Ethylene plays a crucial role in fruit ripening and is perceived by specialised receptor proteins embedded in the endoplasmic reticulum (ER) membrane. As an ethylene antagonist, 1-methylcyclopropene (1-MCP) binds to these receptors and delays papaya ripening, but improper use can cause ripening disorders. The expression of CpERS1 and CpERF-WRI1 is markedly upregulated during ripening yet is suppressed by inappropriate 1-MCP treatments. Similar ripening disorders and expression patterns of CpERS1 and CpERF-WRI1 were observed in immature, chilled and heat-stressed papaya fruits, indicating that these genes may play key roles in ripening disorder. CpERF-WRI1 binds to and activates the CpERS1 promoter both invitro and invivo. Transient overexpression of CpERF-WRI1 in papaya and ectopic expression in tomato accelerated fruit ripening, increased CpERS1 expression and upregulated ripening-related pathways, whereas virus-induced gene silencing (VIGS) of CpERF-WRI1 in papaya delayed ripening and downregulated those pathways. Similarly, overexpressing CpERS1 in papaya and tomato accelerated ripening and boosted the expression of ripening-associated genes, while VIGS-mediated silencing of CpERS1 delayed ripening and suppressed these genes. Together, these results indicate that CpERF-WRI1 regulates CpERS1 expression and modulates ethylene sensing within the system II ethylene signalling pathway to control papaya ripening.

Introduction of Reduced height (Rht) genes into modern wheat cultivars has resulted in 'Green Revolution' that skyrocketed wheat grain yields worldwide since the 1960s. These 'Green Revolution' cultivars show shorter plant height, but higher lodging resistance and harvest index. The identification and exploitation of novel Rht genes are of great significance for the development of high-yielding wheat cultivars. In this study, a semi-dwarf wheat mutant, d14078, with reduced plant height and grain size, was generated by ethyl methanesulfonate (EMS) mutagenesis. Here, through map-based cloning, we cloned the causal gene for the semi-dwarf phenotype of d14078 as TaWAK3-B that encodes a cell wall-associated receptor kinase 3. A single-base mutation occurred in the coding region of TaWAK3-B, resulting in an amino acid mutation from Glu to Lys (E938K) at residue 938, which reduces its stability and the formation of homodimers. The cytoskeletons were changed in both the d14078 and TaWAK3-B knockout mutants, as well as the TaWAK3-B overexpression of transgenic plants. Further investigation revealed that TaWAK3-B directly forms stable protein assembly with TaADF3-A (actin depolymerisation factor), TaKLCR1-A (kinesin light chain-related protein 1), and TaIQD2-D (IQ67-domain protein 2). These interactions and complex formations were significantly attenuated by the TaWAK3-BE938K mutation. Therefore, our findings clarify TaWAK3-B regulating the microfilament and microtubule formation that elucidate on the regulation of wheat stem development.

Diosgenin is a key starting material for the synthesis of steroidal drugs, such as corticosteroids and sex hormones. While the primary commercial source of diosgenin is the tubers of Dioscorea spp., identifying alternative plant hosts capable of diosgenin biosynthesis could enhance its production. In this study, we present Solanum nigrum, a widely distributed species of the Solanum genus, as a novel platform for diosgenin production. S. nigrum naturally accumulates high concentrations of steroidal glycoalkaloids (SGAs) with a closed F-ring (spirostanol type) in green fruits and steroidal saponins (STSs) with an open F-ring (furostanol type) in leaves. Both classes originate from cholesterol and share the early oxidation steps, followed by specific reactions that redirect distinct metabolic fluxes. In SGAs, the CYP450 enzyme SnGAME4 oxidises C26-OH to an aldehyde, enabling subsequent transamination. In STSs, SnGAME25, a 3β-hydroxysteroid dehydrogenase/isomerase, initiates the reduction reactions at the C5 double bond. Disruption of these two genes shifted the metabolic profiles from the native SGAs and STSs toward furostanol-type proto-diosgenin glycosides. However, these open F-ring structures yield low diosgenin levels during acid hydrolysis. To overcome this limitation, we identified endogenous furostanol glycoside 26-O-β-glucosidases and employed spontaneous fermentation to convert the furostanol structure to the spirostanol structure. Altogether, S. nigrum green fruits yielded diosgenin up to 1% of dry weight. In addition, we engineered S. nigrum to increase fruit number in combination with the SnGAME4 mutation. These results establish S. nigrum as a promising and scalable host for diosgenin production.

Base excision repair (BER) is a critical pathway for repairing damaged DNA bases in cells; however, the mechanisms of protein recruitment and interaction in this pathway remain largely unexplored in higher plants. In this study, we used '84K' poplar (Populus alba × P. glandulosa) as the experimental system and applied a low concentration of 5-aminouracil (5-AU) to induce DNA base lesions. Through transcriptome analysis and weighted gene co-expression network analysis (WGCNA), we identified two key BER-responsive genes: the DNA glycosylase family gene PagDMG6341 and the DNA polymerase δ subunit PagPOLD4. PagDMG6341 was significantly upregulated during the arrest phase of 5-AU treatment, whereas PagPOLD4 expression peaked during the subsequent release phase. RNA interference (RNAi) lines for each gene resulted in impaired growth and increased susceptibility to 5-AU in '84K' poplar, supporting their functional roles in DNA repair and development. To further investigate their potential interaction network, we performed yeast two-hybrid (Y2H) screening, AlphaFold3-based structural modelling, confirmatory Y2H, bimolecular fluorescence complementation (BiFC) assays, and luciferase complementation imaging (LCI) assays. These experiments demonstrated that a Transducin/WD40-repeat-like scaffold protein (PagWD40) interacts independently with both PagDMG6341 and PagPOLD4. The yeast three-hybrid (Y3H) assay further showed that PagWD40 functions as a molecular scaffold, linking PagDMG6341 and PagPOLD4 to form a functional complex. This study reveals a new mechanism in which PagWD40 functions as a scaffold protein linking a DNA glycosylase with DNA polymerase δ in the plant BER pathway, thereby providing new insights into the organisation of plant DNA damage repair networks.

Pangenome can reveal a large number of variations, providing a more comprehensive view of the genetic diversity of species that a single reference genome cannot surpass. Here, we assembled the haplotype telomere-to-telomere genome and 10 chromosome-level genomes, integrated with two previously reported genomes, and constructed a graph pangenome for P. mume with 'PmNH_Hap1' T2T genome as the reference. Core gene families accounted for 64.47%, while non-essential gene families comprised 35.53%. The total length of the graph pangenome reaches 412.41 Mb, which is a significant increase of 179.60 Mb compared with the 'PmNH_Hap1' reference genome, and these unique insertion sequences contain 5918 genes. Additionally, by combining with five Prunus armeniaca genomes for pangenome variation detection, we identified a total of 51 461 non-redundant SVs, including 15 217 insertions, 21 683 deletions, 13 509 translocations and 1025 inversions. Among these, 60.50% of presence/absence variations were formed by transposons. Pangenome analysis revealed that a 376 bp SV insertion was universally present in the promoter of this gene in P. mume, PmAGL30 can bind to this SV to enhance PmPH4 gene expression and promoted citric acid accumulation in P. mume fruits, leading to extremely significant differences in citric acid content compared with other stone fruits. Additionally, we developed SV molecular markers for the early screening of germplasm with high citric acid content in P. mume fruits. In summary, we constructed a high-quality graph pangenome that reveals abundant genetic variations, providing valuable insights for variety improvement and molecular breeding in P. mume.

Phosphorus (P) is an essential macronutrient for various biological processes in plant growth. Modern agricultural science has advanced the knowledge of regulatory mechanisms underlying phosphorus starvation responses (PSRs), aiming to develop phosphate-efficient crops with sustainable production under reduced Pi fertilizer application. However, information regarding coordinated shoot and root adaptations in response to combined nutrient stresses is limited. This study investigated the role of Phloem Phosphate Stress Repressed 1 (PPSR1) in modulating PSRs and other nutrient deficiency adaptations. The Arabidopsis functional homologue of Cucumis sativus PPSR1 (CsPPSR1), designated AtPPSR1, was identified. AtPPSR1 encodes a glycine-rich domain-containing protein, and its ectopic expression confers enhanced growth performance to plants. Transcriptomic analyses revealed AtPPSR1 as a regulatory mediator of PSRs, photosynthesis, and root development. AtPPSR1 interacted with PHOSPHATE STARVATION RESPONSE 1 (PHR1) to regulate PHR1-target genes for adaptive root development in response to Pi-starvation stress. Additionally, AtPPSR1 was graft-transmissible, and shoot-borne AtPPSR1 played a role in restoring the root phenotype of the ppsr1 mutant. Physiological analyses revealed that enhanced AtPPSR1 expression enabled resilience to nitrogen (N) and potassium (K)-starvation, as well as to Pi-deficiency. Furthermore, we identified homologues of CsPPSR1 and AtPPSR1 in Brassica napus (canola), which displayed similar expression patterns in response to Pi-starvation stress. Overexpression of PPSR1, identified from Arabidopsis, cucumber, and canola, improved growth performance and seed production in canola under N-, Pi-, or K-deficient conditions, within the controlled environment. These findings provide novel insights into PPSR1-mediated molecular coordination to enhance plant resilience to mineral nutrient deficiency.