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Main conclusion: This study links rice leaf metabolome to yield traits, identifying 13 key metabolites through computational metabolomics. These enable early prediction of high-yield varieties, enhancing screening strategies in crop breeding. Metabolites serve as dynamic indicators of plant phenotype, linking genotype and environment through metabolomics profiling. Here, we used a computational metabolomics approach to correlate leaf metabolites with yield traits in four indica rice varieties. Dani Gora, with the highest yield, showed distinct phenotypic and metabolic profiles compared to Njavera N96. Analysis of robust non-redundant mass features revealed maximal 'metabotype' and trait differences between these two varieties. Dani Gora displayed higher central metabolism diversity, while Njavera N96 showed elevated specialization in secondary metabolism. Comparative pathway impact analysis identified 14 central metabolites, especially involved in six metabolic pathways, significantly enriched and positively correlated with the yield parameters. Machine learning (Random Forest) and fold change analysis finally validated 13 key metabolites predictive of yield traits. This framework demonstrates how leaf metabolite classifiers can enable early, high-throughput screening for high-yield rice varieties, offering a tool for accelerating rice breeding strategies.

Main conclusion: OsPP2C10, a member of the OsPP2C subclass F2, is localized at the endoplasmic reticulum exit sites and interacts with vesicle trafficking components, OsSAR1C and an OsPHYTOLONGIN. Altered accumulation patterns of TLP and GLU2 proteins in the apoplast of OsPP2C10 knockout, knockdown, and overexpression lines suggest potential regulatory roles of OsPP2C10 in protein vesicle trafficking. Protein phosphatase 2Cs (PP2Cs) are key regulators of signal transduction that act through dephosphorylation of target proteins. To identify PP2Cs functioning on membranous organelles in rice (Oryza sativa), we screened all 78 OsPP2Cs and found that OsPP2C10 possesses a functional N-terminal transmembrane domain and is localized at the endoplasmic reticulum exit site. OsPP2C10 interacts with OsSAR1C, a component of the COPII complex, and OsPHYTOLONGIN, a VAMP72 longin-related protein, both of which are essential regulators of vesicle trafficking. Functional analysis using T-DNA knockout, RNAi knockdown, and overexpression lines revealed that OsPP2C10 influences the accumulation of secretory proteins such as TLP/PR5 and GLU2/PR2 in the apoplast. These findings suggest potential regulatory roles of OsPP2C10 in protein trafficking in rice.

Main conclusion: Enormous progress has been achieved in developing reliable in vitro propagation systems, microrhizome induction, genetic fidelity assessment, and conservation strategies in ginger. These advances, combined with modern molecular and genomic tools, ensure production of uniform, disease-free planting material and future genetic advancement in ginger. Ginger (Zingiber officinale Rosc.), a crop of immense culinary, medicinal, and industrial importance, has been the subject of extensive research in tissue culture and molecular improvement. In vitro regeneration systems, including shoot organogenesis, somatic embryogenesis, and microrhizome induction, have enabled the large-scale production of disease-free, uniform planting materials, addressing the limitations of conventional rhizome propagation. Complementary conservation strategies such as slow-growth storage, cryopreservation, and synthetic seed technology safeguard valuable germplasm, while molecular marker-based fidelity testing ensures true-to-type regeneration and enriches genetic diversity. Furthermore, biotechnological interventions such as genetic transformation, induced mutagenesis, and polyploidy induction expand the scope of crop improvement, offering opportunities for enhanced yield, stress resilience, and secondary metabolite production. Despite these advances, challenges remain in up scaling microrhizome-based propagation, optimizing transformation efficiency, and translating genomic insights into applied breeding. This review consolidates the advances in in vitro propagation, conservation, fidelity analysis, and molecular breeding of ginger, while highlighting the untapped potential of CRISPR-based genome editing. Collectively, these approaches present a roadmap for sustainable ginger improvement through the convergence of biotechnology, conservation, and molecular innovation.

Main conclusion: This study is a systematic review of heat stress-driven changes in tomato morphology and physiology, thermotolerance mechanisms, and crop improvement methods. Tomato is a widely cultivated and utilized crop. However, climate change poses a direct threat to food systems by diminishing the productivity and indirectly limiting the genetic diversity of crops and their wild relatives. Consequently, this limits future options for breeding improved varieties and makes it harder to adapt crops to new challenges. This is particularly concerning as the average global surface temperature is anticipated to increase by 0.3 °C over the next 10 years. Because of their sessile nature, tomato plants have developed complex signalling networks that allow them to detect changes in ambient temperature. However, high-temperature stress can negatively impact the morphology, physiology, and biochemistry of tomato plants at every stage of development, from vegetative to reproductive. This heat stress leads to significant yield losses due to induced changes in crop phenology, growth patterns, sensitivity to pests, shrinkage of the maturity period, and accelerated senescence. Finding novel sources of heat tolerance and identifying the genes involved in those pathways have become significant challenges in the modern era due to global warming. This complexity is further increased by significant genotype-environment and epistatic interactions, making it difficult for breeders to develop and select heat-tolerant genotypes. The current review aims to provide insights into physiological processes related to heat stress, the molecular underpinnings of tomato heat tolerance, germplasm and quantitative trait loci governing tolerance, and the different crop improvement techniques utilized in breeding for heat tolerance of tomato. Deciphering various physiological processes and the development of different breeding techniques are critical to assist in the evolution of thermotolerant tomato cultivars.

Main conclusion: Our work identified Ca²⁺-dependent and -independent changes in protein contents upon oxidative stress, showing that Ca²⁺ signaling shapes the early oxidative stress response and identifying potential targets for stress resilience research. Calcium (Ca²⁺) and reactive oxygen species (ROS) are key secondary messengers in plant stress signaling, yet their interplay in regulating proteome-wide responses remains poorly understood. We employed label-free quantitative (LFQ) proteomics to investigate Ca²⁺-dependent and -independent proteome changes in Arabidopsis thaliana leaves upon oxidative stress induced by hydrogen peroxide (H₂O₂). To dissect the role of Ca²⁺ signaling, we inhibited H₂O₂-induced Ca²⁺ transients by pre-treatment with the Ca²⁺ influx blocker LaCl₃. Throughout all four treatment samples - control, H₂O₂-treated, LaCl₃-treated, H₂O₂- and LaCl₃-treated - we identified a total of 3724 and 3757 proteins after 10 and 30 min, respectively. Of these, 581 proteins showed significant changes in abundance between the 10 min and 909 proteins between the 30 min sample groups. The combined LaCl₃ and H₂O₂ treatment resulted in the highest number of differentially abundant proteins (DAPs), indicating a strong attenuating effect of Ca²⁺ signaling on the oxidative stress response. By contrast, only 37 and 57 proteins responded to H₂O₂ alone with distinct subsets of strictly Ca²⁺-dependent, partially Ca²⁺-dependent, and Ca²⁺-independent proteins. Ca²⁺-independent H₂O₂-responsive proteins predominantly showed increased abundance, while strictly Ca²⁺-dependent proteins exhibited decreased abundance, suggesting a role for Ca²⁺ signaling in protein degradation. Furthermore, three proteins-WLIM1, CYP97C1, and AGAP1-underwent shifts in Ca²⁺-dependency between the two time points, pointing to a dynamic Ca²⁺-regulation. This study provides insight into short-term Ca²⁺-dependent and independent regulation of the Arabidopsis leaf proteome in response to oxidative stress, thereby identifying potential new targets for research on plant stress resilience mechanisms.

Main conclusion: TaSLC25A4-7B is closely related to the biological processes involved in drought stress and the ABA signaling pathway through the regulation of stomata, providing a theoretical basis for exploring drought resistance in wheat. The solute carrier family 25 (SLC25) member SLC25A4 plays important roles in plant growth regulation. However, its roles in drought-stress response remain unclear. Here, we determined that the mitochondrial wheat (Triticum aestivum L.) SLC25A4-7B gene (TaSLC25A4-7B) was involved in regulating drought responses by coordinating stomatal aperture and abscisic acid (ABA). Tobacco and rice plants overexpressing TaSLC25A4-7B (OxTaSLC25A4-7B) showed increased stomatal aperture and/or size, as well as impaired drought tolerance. The larger stomata were associated with altered stomatal morphology, downregulated ABA synthesis-related genes and upregulated ABA degradation-related genes. Consistently, the endogenous ABA contents were markedly altered in tobacco OxTaSLC25A4-7B compared with wild type. Additionally, the larger stomata were associated with a higher photosynthetic capacity in rice OxTaSLC25A4-7B compared with Nipponbare. Under drought conditions, the OxTaSLC25A4-7B transgenic plants showed severe wilting phenotypes and increased contents of reactive oxygen species and malondialdehyde compared with the control. Furthermore, we found that wheat protein phosphatase type 2C binds to the promoter of TaSLC25A4-7B and inhibits the gene's activity. The results suggested that TaSLC25A4-7B negatively regulated drought tolerance.

Main conclusion: A desiccation-induced chloroplast DnaJ/HSP40 gene, BhDnaJC6, from the resurrection plant enhances photosynthesis and cotton drought tolerance via interaction with and stabilization of Rieske iron-sulfur protein (PetC) in transgenic cotton plants. Drought stress severely affects cotton productivity and seedling survival. Resurrection plants are known for their unique mechanisms of desiccation tolerance, including the maintenance of photosynthetic proteins during dehydration and rehydration, making their genes valuable for drought-tolerant cotton breeding. Chloroplast DnaJ proteins play roles in protein quality control in plant cells. Here, we report the identification and functional characterization of a chloroplast-localized C-type DnaJ protein-coding gene BhDnaJC6 from the resurrection plant Boea hygrometrica. BhDnaJC6 transcripts accumulate in response to slow desiccation, and rapid desiccation in acclimated (desiccation-tolerant) but not non-acclimated (desiccation-sensitive) B. hygrometrica plants. Microscopic observation confirmed the cellular localization of BhDnaJC6-GFP in chloroplasts in transiently transformed tobacco guard cells, and its interference with Rieske iron-sulfur protein, the PetC subunit of the cytochrome b6/f complex, fused with mCherry. In silico analysis predicted a possible physical interaction between BhDnaJC6 and Rieske iron-sulfur protein, which was experimentally confirmed using bimolecular fluorescence complementation (BiFC) and yeast two-hybrid assays. When overexpressed in cotton, the BhDnaJC6 transgenic lines displayed higher Rieske iron-sulfur protein levels and improved drought tolerance compared to the wild type. The higher levels of Rieske iron-sulfur protein improve photosynthetic performance in transgenic lines under both non-stressed and drought-stressed conditions, increasing the electron transport rates and actual quantum yields of PSII and decreasing the quantum yield of non-regulated energy dissipation. Taken together, our findings unveil a novel component enhancing Rieske iron-sulfur protein stability and improving the drought tolerance of transgenic cotton, offering a valuable genetic resource for drought-tolerant cotton breeding.

Main conclusion: An improved method allows accurate quantification of the maturation strain in developing flax stems and reveals its strong correlation with the area of constitutively deposited gelatinous cell wall in phloem fibers. Improving experimental methods to reliably quantify the maturation strain in herbaceous stems is essential for understanding the mechanical regulation of their growth and for optimizing fiber crop properties. An improved longitudinal stem-splitting method enabled quantitative assessment of the tensile strain in developing flax stems, allowing evaluation of the contribution of phloem fibers with constitutively deposited gelatinous cell walls, while excluding the influence of xylem and parenchyma. The assessment was based on direct measurements of tissue mechanical properties using an inverse three-point bending test and on removing the turgor effects by incubation with the osmoticum. The main source of internal tension in the growing flax stem is the phloem fibers with a gelatinous cell wall, and strain values show a strong correlation with their area. The obtained values correspond to the range characteristic of tension wood, confirming the universality of the tension generation mechanism in vascular plants. This method provides a reliable means of estimating internal stresses at different stages of herbaceous stem development.

Main conclusion: This review summarizes major advances in Persian walnut biotechnology, emphasizing progress in propagation, somatic embryogenesis, genome editing, and computational tools while outlining key challenges for large-scale propagation and genetic improvement. In vitro culture is fundamental for uniform and large-scale propagation of Persian walnut. Over the past decades, significant improvements have enhanced plant adaptability and survival during transfer to ex vitro environments. Commonly used explants, such as shoot buds, nodal segments, and shoot tips, show variable success depending on genetic, physiological, and environmental factors, as well as culture media composition. Somatic embryogenesis and plant regeneration form the basis for several biotechnological approaches, including haploid production for genomic mapping, mutation analysis, and hybrid development. Recent advances in genome editing, particularly CRISPR/Cas9, have accelerated the creation of cultivars with improved rooting ability, enhanced resistance to biotic stresses, and better tolerance to drought and salinity. Moreover, the integration of machine learning and computational tools has facilitated high-throughput phenotyping, reducing experimental time and cost. Despite these achievements, challenges such as genotype-dependent recalcitrance, oxidative browning, and low transformation efficiency continue to limit large-scale applications. Addressing these obstacles through optimized culture systems and molecular tools will be essential for realizing the full potential of Persian walnut biotechnology. This review provides an integrated overview of recent advances, identifies persistent challenges, and highlights future directions for improving propagation efficiency and accelerating genetic enhancement in this valuable tree species.

Main conclusion: Embryos one, two, and three can give rise to plants identical, similar, and different from the mother plant. The size of the embryo does not guarantee its genetic identity. The model of polyembryony in citrus establishes that the larger embryo is identical to the mother plant, and the smaller one is zygotic. This work aimed to determine the percentage of polyembryony, the number of embryos, and the genetic similarity index (GSI) of three embryos (one, two, and three) compared to the mother plant in seeds of Mandarin amblycarpa, to provide a broader view of polyembryony. This is the first study to determine the genetic identity of embryos based on size using microsatellites and categorize them into three groups: identical to, similar to, and different from the mother plant. Open-pollinated fruits were harvested in two cycles (2020 and 2021). The percentage of polyembryony was determined, and the number of embryos per seed was counted. By comparing banding patterns produced by SSR microsatellites, the GSI was calculated. Nei distances were calculated and analyzed by UPGMA (unweighted pair group method with arithmetic mean). Since the variation occurred at different loci, Nei's genetic distances allowed embryos with the same GSI to be regrouped in different dendrogram branches. As plants identical to, similar to, and different from the mother plant were found in embryos one, two, and three, it is evident that embryo size does not determine the genetic identity of the plant; therefore, it is necessary to modify the current model of polyembryony. Additionally, we propose using the term different from the mother' instead of 'sexual origin', as the resulting plant might derive from a mutation.