CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 has been widely utilized for plant genome editing, but the protospacer adjacent motif (PAM) requirement limits its editing scope. CRISPR/Cas12i3 bel...CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 has been widely utilized for plant genome editing, but the protospacer adjacent motif (PAM) requirement limits its editing scope. CRISPR/Cas12i3 belongs to the type-VI Cas system that has gained extensive attention due to its smaller size and less restricted canonical TTN PAM sequence. In this study, we explored the newly developed Cas-SF01 system (Cas12i3 variant) for genome editing in oilseed rape. We established an efficient protoplast transformation system in oilseed rape to compare editing efficiency between Cas-SF01 and Cas9. Cas-SF01 shows cleavage activities at the tested 5'-TTN-3' PAM sites with editing outcomes sharing considerable similarities with the CRISPR-Cas9 system in protoplast. Cas-SF01 also induces high efficiency mutagenesis for multiple target sites in stable transformed oilseed rape lines, generating mutants with multilocular silique and male sterile phenotypes. Furthermore, Cas-SF01-derived cytosine base editors (CBEs) were developed to produce targeted C-to-T base edits. Compared to SpCas9, Cas-SF01 has an expanded PAM range and effectively recognizes TTN PAMs, which has substantially broadened the scope of editable sites within the rapeseed genome. No mutations were identified at the putative off-target sites among the edited plants. This study developed a robust, first-of-its-kind Cas12 system in the allotetraploid Brassica napus, expanding the scope of editing and enriching genome-editing toolkits for biological research and genetic improvement.
Cotton fiber quality-defined by length, strength, and fineness-directly influences the commercial value of textile products, with fiber length being one of the most critical parameters in industrial procurement. In uplan...Cotton fiber quality-defined by length, strength, and fineness-directly influences the commercial value of textile products, with fiber length being one of the most critical parameters in industrial procurement. In upland cotton (Gossypium hirsutum), fiber development occurs through four overlapping stages, of which the elongation phase (2-20 d post-anthesis, DPA) is pivotal for determining final fiber length. Recent studies have identified a diverse set of genes regulating fiber elongation via distinct molecular mechanisms, categorized into six functional classes: Phytohormone-associated genes; transcription factor-associated genes; cellulose-, lignin-, and sucrose-associated genes; lipid-associated genes; cytoskeleton-associated genes; and other functionally diverse genes. By synthesizing their roles and hierarchical interactions, this review constructs comprehensive genetic networks governing fiber elongation. This work provides a molecular blueprint for precision breeding strategies to enhance cotton fiber length, offering actionable insights for breeding programs aimed at improving fiber quality.
Plant growth and productivity are strongly constrained by herbivorous insects, which reduce both yield and quality. Over the past two centuries, extensive efforts have been devoted to identifying natural insect-resistant...Plant growth and productivity are strongly constrained by herbivorous insects, which reduce both yield and quality. Over the past two centuries, extensive efforts have been devoted to identifying natural insect-resistant traits and genes that have evolved in plants. Here, we first review key milestones and advances, including empirical observation, mechanism onset, theoretical emergence, gene identification, and breeding application. Then, we categorize research on plant defenses for insect resistance into four major types: physical, chemical, ecological modulation, and behavioral defenses, and integrate them to highlight the coordination and synergy among different defenses. Finally, we propose priority areas and future directions for research to advance studies on plant-insect interactions and support effective and sustainable pest management.
Shi Y, Chen R, Jiang K
… +4 more, Jiang A, Yang J, Cui H, Chen M
J Integr Plant Biol
· 2026 Jul · PMID 41782214
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Soil salinization is a major abiotic stress factor that reduces soybean production. Studies have shown that application of Chlorella promotes plant growth; however, its potential to mitigate salt stress, and the active c...Soil salinization is a major abiotic stress factor that reduces soybean production. Studies have shown that application of Chlorella promotes plant growth; however, its potential to mitigate salt stress, and the active components involved and the underlying mechanisms, remains unclear. In this study, the application of Chlorella vulgaris significantly mitigated salt stress in soybean seedlings. To identify the active components, we fractionated C. vulgaris and found that the extracellular secretions were primarily responsible for the mitigation. Furthermore, we isolated and characterized exosomes from these secretions. Phenotypic and physiological assessments confirmed that C. vulgaris exosomes alleviated salt stress in soybean seedlings to an extent similar to the intact organism. We identified the key metabolites (linolenic acid and inosine) as the active components within these exosomes. Notably, when applied in combination, they showed a strong synergistic effect, collectively promoting seedling growth, restoring ion homeostasis, and improving redox homeostasis under salt stress. To investigate the molecular mechanisms of salt stress alleviation, the transcriptomes of soybean seedlings subjected to different treatments were analyzed. Salt stress induced widespread changes in gene expression; however, application of linoleic acid (LA), inosine, and especially their combination, led to substantial transcriptomic reprogramming. Enrichment analysis indicated that these modifications were coordinated across energy metabolism, redox homeostasis, carbohydrate metabolism, and ion transport. Importantly, the LA + inosine combination induced a synergistic rather than simply additive transcriptional response, which explains its superior effect on salt tolerance at the molecular level. In this study, we successfully isolated and identified, for the first time, exosomes as the functional components through which C. vulgaris alleviates salt stress in soybean seedlings. Further analysis identified LA and inosine within the exosomes as the key active metabolites. These findings provide a novel theoretical basis for improving crop salt tolerance and are important for developing novel algal nanovesicle-based biostimulants.
Frequent changes in global climate enhance environmental cues, threaten agricultural systems, which jeopardizes food security, and impair the achievements of the United Nations Sustainable Development Goal 2 "Zero Hunger...Frequent changes in global climate enhance environmental cues, threaten agricultural systems, which jeopardizes food security, and impair the achievements of the United Nations Sustainable Development Goal 2 "Zero Hunger". To achieve a sustainable path, use of biostimulants represents a new strategy to enhance plant resilience against abiotic stresses like drought, temperature, salt, waterlogging, and heavy metals. This review explores recent developments in biostimulant technologies, aiming to clarify the processes that underlie their ability to promote plant tolerance. We also highlight the versatile roles of small RNA, peptides, and hormones as emerging molecular regulators, thereby revealing their potential for use as natural biostimulants. Developing on this, transformative effects of microbial biostimulants that use microbiota to strongly regulate plant stress-responsive modules are explored. Furthermore, AI-driven early warning systems provide the opportunity to identify timely stress responses, thus enabling the discovery of multi-omics network modules, allowing rational biostimulant design. These findings are then used to guide the metabolic engineering of tailored biostimulants, where the identified key regulators and network modules become direct targets for formulation or synthetic biology approaches. This review defines a roadmap for crop stress tolerance by clarifying the mechanisms of rationally designed biostimulants, thereby paving the way for climate-resilient agriculture and sustainable food systems.
Dracocephalum moldavica L., an annual herb valued for its medicinal and ornamental properties, produces flavonoid glycosides like apigenin 7-O-glucuronide, scutellarein-7-O-glucuronide, and vitexin, which offer cardiovas...Dracocephalum moldavica L., an annual herb valued for its medicinal and ornamental properties, produces flavonoid glycosides like apigenin 7-O-glucuronide, scutellarein-7-O-glucuronide, and vitexin, which offer cardiovascular benefits. However, the UDP-glycosyltransferases (UGTs) involved in their biosynthesis have not been fully characterized. In the present investigation, we identified five UGTs, which comprise two bifunctional flavonoid UDP-glucuronosyl/glucosyltransferase genes, DmUGT1 and DmUGT2; two flavonoid UDP-glucosyltransferase genes, DmUGT3 and DmUGT4; and one type I di-C-glycosyltransferase gene, DmCGT1. The UDP-glucuronosyl/glucosyltransferase DmUGT1 showed effective glycosylation activity and exhibited a wide substrate promiscuity, facilitating the synthesis of the principal flavonoid glycosides in D. moldavica, including bioactive compounds such as scutellarein-7-O-glucuronide. Homology modeling and site-directed mutagenesis of the bifunctional DmUGT1 indicated that the amino acids Ser127 and Tyr373 are critical determinants of sugar donor specificity. DmCGT1 could catalyze phloretin to form phloretin-3'-C-glycoside and phloretin-3',5'-di-C-glycoside. Additionally, we engineered Escherichia coli strains that utilized DmUGT1 and DmCGT1, complemented with plasmids designed to enhance the intracellular supply of UDP-glucuronic acid and UDP-glucose in E. coli. These engineered strains successfully enabled the in vivo production of scutellarein-7-O-glucuronide and phloretin-3',5'-di-C-glycoside, achieving yields of 195 and 196 mg/L, respectively. This study provides a systematic elucidation of the glycosylation mechanisms of flavonoids in D. moldavica and offers candidate genes and methodologies for the biosynthesis of bioactive glycoside compounds through synthetic biology approaches.
Ma Z, Gao X, An S
… +11 more, Chen M, Zhang B, Zhou L, Sun S, Li M, Yu F, Lü S, Chu Z, You A, Ke Y, Yang P
J Integr Plant Biol
· 2026 Jul · PMID 41782191
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Enhancing crop resilience to guarantee stable, high yields under adverse conditions has long been a central goal of rice breeding, but it remains challenging because of inherent trade-offs. Here, we show that the transcr...Enhancing crop resilience to guarantee stable, high yields under adverse conditions has long been a central goal of rice breeding, but it remains challenging because of inherent trade-offs. Here, we show that the transcriptional activity of the aldehyde-dehydrogenase OsALDH2B1 simultaneously increases grain length and alkaline tolerance. Upon alkali stress, the plasma-membrane leucine-rich-repeat receptor-like kinase SERL1 phosphorylates OsALDH2B1 at Thr-481, thereby blocking its 26S-proteasome-mediated degradation. Stabilized OsALDH2B1 directly represses GS3, a negative regulator of both grain size and alkaline tolerance, and activates all three catalase genes, leading to reduced hydrogen-peroxide (HO) accumulation. OsALDH2B1 over-expression enlarged grains and raised grain yield under field alkalinity, whereas osaldh2b1 mutants were hypersensitive. CRISPR knockouts of SERL1 or the catalase genes phenocopied these defects, confirming that the SERL1-OsALDH2B1 module constitutes an integrated signaling axis that links membrane perception to nuclear reprogramming through GS3 repression and catalase activation. This dual-purpose circuit provides an immediate, breeder-friendly target for high-yield, alkaline-resilient rice.
Prenylated phenolic glycosides, such as nodakenin, represent a class of natural products with diverse bioactivities. Their metabolic engineering production remains largely unexplored, primarily due to the scarcity of eff...Prenylated phenolic glycosides, such as nodakenin, represent a class of natural products with diverse bioactivities. Their metabolic engineering production remains largely unexplored, primarily due to the scarcity of efficient UDP-glycosyltransferases (UGTs) capable of catalyzing prenylated phenolic substrates. In this study, we characterized several UGT93 enzymes from Angelica decursiva that catalyzed the glycosylation of nodakenetin. Enzymatic assays revealed a pronounced catalytic preference of these enzymes toward various types of prenylated phenolic substrates. Notably, this substrate preference is conserved across UGT93s from other species and a reconstructed ancestral enzyme. Structural analysis and mutation experiments revealed that the preference was caused by the substrate binding with several hydrophobic and aromatic residues. This study highlights the biocatalytic potential of the UGT93 family enzymes, offering promising biocatalysts for the glycosylation of plant-derived prenylated phenolics.
This commentary discusses new research showing that six structurally and functionally atypical NLR pairs in wheat confer disease resistance via a sensor NLR-helper NLR module. The functional mechanisms of some NLR pairs...This commentary discusses new research showing that six structurally and functionally atypical NLR pairs in wheat confer disease resistance via a sensor NLR-helper NLR module. The functional mechanisms of some NLR pairs differ from the classical NLR pair model, revealing the complexity and diversity of the wheat immune system.
Shin SY, Park SJ, Park JS
… +5 more, Moon KB, Moon JS, Cho HS, Kim HS, Lee HJ
J Integr Plant Biol
· 2026 Jul · PMID 41765753
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Plant cells can undergo cellular reprogramming, enabling pluripotent callus formation from excised leaves. Despite this pluripotency, organs regenerated from leaf callus have predominantly been confined to conventional s...Plant cells can undergo cellular reprogramming, enabling pluripotent callus formation from excised leaves. Despite this pluripotency, organs regenerated from leaf callus have predominantly been confined to conventional shoots and roots, leaving the potential to regenerate other specialized organs unknown. In this study, we identified that stolons can be regenerated from potato leaf callus. Furthermore, we demonstrate that Agrobacterium tumefaciens stimulation efficiently induces stolon regeneration and subsequent tuber development from potato leaf callus. The induction of stolon regeneration is abolished when biological activity is removed from the bacterial cultures, indicating that viable bacterial cells are required for this process. Comparative assays using various strains reveal that the C58 chromosomal background is essential for this enhancement. Integrating transcriptome analysis with transgenic functional validation, we find that phosphatidylethanolamine-binding protein (PEBP) family genes are closely involved in this response. Furthermore, we observe that viruses do not readily spread to regenerated stolons through the callus, which lacks a continuous vascular system to serve as a pathway for virus movement. Our findings demonstrate that bacterial stimulation triggers stolon regeneration from pluripotent leaf callus, offering a potential approach for the production of virus-free storage organs in potato.
To adapt to environmental challenges, plants have evolved extensive gene families through duplication events, generating multiple-copy genes that mediate stress responses. However, the function of these duplicated genes...To adapt to environmental challenges, plants have evolved extensive gene families through duplication events, generating multiple-copy genes that mediate stress responses. However, the function of these duplicated genes in wheat remains unclear. In this study, we identified ten tandemly duplicated ETHYLENE RESPONSE FACTOR 109 (ERF109) genes in wheat, seven of which showed rapid induction under drought treatment. Overexpressing TaERF109A2 resulted in delayed heading date, increased tiller number, reduced plant height and root length, and enhanced drought resilience. Conversely, the CRISPR/Cas9-generated nonuple Taerf109s mutant showed exacerbated growth inhibition under drought stress. RNA-seq and functional analyses indicated that TaMADS56, functioning as a genetic downstream effector of TaERF109A2, modulates wheat tillering, heading date, and drought recovery responses. TaERF109A2 directly binds to the GCC-box motifs in the promoters of TaIPT8-5B/5D, thereby regulating cytokinin (CK) biosynthesis. Moreover, overexpression of TaERF109A2 enhances nicotianamine (NA) accumulation, which in turn confers tolerance to iron toxicity and drought stress via upregulation of nicotianamine synthase (NAS) genes. Our findings have highlighted the critical role of tandemly duplicated genes in the coordination of stress responses and developmental processes in wheat.
Su Y, Hao Y, Cao X
… +28 more, Wang L, Xu Z, Zhang F, Ma Z, Wang X, Li J, Fan T, Zhao R, Liu Z, Wang W, Zhang Y, Yang X, Yang S, Wang D, Wang K, Sun S, Li Z, Tian W, Sun Y, Liu Z, Xu Y, Xiao H, Peng Y, Xu X, Liu R, Tian X, Zhou Y, Gao Y
Climate change poses an increasing threat to global biodiversity and food security. As a wild relative of cultivated apples, Malus baccata exhibits broad environmental adaptability and robust stress tolerance. However, i...Climate change poses an increasing threat to global biodiversity and food security. As a wild relative of cultivated apples, Malus baccata exhibits broad environmental adaptability and robust stress tolerance. However, its effective utilization in breeding is constrained by the absence of a complete reference genome and insufficient population-level genomic characterization. In this study, we assembled a haplotype-resolved, telomere-to-telomere genome for M. baccata, providing unprecedented resolution for a wild apple reference genome. Population genomic analyses revealed four distinct genetic clusters. Among these, the Hebei Group 2 harbors the highest genetic diversity and heterozygosity, alongside the lowest runs of homozygosity, suggesting a complex history of genetic admixture in this population. By integrating population genomics with genotype-environment association analyses, we identified a series of climate-associated single-nucleotide polymorphisms and structural variants. A substantial proportion of these adaptive variants is localized within the coding and regulatory regions of candidate genes, providing a genomic basis for their roles in environmental adaptation. Notably, DREB1A/D and NAC6 are associated with temperature seasonality and annual precipitation, respectively. Furthermore, future climate projections indicate that the Northeastern (NE) clusters face the highest risk of maladaptation, especially under high-emission scenarios. Collectively, these findings provide critical insights into the genetic basis of climatic adaptation in wild apples, establishing a solid foundation for the conservation of crop wild relatives and the breeding of climate-resilient cultivars.
The circadian clock is an endogenous timekeeping mechanism that coordinates diverse biological processes across diverse organisms. Emerging evidence recently underscores its critical role in modulating plant immune respo...The circadian clock is an endogenous timekeeping mechanism that coordinates diverse biological processes across diverse organisms. Emerging evidence recently underscores its critical role in modulating plant immune responses. Salicylic acid (SA) is a central phytohormone in plant immunity; however, the molecular mechanisms by which clock components influence SA signaling under biotic stress are poorly understood. Here, we report the pivotal role of the core clock components, PSEUDO-RESPONSE REGULATOR 5 (PRR5) and PRR7, in governing Arabidopsis immunity by direct suppression of SA signaling. We found that the transcriptional outputs of SA signaling showed rhythmic expression and were remarkably affected by PRR5 and PRR7. Genetic analyses revealed that PRR5 and PRR7 function genetically upstream of the SA receptor NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1) to inhibit SA-mediated defenses. Biochemical assays confirmed physical interactions among PRR5/7, NPR1, and TGA3, highlighting a direct mechanism whereby PRR5/7 antagonize the transcriptional activity of the NPR1-TGA3 complex. The prr5 prr7 double mutant not only showed enhanced SA signaling but also boosted pathogen-associated molecular pattern-triggered immunity, highlighting their broad inhibitory function in plant immunity. These findings provide critical insights into the temporal dynamics of plant immunity and reveal key molecular targets for breeding crop varieties with an optimized balance between growth and immunity.
Mitogen-activated protein kinase (MAPK) cascades regulate growth, development, stress responses, and immunity in plants by transmitting signals from upstream regulators to downstream components. In this study, we identif...Mitogen-activated protein kinase (MAPK) cascades regulate growth, development, stress responses, and immunity in plants by transmitting signals from upstream regulators to downstream components. In this study, we identify a MAPK cascade composed of MAPK kinase kinase 19 (MKKK19), three MAPK kinases (MKK3/MKK5/MKK9), and MAPK 6 (or MPK6) that is involved in Arabidopsis leaf senescence. The kinase oxidative signal-inducible 1 (OXI1) functions upstream of the MKKK19-MKK3/MKK5/MKK9-MPK6 cascade to promote leaf senescence, whereas two of RESPIRATORY BURST OXIDASE HOMOLOGS (RBOHs), RBOHD and RBOHF, act downstream to mediate the accumulation of reactive oxygen species (ROS). Loss-of-function mutation of OXI1, MKKK19, MKK3/MKK5/MKK9, or MPK6 resulted in delayed leaf senescence associated with reduced ROS levels, whereas transgenic lines overexpressing OXI1, MKKK19, MKK3/MKK5/MKK9, or MPK6 displayed the opposite phenotypes. Epistatic analyses supported the involvement of OXI1, MKKK19, MKK3/MKK5/MKK9, MPK6, and RBOHD/RBOHF in the same signaling pathway for leaf senescence. In conclusion, genetic and biochemical analysis of the Arabidopsis MKKK19-MKK3/MKK5/MKK9-MPK6 cascade through OXI1 and RBOHD/RBOHF revealed a vital role for the MAPK cascade and ROS in natural leaf senescence.
Jasmonates (JAs) are vital to plant defense and stress adaptation. In Salvia miltiorrhiza, JA significantly promotes tanshinone accumulation, a class of bioactive diterpenoids. Although transcriptional regulation of JA s...Jasmonates (JAs) are vital to plant defense and stress adaptation. In Salvia miltiorrhiza, JA significantly promotes tanshinone accumulation, a class of bioactive diterpenoids. Although transcriptional regulation of JA signaling is well characterized, the post-translational mechanisms governing JA-mediated tanshinone biosynthesis remain poorly understood. Here, we identify SmWRKY2 as a critical regulator of JA-induced tanshinone accumulation, which interacts with SmCPK20. SmCPK20 positively regulates JA-induced tanshinone accumulation. JA signaling activates SmCPK20, promoting phosphorylation of SmWRKY2 at Thr-256. This phosphorylation event significantly enhances SmWRKY2's binding to the SmCPS1 promoter and its transcriptional activation capacity, thereby promoting tanshinone accumulation. Furthermore, SmWRKY2 interacts with the JA signaling repressor SmJAZ3. SmJAZ3 inhibits the SmWRKY2-SmCPK20 interaction in the absence of JA. JA-triggered degradation of SmJAZ3 releases SmWRKY2, enabling SmCPK20-mediated phosphorylation and promoting tanshinone biosynthesis. Collectively, our results demonstrate that JA and Ca signaling pathways cooperate to regulate plant secondary metabolism.