Fatty acid methyl esters (FAMEs) are recognized as promising biofuels. While engineering efforts have enabled FAME production in diverse microbes, no such work has been reported in plants. Here, we use an engineered SABATH methyltransferase for plant FAME production. PtJMT1, a jasmonic acid methyltransferase from Populus trichocarpa, displayed low activity toward octanoic acid in Escherichia coli. Guided by structural modeling of the active site, we designed a mutant enzyme predicted to have improved catalytic efficiency with fatty acid substrates. In vitro assays confirmed this prediction. The mutant enzyme displayed activity with several medium-chain fatty acids with highest activity toward octanoic acid. This mutant enzyme was denoted PtFTAMTmut, standing for a mutant fatty acid methyltransferase from P. trichocarpa. To evaluate in planta activity, PtFTAMTmut was transiently expressed in Nicotiana benthamiana. Expression of PtFTAMTmut alone in the cytosol or chloroplast did not yield FAMEs. However, coexpression of PtFTAMTmut with a chloroplast-targeted thioesterase (ChFatB2) enabled FAME production. This study provides the first report of engineered FAME biosynthesis in plants and demonstrates the utility of an engineered SABATH methyltransferase for direct biofuel production.

ABSTRACT Terpenes constitute the largest and most structurally diverse class of plant secondary metabolites, with critical roles in plant-environment interactions and broad industrial applications. Although nuclear genome engineering of terpene pathways has been extensively explored, chloroplast genome engineering remains largely undeveloped, with all reported studies restricted to the model plant Nicotiana . Here we report successful chloroplast genome engineering for diterpene production in the crop plant potato ( Solanum tuberosum ). First we identified the trnT/trnL plastomic locus as optimal for minimizing integration-associated growth penalties. Insertion of a bifunctional diterpene synthase gene into this plastomic site yielded transplastomic plants with successful diterpene production, but with reduced growth. The co-expression of a geranylgeranyl diphosphate synthase gene to enhance precursor supply restored normal growth while elevating diterpene accumulation. Transplastomic plants were otherwise agronomically comparable to wild-type. This work expands chloroplast engineering as a viable strategy for terpene pathway engineering in crop improvement and high-value terpene production.

RNA 5-methylcytosine (m5C) plays an undefined role in plant antiviral defense. Here, we reveal that the wheat methyltransferase NOP2/Sun RNA methyltransferase 2 (TaNSUN2) is an RNA m5C methyltransferase recruited by eukaryotic elongation factor 1-alpha (TaeEF1A) into Chinese wheat mosaic virus (CWMV) replication complexes (VRCs). TaNSUN2 promotes the m5C modification of CWMV RNAs to stabilize them and enhance their translational efficiency. Moreover, m5C modification in RNA 3 ' untranslated region strengthens both TaeEF1A binding, promoting viral replication, and viral coat protein interaction, facilitating viral assembly. A major allele of TaNSUN2 prevents its interaction with TaeEF1A and hinders its entry into the VRCs to suppress m5C modification of viral RNAs. TaNSUN2 knockout enhances wheat resistance to CWMV and increases the weight and size of wheat grains. Our findings provide mechanistic insights into the function of RNA modifications in plant virus infection and a valuable genetic resource for future wheat breeding projects.

Hamamelidaceae, within the order Saxifragales, comprises 27 genera and approximately 120 species. The family has a pantropical and temperate distribution across the Americas, Asia, Africa, and Australia. Previous molecular investigations, constrained by limited taxon sampling and inadequate genetic markers, supported a five-subfamily classification system. However, these studies predominantly focused on Asian taxa, resulting in poor resolution of the evolutionary relationships among American, African, and Australian genera. To address these sampling gaps, we employed near-complete generic sampling (26 of 27 genera) to investigate plastome architecture, structural variation, and phylogenetic relationships. We newly sequenced and assembled 15 plastid genomes representing geographically and taxonomically underrepresented genera and analyzed them alongside 59 publicly available plastomes retrieved from GenBank. Plastid genomes exhibited conserved quadripartite architecture with sizes ranging from 158, 076 bp to 160, 814 bp, minimal structural variation, consistent GC content (37.7-38.2%), and identical gene order. Inverted repeat (IR) regions had limited size variation (26, 211-26, 429 bp). Simple sequence repeat (SSR) distribution (2, 219 loci) showed no clear correlation with the genus-level phylogenetic relationships. We identified ten hypervariable regions, including coding sequences (accD, ycf1, clpP, ndhF, and rpl22) and intergenic spacers (rpl33-rps18, the trnG-UCC intron, trnH-GUG-psbA, accD-psaI, and petA-psbJ), as promising candidate regions for future applications in species delimitation and phylogenetic studies. Phylogenetic analyses revealed largely congruent topologies across datasets and methods, providing improved resolution and strong support for most subfamilial and tribal relationships compared with previous studies. This study highlights the utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae. The genome architecture reflects the high conservation of plastid genomes, while the identified mutation hotspots represent potential resources for future taxonomic and phylogenetic studies. Our results support the existing subfamily classification while improving geographical coverage and generic representation, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.

Heading date is one of the most important indicators to evaluate adaptation in wheat. In this study, we used three association panels to construct a genome-wide recombination landscape consisting of 97 recombination hotspots regions (RHR) in wheat. We further identified 1,043 RHR in six bi-parental populations, and 88 recombination hotspots overlapped with association panels. We next identified 2223 significant SNPs forming 55 clusters for heading date by phenotype-based genome-wide association studies (pGWAS), and 53 stable SNPs associated with 13 candidate genes were detected in at least two environments. Twenty-one QTLs were mapped in bi-parental populations and five QTL intervals overlapped RHR. By integration of collinearity analysis, recombination hotspots, and haplotype analysis, five homoeologous interval pairs were discovered, of which 7D_Hap1 advanced heading by 8.7 days. Further analysis showed that heading date-network genes were involved into transcription regulation and post-translational modification (PTM). Meanwhile, expression GWAS (eGWAS) on heading date regulatory core module identified 307 potential novel genes acting in heading date regulatory network. These findings provide new insights into wheat phenological adaptation and developed resources for developing climate-resilient wheat cultivars.

Methyl salicylate (MeSA) plays diverse roles in the aerial parts of plants. By contrast, its biosynthesis and function in roots remain poorly understood. Here, we investigated root MeSA biosynthesis and function in tomato. Genome-wide association studies (GWAS) were performed using root MeSA levels as the phenotype in a diversity panel of 167 accessions to identify associated loci. Candidate genes were biochemically characterized, and the role of MeSA in defense against root-knot nematode (RKN, Meloidogyne incognita) was evaluated using transgenic plants. MeSA was identified as a major root volatile in tomato and showed a domestication-associated reduction. GWAS revealed multiple loci associated with natural variation in root MeSA, including a major locus on Chromosome 9 encoding the salicylic acid methyltransferase (SlSAMT). SlSAMT-overexpressing plants showed reduced resistance to RKNs, whereas SlSAMT-knockdown plants exhibited enhanced resistance. Our results suggest complex roles of MeSA and the salicylic acid (SA) signaling pathway in belowground plant defense. The SA signaling pathway likely plays critical roles in protecting roots against diverse natural enemies, including RKNs. Nevertheless, RKNs appear to have co-opted MeSA as a host-location signal, and the domestication-associated reduction of root MeSA in tomato has likely contributed to enhanced resistance against RKNs.

Buds are a critical stage in the annual growth-dormancy cycle of perennial woody plants and are essential for survival and biomass accumulation. To safeguard these structures, trees employ both physical and chemical protection. Although Populus buds are known to contain rich phytochemistry, population-level variation remains largely unexplored. Here, we characterized bud phytochemistry across a population of Populus trichocarpa natural variants using gas chromatography-mass spectrometry and examined the antifungal properties of bud extracts. In the reference genotype Nisqually-1, a total of 32 lipophilic metabolites were detected, belonging to four chemical groups: terpenoids, phenylpropanoids, linear hydrocarbons, and others. Analysis of 49 additional P. trichocarpa natural variants revealed both shared features and substantial variation. All lines contained metabolites from the phenylpropanoid, linear hydrocarbon and terpenoid classes, which consistently dominated the profiles. However, quantitative differences in individual metabolites and relative class abundances distinguished the lines, allowing them to be grouped into three chemotypic clusters. To assess potential biological implications of phytochemical variance, we tested antifungal activity of bud extracts against the pathogenic fungus Fusarium oxysporum. Extracts from all 50 lines significantly inhibited fungal growth compared with controls. Correlation analyses between metabolite abundance and inhibition strength identified candidate metabolites that were most strongly associated with antifungal activity. Together, these findings reveal both conserved and variable components of bud phytochemistry in P. trichocarpa. The observed chemical diversity and consistent antifungal effects suggest that bud metabolites contribute to defense and may reflect adaptation across natural populations.

Leaf rust is among the most destructive diseases of wheat globally, incurring significant yield losses and serious economic damage. Characterization and fine mapping of genetic loci for leaf rust resistance can be beneficial for marker-assisted breeding. In the present study, we identified three stable quantitative trait loci (QTL) for adult-plant leaf rust resistance, designated QLr.caas-2AS, QLr.caas-2DS and QLr.caas-5AL, respectively, in a recombinant inbred line population derived from a Zhongmai 175 & times; Lunxuan 987 cross across four environments. Fine mapping of QLr.caas-5AL was subsequently conducted using a secondary population derived from 18 heterozygous recombinants and 19 Kompetitive allele-specific PCR (KASP) markers, which allowed the delimitation of the QTL to a 794.8-kb physical interval from 523.6 to 524.4 Mb based on the Chinese Spring reference genome v1.1. Eighteen high-confidence annotated genes were present in this physical interval, and three genes showing sequence polymorphisms and differential expression between parents were predicted as candidates for QLr.caas-5AL, based on genome and transcriptome sequencing analyses. A KASP marker for QLr.caas-5AL was successfully developed and validated to be significantly associated with leaf rust severity in a natural wheat population of 221 cultivars. The frequency of the resistance allele at this KASP marker locus was 48.0% in the wheat cultivar panel. These findings not only lay a robust foundation for map-based cloning of QLr.caas-5AL, but also provide an efficient molecular tool for marker-assisted selection in wheat breeding. (c) 2026 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Germplasm evaluation is the first step in the utilization and domestication of wild plant resources. Despite the increasing recognition of Primulina eburnea as a valuable plant-based resource for industrial calcium supplement production, systematic evaluation of its germplasm resources remains limited. This study assessed the diversity of 37 wild P. eburnea populations through common-garden experiments, analyzing 26 quality-related traits. Significant variation was found in phenotypic and nutrient traits, with mean coefficients of variation above 20 %, indicating potential for improvement. Phenotypic differentiation coefficient analysis showed that 54.52 % of the total variation was attributable to differences among populations. Principal component analysis and cluster analysis classified the populations into two distinct groups, corresponding to their eastern and western geographical distributions. Correlation analysis identified 95 significant trait relationships, enabling efficient germplasm selection. Environmental factor analysis showed that geographic isolation, which leads to differences in light, rainfall, and temperature, was a key driver of trait differentiation. The membership function models, outperforming PCA in balancing trait selection and genetic diversity, was used to establish a core germplasm bank of 13 populations. Metabolomic profiling further revealed significant differences between eastern and western populations, particularly in flavonoids and phenolic acids, which are potentially linked to bioactivity and medicinal properties. These findings support the robustness of the evaluation model and the reliability of the established core germplasm collection. Overall, these results provide a solid evaluation framework and a reliable core germplasm collection, supporting breeding, large-scale cultivation, and industrial development of P. eburnea as a high-calcium crop.

Abstract Viral suppressors of RNA silencing (VSRs) are crucial for viral infection. Here, we show that a wheat ( Triticum aestivum ) oligosaccharyltransferase ( TaOST1B ) is associated with resistance to Wheat yellow mosaic virus (WYMV). TaOST1B interacts with WYMV-encoded P1 and enhances the VSR function of P1 by N-glycosylating its asparagine residue at position 116. This increases intranuclear accumulation of P1 through interaction with the nuclear transport protein TaIMP-α2 and blocks the interaction between calmodulin (CaM3) and CaM-binding transcriptional activator (CaMTA3) to suppress RNA interference. Nevertheless, nonglycosylated P1 loses its VSR function and forms aggregates triggering endoplasmic reticulum (ER) stress and is subsequently degraded by the 26S proteasome. A natural variant of TaOST1B fails to bind P1 and regulate its N-glycosylation, which induces ER stress and proteasome-mediated degradation to attenuate WYMV infection. Our study identifies an oligosaccharyltransferases as being utilized by VSR to promote viral infection, offering insights into the arms race between plants and viruses.

We present Hi4GS, a hybrid feature selection (HFS) algorithm for selecting SNP subsets from high-dimensional genotypes to improve the prediction of genomic estimated breeding value (GEBV) under genomic selection (GS). Hi4GS combines feature importance weighting with quantity determining to construct a fused feature set from which it extracts an optimal feature subset for subsequent GS. In a study of wheat using four datasets covering 11 yield traits via large-scale GS models, the SNPs selected by Hi4GS increased the average predictive accuracy by over 82% than using all SNPs. Hi4GS was used to identify SNPs potentially affecting wheat yield, and SHAP-based interpretability was applied to explain the contributions of these SNPs and their potential interactions. Hi4GS can be used for assisting in improving the prediction accuracy of GS, wheat and other plants’ yield-associated SNPs identification, and target information for breeding chip development. The free R package Hi4GS is available at https://github.com/shgs19/Hi4GS.

Soybean is a primary source of edible protein and vegetable oil, but salt stress severely limits its quality and yield. Maintaining the intracellular Na⁺/K⁺ (Sodium ion/ Potassium ion) balance is a critical determinant of plant salt tolerance. However, the precise regulatory mechanisms governing K+ acquisition under salt stress is still not fully elucidated. As a pivotal group of K+ transporters, the KUP/HAK/KT family plays a role in regulating K⁺ uptake, translocation, and keep ion homeostasis in plant cells. Here, 29 GmKUP/HAK/KT family members were identified and classified into five subgroups. Protein domain analysis demonstrated that these members possess the conserved architecture characteristic of the K+ transporter superfamily. Promoter analysis showed that these members have various cis-acting elements, involving in hormone-inducible, stress-responsive and so on. Transcriptomic analysis and expression profiling investigated that GmHAK5 had a significant up-regulation in soybean roots and leaves under salt stress. Functional assays in trangenic soybean hair roots demonstrated that GmHAK5 could enhance salt tolerance by increasing K+ content and maintaining a lower Na+/K+ ratio. Notably, we identified that GmHAK5 interacted with protein kinase GmCIPK7 in vivo and vitro, implying a potential phosphorylation-mediated regulatory mechanism. Besides, the up-regulation of predicted interacting protein genes, including several putative GmMDH1 and GmMDH2, along with increased malate dehydrogenase content in GmHAK5-OE soybean hairy roots under salt stress, suggests that GmHAK5 may function as a regulatory hub that not only directly mediates K⁺ uptake but also potentiates energy metabolism in soybean under stress. Collectively, our findings uncover the fundamental characteristics of soybean KUP/HAK/KT family and reveal a functional regulatory module centered on GmHAK5, providing a foundation for understanding K⁺ homeostasis regulation in soybean under salt stress.

The cereal cyst nematode (Heterodera filipjevi) is a highly destructive pathogen responsible for significant annual economic losses. However, its effector repertoire and functions remain poorly resolved. We assembled stage-resolved transcriptomic data, prioritized secreted candidates, and validated their expression, localization, and functions. Seven candidate effectors were up-regulated at parasitism stages; in situ hybridization detected three effectors in subventral oesophageal glands and four in the dorsal oesophageal gland. Transient expression indicated that seven proteins were located in the nucleus and cytoplasm. In vitro RNAi and in planta RNAi demonstrated virulence roles for seven genes, which reduced female numbers by 28.4%-83.8% and 57.2%-87.2%, respectively. In ROS burst assays, Hf70514 and Hf107644 suppressed flg22-induced reactive oxygen species. Overexpression of Hf70514 in Arabidopsis thaliana increased the root length and plant height. Protein-protein interaction tests identified TaCYPA-1 as a wheat target of Hf70514. Transient silencing of TaCYPA-1 significantly enhanced H. filipjevi parasitism, accompanied by down-regulation of defence-related genes. Collectively, these findings expand the H. filipjevi effector compendium and suggest a model in which multiple secreted effectors suppress the PTI-associated ROS, influence plant growth, and engage specific wheat proteins to promote parasitism.

A nuclear-localized G2-like transcription factor, TaGLK-A1 (TraesCS7A02G539600), was identified as a strong candidate gene for grain fructan content in wheat using GWAS, linkage mapping and transcriptome analysis. Fructans, a type of natural polysaccharides or oligosaccharides polymerized from fructose molecules, play important physiological roles in crops and confer great health benefits to humans. In this study, we detected 78 stable loci associated with fructan content across all 21 wheat chromosomes across three environments and in the BLUE, explaining 4.4–10.0

This study employed UPLC-MS/MS and GC-MS metabolomics to analyze quality traits in three red-fleshed kiwifruit cultivars: 'RubyRed', 'Donghong', and 'Hongyang'. 'RubyRed' showed enhanced biosynthesis of flavonoids, particularly anthocyanins, and a volatile profile rich in esters, aldehydes, and ketones contributing to fruity and floral aromas. 'Donghong' and 'Hongyang' were characterized by pyrazines and monoterpenes, respectively. Pathway analysis revealed significant activation of flavonoid and volatile metabolism in 'RubyRed'. Additionally, 'Hongyang' contained higher levels of essential amino acids, highlighting its nutritional value. This study provides critical biochemical insights into the quality traits of red-fleshed kiwifruit. By targeting specific pathways such as flavonoid biosynthesis and volatile compound metabolism, future breeding efforts can optimize traits like pigmentation, aroma, and nutritional value to meet consumer demands and enhance the functional benefits of kiwifruit.

Owing to the continuous increase in industrialization, the extent of soil salinization is escalating globally. Brassica napus is among the most advantageous field crops for the development and utilization of saline - alkali land. Nevertheless, the molecular regulation of salt tolerance during the seedling stage in this species remains unclear. To explore this mechanism, an association population consisting of 202 accessions was subjected to a 257 mmol/L NaCl solution at the seedling (four - leaf) stage. After 14 days of salt treatment, the above - ground and under - ground fresh and dry weights of each accession line were measured, and the correlations between these traits were evaluated. By integrating phenotypic data with resequencing data, a genome - wide association study identified 2043 single nucleotide polymorphisms (SNPs) that were significantly associated with these traits. Ninety SNPs were detected repeatedly, with a single SNP accounting for 1.3%–5.29% of the phenotypic variation. Subsequently, two candidate genes were identified, and six germplasm resources with strong salt tolerance at the seedling stage were selected. These results will guide strategies for breeding salt - tolerant B. napus and will offer a theoretical foundation for the restoration and management of salinized land.

Fruit softening is a critical determinant of shelf life and marketability in sweet cherry (Prunus avium L.). This process is predominantly driven by cell wall disassembly, which is tightly regulated by transcription factors. Despite evidence for ethylene's role in sweet cherry softening, how these signals are transduced to regulate the expression of cell wall-modifying genes is unclear. Here, we identified the ethylene-responsive transcription factor PavERF28 as a key regulator in this process. Overexpression of PavERF28 significantly upregulated the transcriptional levels of genes involved in pectin degradation (including genes encoding polygalacturonase, pectin methylesterase inhibitor, and pectate lyase), thus effectively enhancing fruit softening. Moreover, heterologous overexpression of PavERF28 in tomato confirmed its function in promoting fruit softening. At the molecular level, PavERF28 was shown to directly activate the expression of two polygalacturonase genes (PavPG1 and PavPL5) by binding to their promoters, which catalyze pectin depolymerization and thus drive softening. Collectively, our work provides an in-depth elucidation of the regulatory mechanism by which ERF family members control fruit softening in sweet cherry and offers potential targets for the manipulation of fruit ripening, especially softening.

Terpenes constitute the largest and most structurally diverse class of plant secondary metabolites, with critical roles in plant-environment interactions and broad industrial applications. Although nuclear genome engineering of terpene pathways has been extensively explored, chloroplast genome engineering remains largely undeveloped, with most reported studies restricted to the model plant Nicotiana. Here we report successful chloroplast genome engineering for diterpene production in the crop plant potato (Solanum tuberosum) guided by evolutionary principles. First, we identified the trnT/trnL plastomic locus as a new transgene integration site with minimal integration-associated growth penalties. Insertion of a bifunctional diterpene synthase gene from a fern that is absent in flowering plants into this plastomic site yielded transplastomic potato plants with successful production of new diterpenes, but with reduced growth. The co-expression of an algal geranylgeranyl diphosphate synthase gene of chloroplast genome origin to enhance precursor supply restored normal growth while elevating diterpene production. Transplastomic plants were otherwise agronomically comparable to wild-type. This work expands chloroplast engineering as a viable strategy for evolution-inspired terpene pathway engineering in crop improvement and high-value terpene production.

MYB transcription factors function as main regulatory hubs that integrate environmental signals with multi-hormonal pathways to synchronize plant growth, metabolism and stress responses. This review delineates the regulatory roles of MYB in the signalling pathway of salicylic acid, jasmonic acid, ethylene and abscisic acid signalling. These are responsible for regulating hormone biosynthesis and facilitating interaction between biotic and abiotic stress responses. The post-translational regulation of MYB activity by kinase cascades and the direct regulation of secondary metabolic pathways, such as the biosynthesis of phenylpropanol and lignin, by MYBs through the MYB-bHLH-WD40 (MBW) complex were investigated. MYB transcription factors located at the intersection of hormone signalling, metabolic regulation, and developmental regulation play a unique role in coordinating plant adaptation from the cellular level to the whole plant.