Legume–Rhizobium symbiosis requires rhizobial entry and intracellular persistence without triggering host defense. Recent genetic and biochemical studies support an immune-gating view in which plant immunity pathways are not simply suppressed, but are dynamically regulated throughout rhizobial infection, nodule development and nodule senescence. Here, we review how LysM/LRR receptor complexes and co-receptor availability shape early discrimination of symbiotic signals and immune elicitors and how shared signaling modules (Ca²⁺, ROS and MAPKs) are differentially regulated to permit infection and nodule organogenesis. We then discuss rhizobial surface polysaccharides and type III-secreted effectors as modulators of these thresholds and highlight nodule-local regulators that prevent late immune reactivation and maintain bacteroid accommodation. We also discuss nodule-specific regulators, autophagy-associated processes and, in some legumes, NCR peptides that maintain bacteroids within symbiosomes while preventing plant overactivation of immunity.

Knowing how much information a single pixel can provide is not just a technical issue; it shapes what we learn, and what we will learn, from the field. This article examines how pixel size governs the capture and interpretation of environmental and phenotypic information in remote sensing, phenomics, enviromics, and precision breeding. Spatial resolution, expressed as Ground Sample Distance (GSD), connects image scale to biological meaning, with direct implications for data quality, model accuracy, and the interpretation of genotype?×?environment (GEI) interactions. The discussion spans multiple observation platforms: (i) satellites provide meter-scale data for regional and temporal monitoring; (ii) drones offer centimeter-level imagery suited to within-plot variation and high-throughput phenotyping; and (iii) intermediate resolutions connect detail, comparability, and computational efficiency. When spatial resolution is mismatched with the biological process, information loss occurs through spectral mixing, aggregation biases, and distortion of derived indices such as NDVI, canopy temperature, and biomass. Spatial scale can also be transformed through superpixel aggregation, which converts fine raster grids into homogeneous spatial objects, and through subpixel refinement, which disaggregates coarse pixels to recover local heterogeneity. Empirical evidence shows that predictive ability improves when the spatial scale of environmental covariates aligns with the ecological and experimental scale under study. These concepts extend to experimental design, Target Population of Environments (TPE) mapping, and recommendation zoning through GEI mapping. This review treats spatial resolution strategically as a modeling parameter, not as a fixed technical constraint. Choosing pixel size through sensitivity analysis and study objectives helps align environmental representation, predictive modeling, and comparability across experiments. We also discuss perspectives involving autonomous sensing, multiscale data processing, computational infrastructure, and the use of different spatial scales for genomic and genomic–enviromic prediction.

Grain shape is a key agronomic trait for grain yield and quality in crops. Studies on rice have revealed several complex signaling pathways governing cell proliferation and cell expansion during grain development. Although cell division is critical for these events, the mechanistic integration of cell division into these developmental processes to determine grain shape remains unclear. In this study, we have identified Grain Shape 11 (GS11) as a positive regulator of rice grain shape. Loss of GS11 function leads to mispositioning of the preprophase band (PPB), a cortical ring composed of microtubules and actin filaments that defines cell division orientation. This misregulation results in asymmetric divisions, reduced cell size, increased cell number, and disorganized cell arrangements, ultimately producing shorter and wider grains. GS11 encodes a plant-unique protein that associates with microtubules. GS11 physically interacts with OsTON1a and OsTON2, the components of TON1-TRM-PP2A (TTP) complex, to co-regulate PPB positioning and cell division orientation during mitosis. Moreover, GS11 genetically interacts with GW7 in regulating grain shape. Altogether, our results identify GS11 as a TTP-associated protein that functions in coordinating cell proliferation and expansion likely by modulating microtubule organization and PPB positioning, providing insights into rice grain shape regulation.

Transport and distribution of carbon assimilation products play a crucial regulatory role in rice growth, development, and yield formation. The importance of sugar transport proteins (STPs) in this process is being increasingly recognized. Here, we identified OsSTP26 as a critical regulator of tillering and yield in rice. OsSTP26, which is highly expressed in vascular bundles of leaf blades and leaf sheaths, encodes a plasma membrane-localized transporter with typical conserved sugar transporter domains. A hexose uptake assay in protoplasts demonstrated that OsSTP26 mediates transmembrane transport of glucose and fructose. Analyses of agronomic traits revealed that both knockout and overexpression of OsSTP26 increased tiller number and grain yield. Further physiological, transcriptomic, and hormone analyses indicated enhanced tillering through distinct mechanisms. Knockout of OsSTP26 increased glucose and sucrose levels in leaves and enhanced sugar unloading and sink cell uptake at the shoot base, leading to glucose and sucrose accumulation in the shoot base, thereby promoting tillering and grain yield through the HXK?CK pathway. Overexpression of OsSTP26 elevated sucrose levels in leaves, enhanced sucrose phloem loading in source leaves to facilitate source-sink allocation, and consequently increased tillering and grain yield via the TOR?nitrogen assimilation pathway. This study elucidates the mechanism by which OsSTP26 increases tillering and yield in rice.

In rice (Oryza sativa L.), the vascular bundle tissue in the panicle neck plays a critical role in transporting photosynthetic products, nutrients, and water from the roots and leaves to the panicles, and is positively associated with grain yield. However, the genetic mechanisms regulating vascular bundle number in the panicle neck remain poorly understood. Here, we report the map-based cloning and functional characterization of LVN3, a quantitative trait locus controlling the number of large vascular bundles in rice (Oryza sativa L.) panicle neck. LVN3 encodes OsGA20ox1, an enzyme in gibberellin (GA) biosynthesis. It is expressed in developing panicles and vascular bundles, and positively regulates both the number and cross-sectional area of vascular bundles in the panicle neck and the second internode, as well as flag leaf size and grain number per panicle. Compared with the near-isogenic line NIL-LVN3^LT, NIL-LVN3^TQ showed significantly increased vascular bundle number and area, enlarged flag leaves, and improved panicle morphology, ultimately leading to a 6.6% increase in grain yield. RNA-seq analysis revealed that LVN3 affects the expression of auxin-related genes in the shoot apex, suggesting that LVN3-mediated vascular development is partly driven by crosstalk between GA and auxin signaling. Cultivars carrying the LVN3-2 haplotype exhibited moderate effective panicle number per plant, grain number, and grain weight, yet achieved the highest grain yield among six haplotypes, identifying LVN3-2 as a superior haplotype for optimizing grain yield components. Moreover, natural variation at position rs3:36150392 in the LVN3 promoter may represent a functional site associated with vascular bundle development and grain number per panicle in the japonica (Geng) subpopulation. Together, these findings demonstrate that LVN3 regulates source capacity, sink size, and transport efficiency, showing potential for application in rice breeding programs aimed at increasing grain yield.

The microRNA399-PHOSPHATE2 (miR399-PHO2) module is known to maintain phosphate homeostasis in plants, yet its spatiotemporal control and integration of phosphate signaling under low-phosphate (LP) stress remain unclear. In this study, we show that LP induces distinct OsmiR399/OsPHO2 expression dynamics in roots versus shoots, and root-derived OsmiR399 preferentially suppresses OsPHO2 to facilitate P uptake and translocation. An OsmiR399-resistant OsPHO2-b mutant with deletion of OsmiR399-binding sites within OsPHO2 5′-UTR, significantly reduces shoot P overaccumulation in OsPHR2/OsmiR399 overexpressors under P-replete conditions. Under LP stress, both OsPHO2-b and osmir399 mutants display reduced root plasticity, enhanced shoot growth inhibition and accelerated leaf senescence. Transcriptomic and cellular analyses revealed tissue-specific dysregulation of P-starvation response (PSR) genes, with suppressed expression in roots but elevated in shoots, as well as defective root-shoot P redistribution. Root-split experiments further showed that OsPHO2-b disrupts systemic auxin signaling and root elongation response to local LP stimuli. Genetic evidence revealed that OsPHO2 functionally intersects with OsNLA1 to synergistically regulate PSRs in a P-dependent manner. Meanwhile, overexpression of OsPHO1-2 significantly enhances root elongation and P translocation in OsPHO2-b. Collectively, our findings establish the OsmiR399-OsPHO2 module as a central hub for root-shoot communication, coordinating root plasticity with systemic signaling to facilitate LP acclimation in rice.

Rice blast, caused by Magnaporthe oryzae, is one of the most destructive diseases threatening rice production worldwide. This study aimed to characterize the function of the transcription factor OsEREBP109 and its regulatory network in rice immunity against M. oryzae. We generated OsEREBP109 overexpression lines and CRISPR/Cas9-mediated knockout mutants to evaluate blast resistance phenotypes. The direct binding and transcriptional activation of OsEREBP109 on its downstream target were examined using yeast one-hybrid, electrophoretic mobility shift assay, and dual-luciferase reporter assays. Overexpression of OsEREBP109 enhanced blast resistance, whereas its knockout significantly reduced resistance. OsEREBP109 was shown to directly bind the cis-element in the promoter of OsGRP5 (encoding a glycine-rich RNA-binding protein) and activate its transcription. Loss-of-function of OsGRP5 compromised resistance to M. oryzae, confirming it as a critical downstream target. Moreover, OsGRP5 associated with RNA and modulated the expression of multiple defence-related genes, including OsARF2, OsFBX400, and OsNAC030. Together, these results define a hierarchical ERF-RBP regulatory module in which OsEREBP109 directly induces OsGRP5 to maintain the abundance of key immune transcripts, thereby enhancing rice resistance to M. oryzae.

Tiller number is a pivotal agronomic trait directly determining grain yield in wheat (Triticum aestivum L.). Although TN1 is a key positive regulator of tillering, its regulatory network remains incompletely characterized. In this study, we identify TaMYB72-B and TaGSK3 as convergent regulators of TN1 that together fine-tune tiller number. Promoter analysis established TaMYB72-B as an upstream transcriptional repressor of TN1, and its overexpression reduced tiller number, confirming that TaMYB72-B suppresses tillering through TN1. Independently, the kinase TaGSK3 physically interacts with and phosphorylates TN1, destabilizing the protein and accelerating its degradation; overexpression of TaGSK3 likewise reduced tiller number significantly. Together, these findings define a dual-layer regulatory mechanism in which transcriptional repression and post-translational modification converge on TN1 to precisely control tiller development. Haplotype analysis across global wheat germplasm identified TaMYB72-B Hap 1 as an elite haplotype associated with an optimal balance between reduced tiller number and increased grains per spike, a combination that has been preferentially selected during modern breeding. Collectively, this study uncovers a novel regulatory module governing wheat tillering and provides actionable genetic targets for molecular design breeding aimed at optimizing plant architecture and yield.

Plant architecture is a critical determinant of crop yield, in which plant height serves as a key morphological trait. In this study, we characterized a novel wheat mutant named AS34 carrying a pleiotrophic gene named semi-dwarf and dense-spike 1 (sdd1). AS34 has reduced height, shorter spikes and increased spikelet density. Genetic analysis demonstrated monogenic recessive inheritance of these coordinated traits, with a strong negative correlation between spike length and density. The mutant is insensitive to brassinosteroid (BR), shows a minimal response to applied 24-epibrassinolide and has altered expression of key genes in the BR pathway. AS34 also exhibits enhanced sensitivity to applied gibberellin (GA) and auxin compared with the wild type, suggesting that the phenotype involves modifications in multiple hormone signaling pathways. Transcriptome profiling identified 1869 differentially expressed genes, with upregulation of defense- and cell wall-related pathways and downregulation of sulfur metabolism processes. Sdd1 was localized to a 5.7?Mb interval on chromosome 3B (414.7?420.4?Mb). Among 50 candidate genes located in the interval, TraesCS3B02G260400 was identified as a Sdd1 gene candidate following integrated fine gene mapping, resequencing, expression analysis, and mutant phenotype validation. This study provides new insights into the regulation of wheat architecture and identifies Sdd1 as a new gene resource for breeding for optimized plant architecture.

Grain size and weight are key determinants of wheat yield, yet their genetic basis remains incompletely understood. In this study, we have identified TaPDCD5, a wheat gene encoding a double-stranded DNA-binding domain protein, as a negative regulator of grain size and weight. Overexpression, knockout, and expression studies indicated that TaPDCD5 elevates H₂O₂ levels by suppressing the expression of ROS-scavenging genes, thereby inhibiting grain development. Knockout of TaPDCD5 in the commercial cultivar Xinong 511 similarly increased grain size and weight, confirming its function across genetic backgrounds. A haplotype of TaPDCD5-1B associated with higher grain yield has undergone selection during modern breeding. Collectively, TaPDCD5 is a promising target for molecular breeding to improve wheat yield.

The yield of crops is constrained by abiotic stresses such as heat and drought. In this study, we characterized a wilting maize mutant, wilting leaf1 (wl1-ref), which exhibited leaf wilting, dwarfism, and impaired yield. The wilting phenotype was exacerbated by multiple abiotic stresses, including high temperature, drought, and salt conditions. The wl1-ref mutant showed obvious defects in vascular bundle development, with abnormal or missing protoxylem vessels, leading to compromised water translocation. WL1 encoding a GDSL protein localized to the endoplasmic reticulum and cytoplasm was highly expressed in vascular-rich tissues including roots, stems, and leaf sheaths. Transcriptome profiling revealed substantial changes in pathways related to stress responses and cell wall biosynthesis and modification which are responsible for reduced lignin and disrupted cell wall vasculature. Taken together, our results demonstrated that WL1 contributes to water translocation and abiotic stress tolerance in maize by affecting cell wall integrity and vascular development, highlighting its potential as a target for breeding stress-resilient maize varieties.

Kernel moisture content (KMC) and kernel dehydration rate (KDR) strongly influence grain quality and suitability for mechanical harvesting in maize (Zea mays), yet the underlying genetic architecture is unclear. In this study, using a recombinant inbred line population phenotyped across four environments at 35, 42, 49, and 56?d after pollination (DAP), we identified 38 QTL associated with KMC and KDR, explaining 1.16%–20.88% of the phenotypic variance. The major QTL qKDR3.06 accounted for 4.88%–20.88% of the variance and was fine-mapped to a 219-kb interval in bin 3.06 of chromosome 3. Integrated parental sequence comparison, expression profiling, and regional association analysis identified ZmBAK1a (GRMZM5G815009), which encodes a brassinosteroid (BR) BAK1 family co-receptor, as the leading candidate gene in this interval. Five significant KDR-associated SNPs were located within this gene. A 202-bp InDel in the ZmBAK1a promoter distinguished the two parents, suggesting that this InDel is a causal regulatory variant. RT-qPCR revealed stage-specific differences in gene expression: the PH4CV allele (carrying the 202-bp deletion) showed lower ZmBAK1a expression at 28–40 DAP but significantly higher expression at 45 DAP than the KB020 allele. Consistent with this pattern, genotypes harboring the 202-bp deletion exhibited faster kernel dehydration in the AMP1 and AMP2 maize populations. Bioinformatic analysis identified a canonical salicylic acid (SA)-responsive cis-element within the deleted region. Given that BAK1 family genes regulate cell wall remodeling and water transport during grain maturation, we propose that ZmBAK1a influences late-stage kernel dehydration through BR-mediated signaling, with SA as a potential additional regulator. Our findings provide a functional marker and a novel gene target for breeding maize hybrids with rapidly dehydrating kernels.

Plant cuticular wax forms a hydrophobic barrier that protects plants against various biotic and abiotic stresses, including drought, UV radiation, and pathogen infections. Sorghum (Sorghum bicolor (L.) Moench), a major drought-tolerant crop, is characterized by an abundant cuticular wax layer. In this study, we identified a novel bloomless mutant (bm-sz) with impaired wax biosynthesis in sorghum. The bm-sz mutant displayed significantly reduced levels of very-long-chain fatty acids (VLCFAs), triterpenoids, alcohols, and other wax constituents, resulting in an 80% reduction in total wax content compared with the wild type. Map-based cloning, complemented by allelic mutant analysis and RNA interference (RNAi), verified that BM-SZ is the causal gene, which encodes a putative α/β hydrolase. AlphaFold3 structural modeling further revealed that the causal G198R mutation disrupts the protein’s central hydrophobic catalytic pocket, likely abolishing its ligand-binding or enzymatic capability. Transcriptome analysis indicated that BM-SZ regulates wax and VLCFA biosynthesis by modulating the expression of key wax-producing genes, particularly those in the KCS family. Our findings suggest that BM-SZ functions as a critical regulator of VLCFA-mediated wax biosynthesis, providing a vital genetic target for breeding drought-tolerant crops.

Nuclear male sterility is a valuable trait for hybrid seed production in crops, offering potential yield advantages and enhancing genetic diversity. In soybean (Glycine max), the identification of nuclear male sterility genes is hindered by genome complexity and limited sterile genetic resources. In this study, we employed CRISPR/Cas9 genome editing to disrupt Dysfunctional Tapetum 1 (DYT1), encoding a conserved regulator of pollen development in plants, and successfully induced complete male sterility in soybean. Phylogenetic analysis identified three DYT1 genes in soybean, among which two bHLH genes, GmDYT1a and GmDYT1c, exhibited distinct expression patterns and subcellular localizations. Complete pollen abortion was observed only in the gmdyt1a gmdyt1c double mutant, suggesting functional redundancy between GmDYT1a and GmDYT1c. Cytological observations revealed microspore degeneration in the double mutant, resembling DYT1 loss-of-function phenotypes in other species. Gene expression analysis further demonstrated that the canonical DYT1–TDF1–AMS regulatory pathway is conserved in soybean, supporting its conserved role in regulating male fertility across plant species. Our study establishes CRISPR/Cas9-mediated editing of DYT1 as an effective strategy for generating male-sterile lines and provides a genetic resource for hybrid breeding in soybean.

Seed oil content is a key agronomic trait that defines the quality and economic value of soybean. Although regulatory mechanisms of seed oil accumulation have been investigated using single-omics strategies, the metabolic dynamics during seed development remain poorly understood from a multi-omics perspective. Here, we performed an integrated analysis of metabolomics and transcriptomics across multiple seed developmental stages to dissect the regulatory landscape underlying oil biosynthesis and accumulation in soybean. In total, more than 1000 differential metabolites and 7000 differentially expressed genes (DEGs) were identified in nine soybean cultivars with contrasting oil contents. Through correlation analysis linking metabolic pathways, differential metabolites, and DEGs, we characterized 10 core DEGs significantly associated with seed oil content, which are involved in amino acid metabolism, flavonoid biosynthesis, lipid biosynthesis, and phenylpropanoid biosynthesis. Further integration of oil metabolism pathway analysis and natural population haplotype analysis verified that GmADH1 and GmCrRLK1L34 function as the core hub genes in the regulatory network governing soybean seed oil accumulation. Integrating multi-omics data, our study uncovers the core regulatory circuits controlling oil accumulation in soybean seeds and provides a valuable framework for investigating key agronomic traits across diverse crop species.

Improving lodging resistance without compromising yield is a major challenge in rapeseed (Brassica napus L.), a globally important oilseed crop. Here, we demonstrate that calcium application simultaneously enhances lodging resistance and yield of rapeseed under pot and field conditions. In pot studies, calcium treatment enhanced photosynthetic capacity, increased the number of siliques by an average of 29.4%, and improved thousand-seed weight, resulting in higher yields. Calcium treatment also increased stem bending resistance by altering stem structure and cell-wall composition, with upper- and lower-stem strength increasing by 33.0%–35.2% and 23.9%–30.6%, respectively. We confirmed these beneficial effects at multiple field sites with different soil types and planting densities. Physiological and biochemical analyses revealed that calcium treatment strengthens stem mechanical properties by promoting calcium pectate accumulation and reducing pectin methylesterification, as supported by the upregulation of pectin methylesterase (PME) genes. Furthermore, knockout of BnaPME35 abolished the effect of calcium treatment on lodging resistance, highlighting the role of pectin methylesterification levels in lodging susceptibility. These findings suggest that targeted application of calcium-containing fertilizers offers a practical strategy for improving lodging resistance and yield in rapeseed.

Soil salinity poses a major threat to cotton production. The objective of this study was to identify a novel regulator of salt tolerance in cotton root-tip cells, the initial site of salt perception, and to determine how it confers tolerance, so that it might be used to improve cotton grown on saline soils. Salt-responsive genes were identified by RNA-sequencing of root tips and root-tip protoplasts under NaCl stress, and a candidate hub gene, GhAKR1, was selected using weighted gene co-expression network analysis (WGCNA); its function was characterized by virus-induced gene silencing (VIGS) and overexpression, and its upstream regulator was identified by dual-luciferase and yeast one-hybrid assays. GhAKR1 was progressively induced by salt and belonged to a co-expression module enriched in MAPK and hormone signaling. Silencing GhAKR1 reduced superoxide dismutase (SOD) activity, chlorophyll content, and leaf water content while elevating malondialdehyde (MDA) and reactive oxygen species (ROS), whereas overexpression increased salt tolerance and reversed these physiological effects. GhERF17 bound the GhAKR1 promoter and activated its transcription, and GhAKR1 was associated with ethylene accumulation during salt stress. We conclude that GhAKR1 increases cotton salt tolerance by integrating antioxidant defense and ethylene signaling downstream of GhERF17, making both genes promising targets for breeding salt-tolerant cotton.

The cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) is a major pest of numerous crops. Plant responses to cotton bollworm attack are generally attributed to two primary factors: physical wounding and components of insect oral secretions. Discriminating between these responses is critical for understanding plant defense and developing pest control strategies. In this study, we found that cotton bollworm infestation specifically upregulated the expression of NtNAC29 and NtNAC94, whereas mechanical wounding did not. Functional analyses revealed that silencing either gene promoted bollworm growth, whereas overexpression suppressed larval development. These results demonstrated that NtNAC29 and NtNAC94 had pivotal roles in enhancing plant resistance to bollworm. Further analyses showed that both NAC transcription factors regulated the expression of Cysteine Protease Inhibitor 8 (NtCPI8) by binding to specific sites within the NtCPI8-1 and NtCPI8-2 promoters. Consistently, NtCPI8 exhibited a similar defensive role, significantly inhibiting cotton bollworm growth as reflected by reduced larval weight gain and shorter body length. Overall, our findings suggest that tobacco plants recognize cotton bollworm attack and activate downstream defense responses, including the induction of NtNAC29 and NtNAC94. These transcription factors in turn upregulate NtCPI8 expression, thereby strengthening plant resistance against insect herbivory. Notably, this NAC-CPI regulatory module is conserved among different crop species, providing a promising target for improving crop protection against herbivorous insects.

The purpose of this study was to develop a method for producing high-resolution mapping populations without the disadvantages of rare alleles and population structure, combining the advantages of biparental and association mapping: Advanced Intercross-Derived Recombinant Inbred Lines (AID-RILs). We used male sterility to create an AID-RIL population in rice. Genome-wide association studies in this population achieved high detection power and low false-positive rate for identifying quantitative-trait nucleotides, with the FarmCPU method showing the best performance. The strategy could be extended to multi-parental crosses.

Thinopyrum elongatum (2n?=?4x?=?28) harbors multiple valuable resistance genes and serves as a valuable genetic resource for wheat improvement. Yr1EL was primarily identified on chromosome arm 1EL of tetraploid Th. elongatum, conferring adult-plant resistance to stripe rust. To further map and utilize Yr1EL, we introduced chromosomal rearrangements by crossing the wheat–tetraploid Th. elongatum 1E(1D) substitution line and the T1BS·1EL translocation line with the common wheat Chinese Spring ph1b mutant. In total, eight wheat–Th. elongatum chromosome 1E structural variants were identified by in situ hybridization, the GenoBaits?WheatplusEE panel, and molecular markers. These variants include one large segment translocation, one terminal fragment deletion, one chromosome 1E insertion translocation, and five chromosome 1EL terminal small fragment translocations. Based on phenotyping and genotyping of these variant lines, Yr1EL was mapped to an approximately 20.91?Mb physical interval (532.45 to 553.35?Mb) on the distal long arm of chromosome 1E corresponding to the diploid Th. elongatum reference genome. Genetic analysis confirmed that stripe rust resistance was conferred by the Yr1EL locus with incomplete dominance. Five codominant molecular markers co-segregated with the Yr1EL locus and will facilitate marker-assisted selection. Furthermore, collinearity analysis showed that this interval is structurally conserved among Triticeae species, and 29 candidate genes potentially related to disease resistance were annotated. Those candidates included receptor-like proteins, kinases, nucleotide-binding and leucine-rich repeat receptors, and other disease resistance proteins. The adult-plant resistance gene Yr1EL expands the wheat disease-resistance gene pool and provides valuable germplasm for breeding durable stripe rust-resistant cultivars.

Black point (BP) disease affects wheat (Triticum aestivum) production worldwide, and identifying BP resistance genes is essential for developing resistant cultivars. We previously detected QBB.hau-4A, a major QTL for BP resistance, using the fungal pathogen Bipolaris sorokiniana with a recombinant inbred line (RIL) population from a cross between wheat lines Wanyuanbai 1 and SN4143. Here, we fine mapped QBB.hau-4A using secondary F₂ and F_2:3 populations derived from resistant and susceptible RILs. Using 14 dCAPS markers, the QTL was delimited to a 1.36?Mb interval. With gene-specific markers, we narrowed this interval to a 1.06?Mb region between markers BP-100-d1 and BP-4A-d34 (40.87–41.93?Mb), containing six high-confidence genes in the Chinese Spring reference genome. Based on parental expression patterns and sequence polymorphisms, we identified four candidate genes for QBB.hau-4A: TraesCS4A02G050400, TraesCS4A02G050500, TraesCS4A02G050700, and TraesCS4A02G050800. Of these, TraesCS4A02G050800 is the most likely candidate for QBB.hau-4A. We developed BP-800-d1, a gene-specific marker for TraesCS4A02G050800 based on a SNP and an InDel distinguishing the resistant and susceptible parents. This marker was subsequently validated in two F₂ populations and a diverse panel of 412 wheat accessions. To our knowledge, this study represents one of the first efforts to identify candidate genes associated with BP resistance. In addition to offering valuable information for understanding the complex genetic basis of BP resistance, it provides molecular markers for breeders.

Multi-environment trials (METs) are essential for maize breeding, but their implementation is often constrained by limited resources, particularly the high cost of phenotyping. To optimize resource allocation, 264 testcrosses derived from 100 inbred lines and three testers were evaluated across six locations. Four genomic prediction models, five cross-validation schemes (CV1–CV5), and five training set proportions (S1–S5) were systematically assessed for predicting grain moisture content (GMC), grain yield (GY), and plant height (PH). Together, the five cross-validation schemes and five training set proportions generated 25 sparse testing strategies. Among the four models, the reaction norm model consistently achieved the highest prediction accuracy, and was therefore selected for subsequent analyses. Averaged across S1–S5, CV1 showed the lowest prediction accuracy, with mean accuracies of 0.361 for GMC, 0.413 for GY, and 0.480 for PH. In contrast, CV2–CV5 achieved higher and comparable accuracies. Increasing the training set proportion from 1/6 (S1) to 5/6 (S5) improved prediction accuracy by 48.3% for GMC, 30.3% for GY, and 26.7% for PH, although further gains became limited once the training set proportion exceeded approximately 50% (S3). In addition, CV3 enabled reliable estimation of parental general combining ability based on predicted hybrid performance, particularly at higher training set proportions. Overall, integrating multi-environment sparse testing with genomic prediction enables efficient hybrid evaluation under limited resources, providing a cost-effective strategy to reduce phenotyping demands and accelerate breeding progress.

Heterosis is central to breeding high-yielding maize (Zea mays L.). To dissect the genetic basis of heterosis for yield-related traits, we constructed four testcross populations using four diverse inbred lines as testers and an association mapping panel of 368 inbred lines. We systematically investigated ear diameter, ear length, kernel row number, kernels per row, and kernel weight per ear, as well as their mid-parent heterosis values, across two environments. Using whole-genome sequencing and genome-wide association analysis, we mapped genomic regions and identified candidate genes associated with these traits and their heterosis. We detected a total of 94 genomic regions containing 389 candidate genes, of which Zm00001d051889 (ETHYLENE INSENSITIVE 4 [EIN4]), involved in ethylene signaling, was a key candidate locus. We identified a 59-bp insertion–deletion (InDel) variant in its promoter region, and EIN4 showed non-additive expression in hybrids. Haplotype analysis revealed that the stacking of Hap 3 of EIN4 in hybrids is associated with greater ear diameter and kernel row number. EMS-induced loss-of-function mutation of EIN4 resulted in altered ear length in hybrids, indicating an impact on ear length heterosis. These findings demonstrate that promoter variation, haplotype changes, and EMS-induced premature termination of EIN4 all affect heterosis or yield-related traits, providing convergent genetic evidence for the contribution of EIN4 to yield-related heterosis in maize. The identification of EIN4 and its natural polymorphisms provides a useful molecular resource for maize hybrid breeding, facilitating marker-assisted selection and the development of high-yielding and stable maize varieties.

The objective of this study was to characterize genetic resistance to bacterial wilt (BW) of peanut caused by Ralstonia solanacearum. We fine-mapped qBWA12, a major quantitative trait locus for BW resistance, and identified AhBWR1, which encodes a CC-NBS-LRR protein, as the most likely candidate gene. Interaction studies revealed self-association of the AhBWR1 CC domain and its interaction with MYB56, GRAS and a pentatricopeptide repeat protein. A polymorphism at locus A12_4,323,949 permitted selecting BW-resistant accessions from a peanut germplasm collection of 325 accessions. AhBWR1 could be used to breed novel disease–resistant cultivars.

The objective of this study was to identify how strigolactones (SLs) coordinate canopy architecture and yield plasticity in winter wheat at varying planting densities and genotypic tillering potentials. We examined whether exogenous SLs regulate tiller hierarchy and yield plasticity in winter wheat by conducting two-year field experiments at Jinan and Laizhou with a sowing-density gradient, contrasting tillering cultivars, and foliar application of a natural SL compound or the synthetic analog rac-GR24 at the jointing stage. SL application induced position-specific tiller suppression, reducing total tillers per plant and peak tiller number under high density stress. This adjustment in canopy structure favored assimilate allocation to grain, increasing grain yield under high-competition conditions. We conclude that SLs act as conditional regulators that increase phenotypic plasticity and could be used as a post-establishment agronomic intervention to mitigate overcrowding stress in intensive wheat cropping systems.

Optimizing phenology and dry matter partitioning will increase wheat yield in dryland regions. The objective of this study was to determine how high-yielding dryland wheat cultivars achieve greater grain number per spike through phenological and physiological adjustments under increased soil fertility. In a field experiment conducted over two growing seasons with 18 winter wheat cultivars under two soil fertility treatments, spike differentiation dynamics were tracked for six representative cultivars contrasting in yield level. High-yielding cultivars (HYG) displayed a prolonged pre-flowering and a shortened post-flowering phase. In this extended developmental window, HYG accumulated more total biomass and allocated a higher proportion to spikes, strengthening sink capacity. Increased soil fertility advanced spike initiation and increased assimilate allocation to spikes, increasing spike differentiation and fertile floret formation.

The objective of this study was to identify the soil–root regulatory mechanisms by which nitrogen (N) application at varying soil depths increases nutrient use efficiency and grain yield in wheat. In a two-year field experiment on the Loess Plateau, 240?kg N ha^?1 applied in a 1:2:1 ratio to the 8-, 16-, and 24-cm soil layers redistributed NO₃^?-N, soil organic carbon, available P, and enzyme activities relative to application only at the 8-cm depth. It also extended N- and P-cycling enzyme hotspots into deeper soil layers. These changes were associated with enhanced root growth in deeper soil, including greater specific root length and area, higher nitrate reductase activity, and increased root N and P concentrations. Root functional analyses indicated a shift toward more acquisitive strategies, supported by the upregulation of genes related to lateral root formation and root hair development. The 8–16?cm soil layer contributed most to yield formation, explaining 43.0% of yield variation. Layered N placement increased subsoil nutrient availability, root functional differentiation, and depth-specific transcriptional activation, promoting nutrient accumulation and increasing grain yield.

A persistent trade-off exists between yield gains and quality improvement, but achieving their synergistic enhancement is a critical challenge for modern agricultural production. Green manure has long been recognized for enhancing either grain yield or quality, yet its potential to simultaneously enhance both remains poorly understood. A 6-year field experiment was conducted in an arid irrigation area of northwestern China to examine whether green manure can simultaneously improve wheat grain yield and quality through increased mineral nitrogen supply and plant nitrogen assimilation. The experiment included two nitrogen rates (N1, 180?kg ha^?1 and N0, no nitrogen), along with four green manure rates, namely fallow after wheat harvest (G0) and multiple cropping green manure after wheat harvest with incorporation rates of 15,000?kg ha^?1 (G1), 30,000?kg ha^?1 (G2), and 45,000?kg ha^?1 (G3), respectively. Results showed that green manure strengthened the yield-increasing and stabilizing effects of chemical nitrogen, while also mitigating its limitations and improving overall wheat grain quality. These benefits became increasingly pronounced with increasing duration of green manure application. Compared to N1G0, N1G2 increased wheat grain yield, yield stability index, and the comprehensive evaluation index by 20.7%, 278.5%, and 86.1%, respectively. These improvements under N1G2 were mainly attributable to increased soil nitrate and ammonium nitrogen contents of 24.4% and 22.4%, respectively. Furthermore, N1G2 enhanced nitrogen translocation and distribution to grains by 12.4% and 9.5%, respectively. It also increased the activities of nitrate reductase and glutamine synthetase, thereby promoting nitrogen assimilation capacity in grains. In arid irrigation areas, with the application of 180?kg ha^?1 of chemical nitrogen, returning green manure at a rate of 30,000?kg ha^?1 is a practical strategy to simultaneously improve wheat yield, yield stability, and grain quality.

Intercropping maize (Zea mays) and soybean (Glycine max) is an appealing strategy for improving land-use efficiency. However, the shade stress imposed by maize severely constrains soybean growth and yield. Most intercropping studies conducted to date have been based on artificial shading or relay intercropping, and neither the characteristics of the shade environment under simultaneous intercropping conditions nor the changes in soybean architectural traits have been systematically studied. In this study, we evaluated 907 soybean accessions grown in a simultaneous maize–soybean intercropping system over two consecutive years to identify phenotypic traits associated with yield performance. Intercropping with maize produced a dynamic and heterogeneous shade environment within the soybean canopy, characterized by reductions in the red-to-far red light (R:FR) ratio, blue light fluence, and total photosynthetically active radiation. Shading began after the soybean stage V3 and persisted throughout reproductive development, triggering the shade avoidance response and resulting in substantial yield losses in soybean. Stem diameter showed the strongest positive correlation with yield per plant under intercropping conditions, outperforming the other architectural traits tested. In addition, general shade tolerance was positively associated with intercropping yield but negatively associated with monocropping yield. We compared a shade-tolerant soybean genotype (BX11) with a shade-sensitive genotype (72021). BX11 maintained upright growth under intercropping conditions and exhibited larger stem diameter with a well-developed vascular system while maintaining high expression levels of genes involved in radial growth and vascular development. By contrast, 72021 showed excessively elongated thin stems and lodging under intercropping conditions, exhibiting extensive intercropping-induced transcriptional reprogramming consistent with the repression of secondary cell wall biosynthesis and the induction of auxin-responsive cell elongation pathways. We conclude that shade tolerance in simultaneous intercropping systems depends on the ability to sustain radial stem development and mechanical strength, providing important insights to guide the breeding of soybean varieties optimized for intercropping.

Leaf age is one of the important parameters for describing crop growth stages. In actual production, cultivation methods can be adjusted in a timely manner according to leaf age, which can promote rapid seedling transformation and lay a solid foundation for achieving high yields of winter wheat. However, most existing image segmentation methods focus on leaf recognition and lack consideration for the impact of growing degree days (GDD) on winter wheat growth. This study takes Shandong province as the research area. Firstly, based on MOD09Q1 images, the normalized difference vegetation index (NDVI) time series was reconstructed using cubic spline interpolation and Savitzky-Golay (S-G) filter. Secondly, the dynamic threshold method was used to extract the winter wheat emergence date, the NDVI slope (β) was calculated from the emergence date to the monitoring date, and the GDD during this period was calculated based on ERA5-Land reanalysis temperature data. Finally, a GDD-based leaf age (LA_GDD) model and a Random Forest-based leaf age (LA_RF) model were constructed separately to monitor winter wheat leaf age at the start of the overwintering stage. The research results indicate that compared with the phenological observation data in Shandong province, the winter wheat emergence date extracted using the dynamic threshold method has high accuracy (bias?=?0.47?d, R²?=?0.77, and RMSE?=?3.93 d). Compared with the LA_GDD model (R²?=?0.59, RMSE?=?0.68 leaves), the LA_RF model significantly improves leaf age monitoring accuracy and performs well in both the training and validation sets, showing strong correlation with measured data (training set: R²?=?0.85, RMSE?=?0.39 leaves, validation set: R²?=?0.67, RMSE?=?0.56 leaves). In terms of spatial distribution, the leaf age in the southern and northern regions of Shandong province is relatively stable during the pre-wintering growth stage, with an overall higher leaf age of over 5 leaves in most years. However, the Jiaodong Peninsula has relatively lower leaf ages, but the seedlings are also developing well. In terms of temporal distribution, the leaf age is generally lower in 2021, while the leaf age in other years is moderate, and the region has favorable seedling conditions. This study integrates remote sensing phenological information, vegetation dynamic parameters, and meteorological factors to monitor winter wheat leaf age on a regional scale. The proposed model demonstrates high accuracy and stability, providing scientific support for seedling assessment and precise field management at the pre-overwintering stage.

Some introns can act as cis-elements to enhance gene expression without altering promoter specificity. Here, we engineered the castor bean catalase 1 first intron (CatI) by mutagenesis and identified CatI-mu7, which exhibited enhanced fusion-gene expression and improved splicing accuracy in Nicotiana benthamiana, Arabidopsis, Solanum lycopersicum, and rice. Knock-in of CatI-mu7 into HSP101 increased male fertility under heat stress in rice and Arabidopsis compared with wild-type and CatI knock-in controls, highlighting its potential applications in crop breeding.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease that threatens global wheat (Triticum aestivum) production. Given the rapid evolution of the Pst pathogen and the scarcity of effective resistance genes in cultivated wheat, resistance sources from wild relatives of wheat are being explored. Haynaldia villosa (2n?=?2x?=?14, VV), an annual wild relative of cultivated wheat, exhibits strong resistance to multiple wheat diseases. We previously synthesized a series of Triticum durum–Haynaldia villosa amphiploid lines to facilitate the transfer of beneficial traits into wheat. In this study, we evaluated the resistance of these amphiploid lines to stripe rust at the seedling stage and further identified a novel resistance gene. In total, eleven amphiploid lines derived from seven H. villosa accessions exhibited high resistance to Pst, among which STH55-1 showed high resistance to multiple Pst races. Genetic analysis using F₁, F₂, and F_2:3 populations indicated that the Pst resistance was controlled by a single dominant gene. We mapped the resistance gene, designated Yr2VS, to chromosome 2VS via bulked-segregant exome-capture sequencing, delimiting it to a 5.6-cM interval (spanning 1.84?Mb in the H. villosa RefSeq) flanked by markers InDel411 and InDel1393. Allelism tests revealed that the resistance gene in STH55-1 was likely allelic to that in STH63-1, but not to those in STH36-3 or STH59-1, and was closely linked to the resistance genes in STH50-4 and STH65-4. These findings demonstrate that the H. villosa-derived amphiploid lines harbor multiple, distinct stripe rust resistance genes, reflecting the high genetic diversity of the species. This combination of high-throughput synthesis, resistance screening, and allelism tests provides an efficient strategy for identifying superior resistance loci. The newly identified Yr2VS gene and the resistance germplasm developed herein represent valuable genetic resources for breeding stripe rust-resistant wheat.

Type I-C CRISPR systems induce unidirectional long-fragment DNA degradation and offer promising?tools for targeted large-fragment deletion and broader-window base editing. However, Dvu I-C is the only Type I-C system shown to possess genome-editing activity in plants. In this study, we developed a bioinformatics pipeline to systematically mine Type I-C systems and identified 4258 candidates from approximately 10.35?TB of genomic and metagenomic data. Among these, we characterized two novel systems, Aca I-C and Cja I-C, that exhibited genome editing activity in maize (Zea mays). In stable transgenic maize plants, Aca I-C and Cja I-C induced large-fragment deletions in the target gene GA20ox3, with editing efficiencies of 46.30% and 23.81%, respectively. Furthermore, we repurposed these two systems as adenine base editors by fusing them to the adenine deaminase TadA8e (V106W), enabling A-to-G base substitutions in maize within an editing window of approximately 20?bp and with negligible unwanted indels. Using these systems, we generated heritable GA20ox3-edited maize lines with reduced plant height. Together, these results expand the plant genome-editing toolbox and demonstrate the potential of the Aca I-C and Cja I-C systems for targeted large-fragment deletions and base editing in crop improvement.

Triticum monococcum ssp. aegilopoides (syn. T. boeoticum) is a wild diploid species that harbors the A^bA^b genome containing many disease resistance genes useful for wheat improvement. Genetic analysis conducted on an F₂ population from a cross between T. boeoticum accessions PI 427741 and PI 427560, which are contrasting in powdery mildew responses, indicated that the resistance in PI 427741 was controlled by two dominant genes, PmNCA6 and another unknown gene. Bulked segregant exome capture sequencing (BSE-Seq) analysis of a segregating F₃ family without PmNCA6 demonstrated a new powdery mildew resistance gene, Pm72, on the long arm of chromosome 6A. Through linkage analysis, Pm72 was mapped to a 1.28-cM genetic interval defined by markers XTb6AL04 and XTb6AL06. According to the reference genome of T. boeoticum accession TA299, the Pm72 locus corresponded to a 940-kb physical region (Chr6A: 635,963,867–636,888,696), containing 21 nucleotide-binding leucine-rich repeat receptor (NLR)-like disease resistance genes. Phenotyping showed that Pm72 confers effective resistance to powdery mildew at both the seedling and the adult-plant stages in the hexaploid wheat background. The co-segregating marker XTb6AL05 was useful for marker-assisted selection of Pm72. The identification of the new powdery mildew resistance gene Pm72 will contribute to its positional cloning and breeding application in wheat.

A high-throughput genotyping platform is essential for genetic research and molecular breeding in flax. We present GenoBaits Flax45K, a targeted sequencing SNP array designed by integrating whole-genome resequencing data from diverse accessions. The array features 45,410 target regions, comprising 44,697 background SNPs for genome-wide coverage and 713 foreground SNPs associated with 14 important agronomic traits. Genotyping of 200 accessions demonstrated high reliability (average call rate 99.04%) and ability to capture substantial genetic diversity. Population structure analysis with the array clearly delineated the two major genetic groups corresponding to fiber and oilseed flax, and identified a distinct sub-cluster of landraces, consistent with previous resequencing studies. A genome-wide association study (GWAS) for plant height validated the array’s utility, identifying 201 QTL, of which 63.18% were novel. A key locus on chromosome 14 was refined to an 85.2?kb interval containing a strong candidate gene, Lus10039143 (LuPHI-1), whose allele distribution suggested divergent selection between flax types. Haplotype analysis of four known major plant height QTL demonstrated consistent additive and pyramiding effects between the array-genotyped population and resequenced population, validating the array’s utility for marker-assisted selection. The GenoBaits Flax45K array provides a high-throughput, accurate, and cost-effective tool for germplasm characterization, genetic dissection of complex traits, and molecular breeding in flax.