucus carota) possess two genes encoding lycopene β-cyclase, namely DcLcyB1 and DcLcyB2. Little is known regarding the functional disparities between these two proteins in regulating carrot carotenoid accumulation. We found that the expression level of DcLcyB2 was higher than that of DcLcyB1 in carrot roots. Enzyme reaction in E. coli demonstrated that both two DcLcyB proteins were capable of cycloconverting lycopene to β-carotene, but DcLcyB2 tended to have a higher preference for monocyclic carotene substrates, resulting in more α-carotene production. After the DcLcyBs were separately overexpressed in red carrots, the roots turned yellow, accompanied by the reduction of lycopene and β-carotene content and the entire carotenoid metabolism flowed downstream towards xanthophylls. The expression levels of DcCHXE, DcCYP97A3, DcCHXB1 and DcCHXB2 in the DcLcyB-OE lines raised sharply. After gene editing of DcLcyB1/2, the α-/β-carotene ratio changed conspicuously, particularly in the dclcyb2 mutants, where α-carotene content dropped sharply, while β-carotene remained high. The expression levels of most structural genes in carotenoid pathway responded dynamically. Our results enriched the understanding of functionally redundant but differentiated roles of two DcLcyB isoenzymes in carrot root coloring.
Medicinal plants are rich in bioactive constituents and are extensively utilized in the healthcare sector, holding significant value for both industrial and daily applications. In the context of economic development and escalating environmental challenges, there is an increasing societal demand for medicinal plants with superior quality and enhanced environmental adaptability. Molecular breeding is emerging as a pivotal strategy for the genetic improvement of medicinal plants. Given that traditional breeding methods are often constrained by low efficiency and lengthy developmental cycles, the necessity for innovative approaches is underscored. Advancements in modern molecular breeding technologies, such as marker-assisted breeding, genetic engineering, and molecular design breeding, have revolutionized the paradigm of medicinal plant breeding. This article reviews the research progress in molecular breeding of medicinal plants, encompassing its characteristics, advantages, technical classifications and applications. Based on these advancements, we discuss the major challenges and future prospects in this field. It is evident that the rapid evolution of molecular breeding holds substantial potential for facilitating plant genetic improvement and effectively addressing the growing societal demands for high-quality medicinal plants.
The quality and quantity of plant traits are critically linked to the coordinated onset of leaf senescence. However, both external environmental factors and internal hormones may accelerate leaf senescence process, resulting in various physiological changes, including chlorophyll degradation, anthocyanin biosynthesis, nutrient recycling, and the activation of senescence-associated genes (SAGs). A comprehensive understanding of the signaling pathways involved in stress-induced leaf senescence is essential for plant breeding aimed at enhancing resistance and productivity. This review provides an extensive overview of the signaling mechanisms associated with leaf senescence triggered by abiotic and biotic stresses, including abscisic acid (ABA), darkness, nitrogen deficiency, carbon deficiency, and pathogen attack. Additionally, we discuss strategies to improve stress tolerance, yield, and quality through innovative synthetic biology approaches. Furthermore, we explore the potential applications of machine learning (ML) and deep learning (DL) in the context of senescence- and stress-related plant breeding.
