The Green Revolution genes Rht-B1b and Rht-D1b encode truncated DELLA proteins that confer gibberellin (GA)-insensitive semi-dwarfism in wheat. Their roles in reducing plant height and enhancing lodging resistance are well established, but their pleiotropic effects on specific components of plant architecture require further genetic dissection. Here, we reveal a previously unrecognized role of Rht-D1b in regulating tiller angle, a key determinant of canopy architecture. Quantitative trait locus (QTL) mapping identified Rht-D1b as a major locus controlling tiller angle. Functional validation showed that Rht-D1b not only reduces plant height but also increases tiller angle and tiller number, thereby optimizing canopy structure for enhanced yield potential. Transcriptome profiling indicated that Rht-D1b modulates the expression of genes involved in auxin signaling and polar auxin transport. Broad-scale phenotyping across diverse wheat accessions demonstrated that both Rht-B1b and Rht-D1b significantly increase tiller angle and leaf area index, with double mutants exhibiting the strongest effects on tiller architecture. Notably, the frequency of Rht-B1b and Rht-D1b has risen in modern cultivars, coinciding with a historical trend toward wider tiller angle. Together, these findings establish a novel pleiotropic role for the Green Revolution genes, demonstrating that they not only reduce plant height but also coordinate tiller angle and tiller number to optimize canopy architecture, ultimately elevating yield in wheat.

Deep rooting is an important factor affecting rice drought avoidance. However, few genes that control this trait have been identified in rice. In the present work, we cloned a gene, OsIAA8, associated with a rice quantitative trait locus for deep rooting. Overexpression of OsIAA8 increased deep rooting and yield under drought stress. OsIAA8, which encodes an Aux/IAA protein, interacts with auxin response factor OsARF12, and osarfl2 mutant plants also displayed increased deep rooting. The expression of several auxin transport genes (e.g., OsPIN2 and OsPIN8) was down-regulated in OsIAA8-overexpressing rice plants. OsARF12 promotes the transcription of these genes, whereas OsIAA8 inhibited this transcription activation. Furthermore, the auxin content in the roots of OsIAA8-overexpressing plants was reduced compared with wild type plants. Of five haplotypes at the OsIAA8 locus, accessions carrying Hap 2 had higher deep rooting. This study revealed that OsIAA8-OsARF12 module regulates deep rooting by inhibiting auxin transport, providing the insights into improvement of root architecture and drought resistance in rice breeding.

Plant mechanical strength affects lodging resistance and stress tolerance, highlighting the importance of elucidating the regulatory mechanisms underlying cell wall development. In this study, we identified a novel dwarf and brittle culm mutant, dbc3, which exhibited reduced culm mechanical strength due to a thinner secondary cell wall, irregular distribution of the sclerenchyma cells under the epidermal layer and vascular bundle cells, as well as a significant reduction in cellulose and lignin content. Map-based cloning revealed that DBC3 encodes a xylan arabinosyltransferase belonging to the GT61 family. GUS staining and qRT-PCR showed that DBC3 was expressed in all tested tissues. Yeast one-hybrid, dual-luciferase assays and EMSA demonstrated that OsMYB63 directly bound to the DBC3 promoter to activate its expression. In the osmyb63 knockout mutant, DBC3 expression was significantly reduced, accompanied by a moderate decrease in stem mechanical strength. Taken together, these findings suggest that DBC3, as a direct target gene of OsMYB63, plays an important role in regulating plant mechanical strength by modulating cell wall development.

Heat stress induces severe meiotic defects in plants, leading to significant male sterility and substantial yield losses in crops. However, few genes involved in meiotic thermotolerance have been characterized. In this study, we demonstrate that HSP101, a conserved heat shock protein, plays a critical role in protecting pollen mother cells from heat-induced meiotic defects in both rice and Arabidopsis. HSP101 is highly expressed during early pollen development, and its loss of function leads to meiotic instability under heat stress. Transcriptomic analysis revealed that HSP101 deficiency disrupts the transcriptional network essential for cellular homeostasis during heat stress. Importantly, overexpression of HSP101 enhanced thermotolerance during microsporogenesis without obvious adverse effects on plant growth. Our findings establish HSP101 as a positive regulator of meiotic thermotolerance during microsporogenesis using rice and Arabidopsis as model systems, providing critical insights for improving adaptation of male meiocytes to high temperatures in crops.

Drought is a major limiting factor for growth, development, and yield in wheat. TaPP2C62-2A, a clade A type phosphatase (PP2C) member in T. aestivum, was identified as a mediator of drought response. TaPP2C62-2A expression was downregulated in tissues in response to drought and abscisic acid signaling, which is linked to a transcriptional silencer in the promoter region. Yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays revealed interaction between TaPP2C62-2A and SnRK2 kinase TaSnRK2.5-2D and that TaSnRK2.5-2D also interacted with bZIP transcription factor TaABI5-3B with both interactions occurring via distinct conserved domains to establish a regulatory module of TaPP2C62-2A with the above partners. Transgene analyses revealed that this module is essential in modulating drought responses. TaPP2C62-2A negatively regulates drought tolerance, whereas TaSnRK2.5-2D and TaABI5-3B positively regulate plant growth and agronomic traits under drought conditions. The modified drought response mediated by TaPP2C62-2A and its associated components was ascribed to their functions in regulating osmotic stress-related physiological processes, including stomatal movement, osmolyte biosynthesis, leaf water retention, root morphology, and homeostasis of reactive oxygen species. TaABI5-3B binds with the promoters of stress-responsive genes, including S-type channel gene TaSLAC1-3, P5CS gene TaP5CS1, PIP gene TaPIP2;1, PIN-FORMED gene TaPIN4, and catalase gene TaCAT6, leading to their transcriptional activation. Transgene analysis confirmed the positive roles of these stress-responsive genes in regulating drought tolerance. Significant correlations were observed between yield and TaPP2C62-2A transcription and its module genes in a wheat variety panel subjected to drought conditions, with haplotype TaPP2C62-2A_h1 enhancing drought adaptation capacity. Our study presents novel insights into plant drought response associated with PP2C regulatory module and provides substantial genetic resources for breeding drought-tolerant wheat cultivars.

The plasticity of crop development is crucial for survival and yield stability under adverse conditions. Saline-alkaline soil is a major environmental constraint limiting wheat productivity. Elucidating the regulatory basis of wheat developmental plasticity under salt stress is crucial for improving salt tolerance and yield stability. In this study, salt stress promotes the initiation of lateral root (LR) primordia while inhibiting LR emergence in wheat. Upon return to non-stress conditions, these primordia rapidly develop into LRs, enabling swift recovery and root system expansion. We identify glycogen synthase kinase 3 (TaGSK3) as a molecular switch that regulates this plastic response via brassinosteroid and auxin signaling pathways. By this mechanism, environmental signals are transduced into root development plasticity via TaGSK3 phosphorylation. This work provides new insights into how crops control developmental plasticity under stress.

The monoacylglycerol lipase (MAGL) is a key enzyme in the lipid metabolism pathway which products fatty acids and could play an important role in plant growth and stimulus response. However, the underlying mechanism through which MAGL regulates chilling tolerance in plants is unclear. Here, we demonstrate that the ZmMAGL could be a positive regulator in plants to enhance chilling tolerance. Loss of function on MAGL resulted in slow growth, leaf chlorosis, and decreased photosynthetic capacity in both maize and Arabidopsis under chilling conditions. We show that the ZmMAGL directly interacts with ZmEULS3 for regulating chilling tolerance together. In addition, the ZmFBIP could enhance the ZmMAGL activity by binding to its promoter region. Further multi-omics analysis revealed that the ZmMAGL could be involved in fatty acid remodeling under chilling stress to maintain photosynthesis capacity and regular growth. These results uncover a ZmFBIP-ZmMAGL/ZmEULS3 regulation module which plays an essential role for growth and development through regulating the photosynthesis and lipid metabolism in maize under chilling stress.

Pratylenchus coffeae is a widespread migratory endoparasitic nematode that causes substantial yield losses across a broad range of crops. Successful parasitism depended on the secretion of effector proteins that modulate host cellular processes. In this study, we identified a novel β-1,4-endoglucanase effector, PcENG3, which was specifically expressed in the esophageal gland cell and gonadal tissues of P. coffeae and was significantly upregulated during parasitic stages. A yeast signal sequence trap assay confirmed the N-terminal signal peptide of PcENG3 was functional, suggesting its potential for secretion. Silencing PcENG3 in P. coffeae markedly impaired its infectivity on maize (Zea mays L.). Transgenic expression of PcENG3 in Arabidopsis thaliana suppressed flg22-triggered reactive oxygen species (ROS) accumulation, leading to enhanced susceptibility to nematode infection. Yeast two-hybrid and luciferase complementation imaging assays revealed a direct interaction between PcENG3 and maize ZmTCTP2a, a translationally controlled tumor protein involved in cell proliferation and immune regulation. Notably, suppression of ZmTCTP2a expression in maize increased susceptibility to P. coffeae and compromised basal immunity against multiple pathogens. Collectively, our findings uncovered a previously uncharacterized effector-host interaction in which PcENG3 targeted ZmTCTP2a to suppress immunity and alter root cap cell proliferation and differentiation, thereby promoting nematode parasitism. This work provided new insights into the molecular mechanisms underlying P. coffeae pathogenicity and host susceptibility.

As covalently closed non-coding RNAs, circular RNAs (circRNAs) play important roles in microRNA (miRNA) function regulation. To identify sorghum circRNAs and investigate functional roles they play in salt tolerance, high throughput transcriptome sequencing was performed for a salt-tolerant sorghum genotype M-81E and one salt-sensitive sorghum genotype Roma. Comparative analysis identified 87 significantly differentially expressed circRNAs (DEcircRNAs) in M-81E, of which 27 were up-regulated and 60 down-regulated. In contrast, 22 up-regulated and 62 down-regulated DEcircRNAs were identified in Roma. Competing endogenous RNA (ceRNAs) network construction identified different networks in M-81E and Roma, suggesting different circRNA-miRNA-mRNA regulatory modules in response to salt stress in the two genotypes. We then studied the functions of two circRNAs, circRNA1562 and circRNA910, from M-81E that participated in network regulation. Both transgenic plants overexpressing these two circRNAs showed increased tolerance against oxidant and ion stress caused by salt treatment. Expression patterns of these genes suggest a role of circRNA1562 in regulating the expression of SbOXS3 by competitively binding sbi-MIR399i-p5, whereas circRNA910 may be involved in regulating SbIBH1 expression by competitively binding to PC-3p-23854_516, suggesting a role of circRNAs as miRNA “sponge” by increasing target gene expression and decreasing the ROS content, so as to enhance tolerance against salt stress. Together, our work reveals the potential molecular mechanism of circRNAs in response to salt stress and provides important information for crop breeding.

Saline–alkali stress is becoming a major global issue due to environmental degradation, hindering plant growth and reducing both seed yield and quality of many crops, including soybean. Improving stress tolerance through genetic resources is crucial for sustainable production. In this study, overexpression of the Arabidopsis SRRM1L gene increased soybean (Glycine max) tolerance to saline–alkali stress by reducing reactive oxygen species and malondialdehyde accumulation and promoting antioxidant enzyme activities, whereas knockdown of GmSRRM1L1/2 genes reduced stress resistance and overexpression of GmSRRM1L1/2 increased it. These findings highlight that the AtSRRM1L and GmSRRM1L proteins are valuable genetic resources for breeding stress-resistant cultivars without yield penalty.

OVATE family proteins (OFPs) are key regulators involved in plant development and stress responses. However, their biological roles in soybean remain largely unclear. In this study, we identified GmOFP8, a member of OVATE family in soybean, which exhibits root-specific expression and is transcriptionally responsive to both brassinolide and drought stress. Overexpression of GmOFP8 increased drought tolerance and nodule numbers, whereas knockout of GmOFP8 resulted in reduced drought resistance and fewer nodules, indicating its positive role in regulating drought stress responses and nodulation. Protein-protein interaction analyses demonstrated that GmOFP8 physically interacted with the glycogen synthase kinase 3-like kinase, GmSK2, and this interaction promotes the nucleocytoplasmic shuttling of GmOFP8. Furthermore, overexpression of GmSK2 in soybean hairy roots suppressed both drought tolerance and nodulation. Based on these findings, we propose that GmSK2 plays a conserved role in mediating the phosphorylation status of GmOFP8, as observed in rice, thereby contributing to the regulation of drought tolerance and nodulation in soybean. These results provide valuable genetic resources for molecular breeding strategies aimed at improving stress resilience and nitrogen fixation capacity in soybean.

While high-temperature stress severely inhibits the growth, development, and tuberization of potatoes (Solanum tuberosum L.), moderate high temperatures can trigger thermomorphogenesis. However, the molecular mechanisms underlying thermomorphogenesis in potato remain largely elusive. In this study, we identified a heat-responsive, nucleus-plastid shuttling transcriptional activator, StHEMERA (StHMR), whose nuclear translocation was enhanced under high-temperature conditions. Transgenic analyses revealed that the high-temperature induced increase in plant height and cell elongation in potato depends on the function of StHMR. The StHMR-silenced lines displayed a phenotype insensitive to elevated temperatures. Biochemical evidence further revealed that StHMR forms a regulatory module with PHYTOCHROME INTERACTING FACTOR 4 (StPIF4), a potato homolog of the central Arabidopsis thermosensory. StPIF4 is indispensable for high-temperature-induced stem elongation and directly binds the promoters of the auxin biosynthesis gene YUCCA8 (StYUC8) and the cell-elongation gene α-EXPANSION A8 (StEXPA8). StPIF4 regulates cell elongation under high-temperature conditions by binding to E-box elements within the promoters of these genes. Notably, StHMR functions as a transcriptional co-activator that enhances the ability of StPIF4 to activate the transcription of StYUC8, especially under heat conditions. Collectively, this study characterizes the StHMR-StPIF4 module as a key molecular unit of potato thermomorphogenesis and highlights its potential relevance to tuber formation, providing promising molecular targets for breeding heat-tolerant potato varieties.

Photoluminescence (PL) is a crucial property of carbon dots (CDs), which are promising carbon nanomaterials for agricultural applications. Red light signaling positively influences various physiological processes in plant salt tolerance. However, the potential for designing CDs based on light signaling theory to enhance agronomic traits in field crops remains unexplored. In this study, foliar spraying of red-emissive CDs (RCDs) improved salt tolerance in sweetpotato (Ipomoea batatas (L.) Lam) by enhancing nitric oxide (NO)-mediated Na⁺ homeostasis in roots. A mechanistic investigation attributed this beneficial effect primarily to the PL properties of the RCDs. The expression of genes related to RCD-enhanced Na⁺ transport in roots was found to be dependent on NO-mediated histone acetylation. For instance, RCDs, including genes encoding the red-light receptor (IbPHYB) and the Na⁺/H⁺ antiporter (IbSOS1), triggered comprehensive histone H4 hyperacetylation in salinized sweetpotato roots. IbHY5 was identified as a potential shoot-to-root mobile signal that triggered the hyperproduction of NO in sweetpotato roots under stress conditions. In summary, the RCDs enhanced salt tolerance in sweetpotato via the IbHY5-NO-IbHAM1-IbSOS1 signaling. These findings revealed that the PL properties of CDs could target specific light signaling pathways for field crop improvement.

The objective of this study was to identify functional genes regulating root branching and drought resistance that could be used in developing drought-tolerant alfalfa (Medicago sativa L.) cultivars. Heterologously expression of an Arabidopsis orphan gene QQS was found to enhance root branching and drought tolerance in alfalfa. By yeast two-hybid (Y2H) and luciferase complementation imaging (LCI) assay, a transcription factor MsNF-YC4 was confirmed as an endogenous interactor of QQS. We speculated it could play a positive role in regulating alfalfa root branching and drought tolerance. Transgenic alfalfa plants overexpressing MsNF-YC4 were generated by Agrobacterium-mediated transformation. Through RNA sequencing (RNA-seq), we noticed that the abscisic acid and auxin signaling pathways were affected in the MsNF-YC4 overexpressing plants. Consistently, exogenous application of indoleacetic acid also enhanced root branching and drought tolerance of alfalfa seedlings. Further, MsNF-YC4 was found to activate the transcription of MsARF8 by yeast one-hybrid (Y1H) and dual-luciferase (LUC) reporter Assay. Silencing of MsARF8 by antisense oligonucleotide (as-ODN) method suppressed both root branching and drought tolerance of alfalfa seedlings. Collectively, we prove that an endogenous transcription factor MsNF-YC4 interacts with foreign protein QQS, and by activating MsARF8 to regulate alfalfa root branching and drought resilience. Our study also provides a regulatory pathway for drought tolerant alfalfa breeding.

The symbiotic nitrogen fixation process between legume roots and rhizobia initiates at the root hairs. Rhizobia initially colonize the tip of the root hairs and induce its curling to become entrapped. However, the specific molecular mechanisms underlying root hair deformation and curling in response to rhizobial infection remain unclear. In this study, transcriptome analysis of wild-type JiMa389 and nodulation-deficient mutant jima61 of Melilotus albus, the Rho-like small GTPase MaROP10. Our results show that MaROP10 functions as an interacts with the Nod factor receptor NFR5 to regulate rhizobia-induced root hair deformation and infection thread formation during the early stages of rhizobial infection. To elucidate the mechanism of MaROP10, we further identified its downstream potential effector protein, MaRIC6, which positively regulates root hair deformation and infection thread formation. Taken together, MaROP10 likely integrates signals from the symbiotic receptor NFR5 to regulate downstream signaling pathways through its effector MaRIC6, thereby coordinating root hair deformation and infection thread development during the early stages of rhizobial infection.

Optimization of heading date (HD) and spike formation, two sequential development phases, is essential for improving wheat acclimation and yield. Identification of quantitative trait loci (QTL) for HD and spikelet number will contribute to breeding early maturing and high-yielding cultivars. Zhongmai 578 (ZM578) and Jimai 22 (JM22) are elite cultivars with significant differences in HD and spikelet number. Here, 14 environmentally stable QTL for HD, spikelet number per spike (SNS), and fertile spikelet number per spike (FSN) were identified in a population of 262 recombinant inbred lines from the cross ZM578/JM22. Among them, QHd.caas-3A.1, QHd.caas-4A, QHd.caas-5B, QHd.caas-7A, QHd.caas-7D, QFsn.caas-7A, QSns.caas-7A, and QSns.caas-7D explained up to 13.4%, 14.5%, 49.7%, 14.6%, 11.3%, 35.6%, 34.1%, and 16.2% of the phenotypic variances, respectively. Genome resequencing, transcriptome, and genetic linkage analyses identified TaFT-A1 and TaSEP3-D1 as candidate genes for QHd.caas-7A and QTL pair QHd.caas-7D and QSns.caas-7D, respectively. WAPO-A1 was identified as a candidate gene for the QTL cluster that included QSns.caas-7A and QFsn.caas-7A. We also predicted candidate genes for the remaining stable QTL based on genome and transcriptome analyses. Considering that the genetic effect of WAPO-A1 was confirmed previously, we developed breeder-friendly markers for the other major QTL to validate genetic effects in a diverse wheat cultivar panel. Marker-trait association analyses revealed that the favorable alleles of these QTL, except QHd.caas-5B, conferred early HD without yield penalty, which was also confirmed by pyramiding effects. These results provide useful genetic resources and molecular tools for improving adaptation and yield potential in wheat.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major disease constraining global wheat production. The Chinese wheat landrace Baikeheshangmai (BK) exhibits high-level, all-stage resistance (ASR) to this disease. The genetic basis of this resistance was investigated by analyzing a recombinant inbred line (RIL) population derived from cross BK × Avocet S using bulked-segregant exome capture sequencing (BSE-seq). Two resistance genes were identified: a major ASR gene, provisionally designated YrBK, and the adult-plant resistance (APR) gene Yr18. Across multiple environments, YrBK and Yr18 explained 12.47%–30.32% and 9.74%–20.56% of the phenotypic variance, respectively, and the two genes displayed a significant additive effect. Genetic mapping using a population of 4474 individuals, derived from the residual heterozygous lines, narrowed YrBK to a 0.181?cM genetic interval on chromosome arm 1BL. This genetic interval corresponds to a 56.16?Mb physical region characterized by suppressed recombination, precluding further map-based cloning. Within this interval, integrative candidate analysis combining expression profiles and SNP variation did not reveal a clear candidate from canonical resistance gene families, such as NLRs or kinases. Nevertheless, robust KASP markers co-segregating with YrBK were validated across diverse germplasm, enabling efficient marker-assisted selection. This study reports an effective genetic resource (YrBK) and provides molecular tools for marker-assisted selection. This gene will contribute to diversification of stripe rust resistance in wheat breeding.

Leymus mollis Trin. (2n?=?4x?=?28, NsNsXmXm), an important wild relative of common wheat (Triticum aestivum L.), harbors abundant genes for disease resistance and excellent agronomic traits genes, representing a valuable genetic resource for wheat improvement. Cytological observation and genomic in situ hybridization (GISH) analyses confirmed that both lines contain 40 wheat chromosomes and a pair of L. mollis chromosomes. Fluorescence in situ hybridization (FISH) revealed that DM160 lacked chromosome 6B and exhibits structural variations in chromosome 5A and 7B, while DM252 lacks chromosome 6D and carries a mutated chromosome 7B. Combined molecular markers and liquid array analyses confirmed DM160 was a wheat–L. mollis 6Ns (6B) disomic substitution line, and DM252 was a wheat–L. mollis 6Ns (6D) disomic substitution line. Agronomic and disease resistance evaluations demonstrated that DM160 produces more tillers and exhibits stripe rust resistance, whereas DM252 displays reduced plant height, and confers resistance to both powdery mildew and stripe rust. Transcriptome sequencing revealed distinct gene expression profiles among DM160, DM252, and 7182, leading to the identification of six key candidate disease resistance genes. Furthermore, 15 DNA markers specific to Lm#6Ns were developed to track this chromatin in wheat backgrounds. These novel substitution lines provide valuable germplasm for enhancing disease resistance and agronomic traits in wheat, and serve as essential materials for further characterization and utilization of Lm#6Ns chromosomes.

Root architecture is intricately linked to the acquisition of water and nutrients in maize seedlings. Despite its functional importance, few genes controlling root development have been targeted for drought resistance in breeding. Here, we performed a genome-wide association analysis to detect genetic variants linked to primary root length (PRL) across 307 inbred lines grown under hydroponic conditions. We identified 28 SNPs significantly associated with 25 candidate genes, accounting for 6.09%–11.07% of the phenotypic variation. Among them, ZmHSP20-5, encoding a cytoplasm-localized small heat shock protein (sHSP) with preferential expression particularly in lateral root primordia emerged as a promising candidate. Functional validation using knockout mutants revealed that disruption of ZmHSP20-5 impaired root architecture, causing reduced primary root elongation, shorter lateral roots, decreased lateral root density, and compromised drought tolerance. Further analysis revealed that InDel-1224 in the ZmHSP20-5 promoter likely contributed to differential gene expression and variation in root development among inbred lines. Evolutionary evidence suggested that the ZmHSP20-5 locus may have undergone selection during domestication, with the favorable ZmHSP20-5^In-1224 allele increasing in frequency over time. Overall, these findings establish that natural variation in ZmHSP20-5, particularly the ZmHSP20-5^In-1224 allele, contributes to root growth and drought resistance, providing a valuable genetic resource for the breeding of drought-resistant maize varieties with optimized root systems.

Optimizing plant architecture is essential for improving mechanized harvesting and yield potential in peanut (Arachis hypogaea L.), yet its genetic basis remains unclear. This study aimed to identify stable major-effect QTL associated with main stem length, basal branch length, and the main stem length to basal branch length ratio, and to predict candidate genes using gene expression data and genome sequencing. A previously constructed population of recombinant inbred lines (RIL) derived from a cross between erect-type JH5 and bunch-type KX01-6 was evaluated across three field environments. Statistical analysis identified six QTL with LOD scores ranging from 3.27 to 9.77, explaining 6.14%–24.14% of the phenotypic variation. Among them, qMSL_B09, qBBL_B09, qBBL_B05, and qMBR_B05 were identified in at least two environments. By integrating QTL analysis based on Best Linear Unbiased Prediction (BLUP) values, we narrowed these four stable QTL to two loci, Rpa1 (Regulating plant architecture 1) and Rph1 (Regulating plant height 1) that were delimited to a ～6.840?Mb region (B05: 154.040?Mb to the end) and a ～400?kb physical interval (B09: 158.05–158.45?Mb), respectively. Phenotypic validation using near-isogenic lines (NILs) demonstrated that Rpa1 increased basal branch length by 27.22% and branch angle by 140.08%, while reducing the main stem-to-branch ratio by 22.91%. In contrast, Rph1 decreased main stem length by 42.31% and basal branch length by 46.84%. Map-based cloning of Rph1 identified an 1816-bp deletion in parental line JH5 that influenced the expression of two candidate genes: Ah19g561300 (encoding a bifunctional inhibitor/lipid-transfer protein) and Ah19g561500 (encoding a proteasome subunit). A diagnostic InDel marker to facilitate marker-assisted selection for ideal plant height in breeding programs was developed to track the deletion. Haplotype analysis of 241 accessions confirmed the association of Rph1 with plant architecture, and accessions carrying Hap^rph1 exhibited significantly higher main stem and basal branch lengths (by ～10%; P?<?0.01). These findings provide novel genetic insights and molecular tools for improving plant architecture and enhancing yield potential in peanut.

Sucrose content dictates processing quality and consumer preference in edible peanuts, but its genetic control remains poorly characterized, limiting progress in breeding. In this study, using a breeding-informed F₂ population derived from a cross of high-sucrose germplasm JMT and elite cultivar Fushunsilihong (FSH) with normal-sucrose content, we integrated QTL mapping with functional genomics to decode the genetic architecture of sucrose accumulation. A major-effect locus (qSCB06) was precisely mapped to a 131-kb interval on chromosome B06 (148.03–148.16?Mb), accounting for 41.83% of the phenotypic variance (PVE). Comprehensive variant-to-function analysis identified five genes harboring exonic mutations, with Arahy.3URM83 validated as a key sucrose regulator through tissue-specific qRT-PCR profiling. To translate genomic discovery into breeding tools, we developed two cost-effective KASP markers (Arahy.06_115805462 and Arahy.06_148167024) that demonstrated 100% genotyping accuracy of F₂ individuals validated by SNP sequencing and 91.30% selection efficiency across 46 diverse cultivars. These markers enable rapid screening of sucrose-rich genotypes within 3?h, establishing a ready-to-implement molecular toolkit for expediting breeding of premium-quality peanuts. This work bridges gene discovery with field application, delivering both mechanistic insights and industrial solutions for flavor-driven peanut improvement.

Late leaf spot (LLS) is a major foliar disease that significantly reduces yield and compromises the quality of peanut (Arachis hypogaea L.). To identify genes conferring LLS resistance, a recombinant inbred line (RIL) population of 257 lines from a cross between the susceptible cultivar Baisha 1016 and the resistant germplasm ICGV 86699 was analyzed using whole-genome resequencing. A high-density genetic map was constructed with 4908 bin markers, leading to the identification of 19 quantitative trait loci (QTL) for LLS resistance. A major QTL, qLLS.A02.1, was consistently detected on chromosome A02 across six environments, explaining up to 37.49% of the phenotypic variance. Fine mapping delimited the qLLS.A02.1 locus to a 319?kb region flanked by KASP markers S4 and S5, which contained a cluster of ten NBS-LRR genes. Validation in 266 accessions confirmed a significant association of these flanking markers with LLS resistance. Transcriptome analysis revealed that four NBS-LRR genes within the cluster were specifically upregulated in the resistant parent. This study provides valuable genetic resources and molecular markers for breeding LLS-resistant peanut varieties.

Nitrogen (N) deficiency critically impairs leaf photosynthetic capacity and triggers premature senescence. However, the physiological metabolism underlying N deficiency-induced leaf senescence and its relationship with the varying mineral nutrients and reactive oxygen (ROS) concentration in leaf tissues are not well understood. In this paper, the premature senescence of flag leaves (psf) mutant and its wild type (WT) were employed to clarify the senescent-associated changes in the contents of several mineral elements, including potassium (K), manganese (Mn), magnesium (Mg), and iron (Fe) in leaf and root tissues under different N regimes. The roles of K and Mn in regulating ROS generation during N deficiency-induced senescence were further verified by exogenous K and Mn treatments. Results showed that N deficiency accelerated leaf senescence and led to a significant increase in ROS and Mn content in both leaf and root tissues, concurrently with N deficiency-induced declines in K, Mg and Fe contents in senescing leaves. In contrast,?sufficient N supply delayed leaf senescence and reduced ROS and Mn accumulation in leaf tissues. The changes in ROS and Mn under varying N conditions exhibited an inverse relationship with the variations in K, Mg, and Fe. K deficiency exacerbated N starvation-induced leaf senescence and promoted ROS accumulation by suppressing antioxidant enzyme activity. Conversely, exogenous K incubation at higher concentration inhibited excessive ROS accumulation and retarded leaf senescence under N deficiency. Furthermore, the elevated Mn accumulation under N-deficiency impaired ROS scavenging capacity of antioxidant enzymes, leading to oxidative stress and excessive ROS. Increased Mn levels in leaves and roots further aggravated?N deficiency-induced leaf senescence by triggering ROS burst. N deficiency upregulated the expression of key K⁺ transporter genes (OsHAK1 and OsHAK5) and stimulated K⁺ efflux from leaf tissues. The elevated accumulation of Mn coupled with the loss of K in senescing leaves acts as an important regulatory mechanism driving N deficiency-induced leaf senescence.

Light intensity plays a critical role in determining spike fertility of wheat (Triticum aestivum L.) by influencing floret development. However, whether a light signal directly perceived by the juvenile spike is essential for spike fertility remains unknown. To address this, we conducted two experiments imposing light blocking (LB) treatments from jointing to either anthesis (LB_J-A) or booting (LB_J-B) as well as a control (CT). LB was imposed through an innovative procedure employing aluminum foil. We found that LB_J-A did not affect floret primordia initiation, only increased distal floret mortality, and drastically impaired pollen viability in the anthers, resulting in a slight reduction in the number of competent florets but a massive sterility of all florets across all spikelets compared to CT, and LB_J-B exhibited results closer to the CT. For instance, under field conditions, the number of fertile florets was 42.92 in CT and 36.10 in LB_J-B, whereas no fertile florets (0) were observed in LB_J-A. While re-exposing juvenile spikes to light at booting restored fertility, highlighting that light signal perceived by juvenile spike from booting to anthesis played a crucial role for floret fertility. Furthermore, a strong correlation was observed between the number of fertile florets and the number of floret primordia with green anthers, suggesting that light blocking may impair fertility by preventing anther greening. These novel findings provide evidence that light signal directly perceived by juvenile spikes qualitatively may affect spike fertility possibly through affecting anther greening and inducing sterile pollen formation.

Knowledge of the maize pollen development stages at which high temperature (HT) stress leads to male sterility and yield loss would support targeted breeding strategies. In a cross between Zhengdan 958 (HT-tolerant) and Xianyu 335 (HT-sensitive) the contributions of maize traits to effective grain number (EGN) loss under HT stress were measured during pollen development stages, with loss increasing with the approach of flowering. Traits including pollen number per anther, total tassel spikelets, and pollen germination and shedding were the strongest contributors at various stages. The stage-specific vulnerabilities of maize tassels to HT stress suggest increasing pollen production before the tetrad stage and increasing pollen fertility and shedding during the microspore development stage. In the short term, increasing pollen developmental quality offers the greatest potential for reducing HT-caused EGN loss.

To increase the yield of indica-japonica hybrid rice, it is crucial to explore their photosynthetic and population characteristics at different yield levels and quantify their response to varying planting densities. In this study, a two-year field experiment was conducted to test two indica-japonica hybrid rice varieties with different yield potentials (12?t ha^?1 and 15?t ha^?1, respectively) at four planting densities (D1: 21?cm?×?30?cm; D2: 18?cm?×?30?cm; D3: 16?cm?×?30?cm; D4: 14?cm?×?30?cm). High yield indica-japonica hybrid rice was primarily charcterized by a high number of spikelets per panicle and a greater spikelet weight, which increased the single panicle’s weight. In addition, rational material translocation and a coordinated source-sink relationship contributed to dry matter accumulation. Open plant morphology optimized leaf enzyme activity at all stages, improved photosynthesis, and increased yield by 20.54%–21.60%. Increasing the planting density of indica-japonica hybrid rice somewhat restricted the growth of the rice population, leading to decreases in spikelets per panicle, 1000-grain weight, seed-setting rate, plant height, length of the top three leaves, leaf width, leaf angle, and the number of primary and secondary branches. However, the higher number of basic seedling resulted in more effective panicles and an increase in total spikelets, increasing the yield of each variety by 4.17%–8.48% and 2.39%–12.71%, respectively. Optimum dense planting of indica-japonica hybrid rice will benefit the sink capacity and a synergistic increase in both yield and economic benefit. This study offers crucial theoretical insights and practical significance for increasing indica-japonica hybrid rice yield and ensuring food security.

Intrinsic water use efficiency (iWUE), the ratio of leaf carbon assimilation (A_n) to stomatal conductance to water vapour (g_s), is an important crop trait. The effect of environmental fluctuations, such as light transitions, on iWUE are mediated via the stomatal kinetic responses to these fluctuations. We screened for variation in stomatal kinetic response to changes in light intensity in a sorghum population containing different haplotypes, selected based on variation in aquaporin (AQP) alleles. We assessed the role of stomatal anatomy in determining iWUE. Furthermore, we grew plants under water stress to reveal the trade-offs between water use and conservation underlined by stomatal kinetics and behavior. The results showed that iWUE measured from steady state A_n/g_s and iWUE calculated from A_n and g_s responses to transient light change (dynamic iWUE) correlated, propelled by prolonged stomatal opening time (k_open) but independent of stomatal closing time (k_close). Stomatal size and density played a minor role in determining those responses but still might have an indirect effect. Leaf width correlated instead with faster stomatal opening and increased anatomical conductance. “Faster” stomata were significantly determined by decreased regulation of leaf water potential (increased anisohydry) because they had reduced sensitivity to changes in leaf water status, while “slower” stomata were characterized by water conservation and heightened sensitivity to changes in leaf water potential. We found those two sets of behaviors can be distinguished by an AQP-associated haplotype (SbTIP3.2), opening the door for newer genetic determinants of iWUE that can incorporate possible trade-offs.

The objective of this study was to identify an application strategy for a blend of two controlled-release nitrogen fertilizers (CRNFs) that optimized yield and N-use efficiency of late japonica rice in the Yangtze River Delta. In a two-year field experiment using high-yield split-applied urea (CK) and no-N fertilization as control (N0), nine CRNF treatments were evaluated for their effects on grain yield, N uptake (N_UP), soil ammonium nitrogen (NH₄⁺-N) dynamics, and ammonia volatilization (AV). The treatments included sulfur-coated urea (SCU), urease inhibitor urea (AHA), 90-d polymer-coated urea (P₉₀), 120-d polymer-coated urea (P₁₂₀), and five BBFs prepared by mixing CRNFs at a 3:7 ratio (AHAP₉₀, SP₉₀, AHAP₁₂₀, SP₁₂₀, and P₉₀P₁₂₀). Based on N release characteristics, CRNFs were categorized into four release modes: pre-positioned single-peak (PrSRM), post-positioned single-peak (PoSRM), decreasing double-peak (DDRM), and increasing double-peak (IDRM). Synchronization between soil NH₄⁺-N dynamics under CRNFs and plant N uptake rate (N_UPR) under CK was quantified using dynamic time warping (DTW), with smaller values indicating higher synchrony. Results showed that single-peak release modes significantly reduced grain yield and N_UP by 12.6% and 10.5%, respectively. The IDRM treatment, a blend of 90-d and 120-d polymer-coated urea, showed NH₄⁺-N supply dynamics most closely matching the N demand of high-yielding rice, with lower two-year average DTW values (SSR_DTW 1.01, N_UPS_DTW 1.72) than DDRM (1.03 and 2.00), which translated into increases in spikelet number, grain yield, and N_UP by 4.49%, 6.03%, and 4.85%, respectively, while decreasing AV by 86.7% compared with CK. One-time application of IDRM fertilizer can align soil NH₄⁺-N supply with rice N demand, ensure high yield, and reduce N losses, providing an optimized fertilization strategy for sustainable rice production in the Yangtze River Delta.

Maize–soybean relay cropping increases land-equivalent ratio, but shading often limits soybean productivity. Optimizing strip relay configurations improves the light environment for soybean, enhancing its photosynthetic capacity and yield. In a four-year trial, we tested maize–soybean relay strip cropping at interspecific distances of 30, 45, 60 and 75?cm, and monocropping soybean. We measured photosynthetic characteristics, photosynthate allocation, root traits, nitrogen (N) uptake and yield to elucidate the canopy-root synergy driving spacing-induced yield gains and identify the optimal interspecific distance. Increasing interspecific distance significantly improved canopy transmittance and photosynthetically active radiation (PAR). The 60?cm treatment (MS60) increased transmittance and upregulated leaf antioxidant enzyme activity, thereby enhancing leaf area index, SPAD and net photosynthetic rate. Compared with other relay cropping treatments, MS60 increased ¹³C content and sucrose accumulation by 17.8%–69.7% and 7.1%–34.9%, respectively, and increased N uptake by 20.1% on average. The dual boost in carbon and nitrogen accumulation led to an 11.6%–29.3% yield increase under MS60, with a soybean yield of 1.9?t ha^?1 that was close to the monocropped soybean yield of 2.1?t ha^?1. This yield advantage was attributed to increased canopy radiation and carbon (C) accumulation that increased root development and N uptake. MS60 optimizes the balance between interspecific compensation and intraspecific competition in the relay strip cropping system, increasing maize yield while maintaining soybean yield at monoculture levels.

The objective of this study was to identify a combination of N application site and application rate that maximized maize yield and nutrient efficiency in soybean–maize strip intercropping systems in southwest China. A two-year, two-factor split-plot experiment was performed, with the N application site (S) and N application rate (N) as the primary factor and the sub-factor, respectively. S1 represents narrow row N application site, while S2, S3, and S4 represent wide row N application site at distances of 10?cm, 20?cm, and 30?cm from the maize plants, respectively. N0 represents 0?kg?N?ha^?1, while N1, N2, and N3 represent 225?kg?N?ha^?1, 300?kg?N?ha^?1, and 375?kg?N?ha^?1, respectively. Results indicated that S3N2 significantly increased maize yield by 19.77% and system yield by 16.92% relative to S1N2. This yield advantage was mainly attributed to increased biomass allocation to ears rather than stems or leaves. Compared with S1N2, S3N2 significantly increased the root dry weight (RDW) in 0?20?cm layer by 95.02%, and root length (RL), root volume (RV), and root surface area (RSA) in 30?50?cm layer by 42.76%, 28.82%, and 26.67%, respectively. Additionally, compared with S1N2, S3N2 significantly increased root sap rate, ammonium N, nitrate N, and root N metabolism enzymes activity, ultimately increasing N harvest index. Interactions between N application site and N application rate significantly increased RDW, RL, RV, RSA, root physiological activity, and improved nutrient use efficiency and strip-intercropped maize yield. In summary, S3N2 is recommended as the N management strategy for soybean–maize strip intercropping systems, as it can achieve the win–win goals of increasing maize yield and improving nutrient efficiency.

Timely and accurate estimation of component biomass of winter wheat, including leaf dry biomass (LDB), stem dry biomass (SDB), and reproductive organ dry biomass (RDB), is critical for crop growth monitoring and yield assessment. Canopy spectra mainly reflect leaf information, allowing for effective LDB estimation, whereas estimating SDB and RDB requires consideration of growth stage effects. To address this, we developed a hybrid biomass estimation framework by combining deep learning with biomass allocation law. Specifically, (1) a component biomass hierarchical (CBH) model was proposed based on accumulated growing degree days (AGDD) and biomass allocation laws; (2) a deep learning model (LBNet), based on two-dimensional fractional-order differential (2DFOD) hyperspectral images, was pre-trained on PROSAIL-simulated data and fine-tuned with field data to improve LDB estimation; and (3) the LBNet and CBH models were integrated to estimate and map component biomass across multiple scales. The hybrid framework achieved robust performance across interannual, regional, and UAV-based validations. For LDB, the root mean square error (RMSE) was 0.28–0.38?t?ha^?1, with a normalized RMSE (nRMSE) of 9.79%–14.50%. The RMSEs for SDB and RDB were 0.88–1.63?t?ha^?1 (nRMSE?=?11.05%–19.25%) and 0.76–2.22?t?ha^?1 (nRMSE?=?9.29%–22.66%), respectively. Overall, the proposed method provides an effective approach for multi-stage biomass estimation of winter wheat and demonstrates highly promising potential for applications in smart agriculture and crop yield assessment.

Root phenotyping is crucial for advancing our understanding of plant development and adaptation. However, existing platforms often face challenges in balancing high-throughput capacity with long-term, high-frequency monitoring. To overcome this limitation, we present HTPRootSlides, an integrated root phenotyping platform designed for dynamic and scalable trait analysis. Its design features a circulating zone that accommodates 141 specialized root boxes for high-throughput operation synchronously. Root boxes follow a continuous S-shaped trajectory step by step, facilitating repetitive imaging for high-throughput, time-series data acquisition. To address challenges such as water vapor condensation and fine root entanglement, we developed a dedicated segmentation algorithm, achieving 89.56% accuracy in root isolation. Combining morphological and skeleton-based feature extraction techniques, the platform ensures comprehensive and efficient phenotypic trait quantification. We validated HTPRootSlides by dynamically monitoring root development in four staple crops (soybean, maize, wheat, and rice) during early-stage germination (< 14 d). The results demonstrate the capability of HTPRootSlides for high-frequency, high-precision and large-scale root phenotyping (< 1 h with 141 root boxes per run), offering researchers a powerful tool to investigate root dynamics and optimize crop performance through trait selection.

Rice blast is one of the most devastating diseases, particularly panicle blast leads to significant yield losses. Utilization of panicle blast resistance genes is one of the effective ways to control this disease. However, genetic resources with panicle blast resistance are rare. The objective of this study was to identify the role of OsEXOIII-1, a previously identified candidate gene, in Pigm-mediated panicle blast resistance in rice. There were two main haplotypes in rice germplasm, with OsEXOIII-1^Hap1, the product of the resistant haplotype, binding more strongly to PiBP1 than OsEXOIII-1^Hap2. OsEXOIII-1/PiBP1 positively regulates Pigm-mediated panicle blast resistance by regulating expression of PR1 subfamily genes. OsEXOIII could be a target for breeding panicle blast-resistant cultivars.

Cadmium (Cd) in agricultural soils readily accumulates in crop grains and shoots, posing serious risks to food and feed safety, especially in maize (Zea mays L.). Natural resistance-associated macrophage proteins (NRAMPs) constitute a key family of metal transporters; however, their role in Cd uptake in maize remains unclear. In this study, the maize gene ZmNRAMPL5 mediated Cd uptake when expressed in yeast. ZmNRAMPL5 knockout mutants, which exhibited no differences from wild type under normal conditions but showed reduced Cd accumulation, alleviated toxicity, increased tolerance under Cd stress. Pot experiments under simulated light and moderate Cd-contaminated soils further showed that knockout lines maintained silage biomass and exhibited over 60% and 80% increases in grain yield per ear compared with wild type, respectively. Moreover, Cd concentrations in stems, leaves, and grains of knockout lines were significantly reduced and remained well below China’s national safety thresholds. Thus, ZmNRAMPL5 might be used in developing Cd-tolerant, low-Cd maize germplasm for grain and feed production in Cd-contaminated farmlands.

Soybean (Glycine max), a key food and oilseed crop, is derived from wild soybean (Glycine soja). Compared with cultivated varieties, wild soybean exhibits significantly higher genetic diversity, harboring stress-tolerance genes, broad-spectrum disease-resistance genes, and superior alleles that regulate seed nutrition, which were lost during domestication. These genetic resources have remained “visible yet underutilized”, primarily due to the lack of mature transformation and gene editing systems. In this study, we established stable genetic transformation and gene editing systems for Glycine soja. We identified three major bottlenecks to the genetic transformation of Glycine soja: its thick, rigid seed coat impairs water absorption and germination; its Agrobacterium infection efficiency is low; and regenerated shoots exhibit severe chlorosis and death. To address these issues, we employed 1) seed coat sandpaper abrasion enables wild soybean seeds to absorb water and germinate within 1 d; 2) sonication at 45?kHz for 60?s, which increased the Agrobacterium infection rate from 11.76% to 55.26%; and 3) supplementation of the culture media with an additional 12?mg L^?1 ferrous sulfate and 30?mg L^?1 disodium ethylenediaminetetraacetic acid (EDTA), which alleviated chlorosis in regenerated shoots. The transformation efficiencies of two wild soybean accessions reached 1.54% and 6.33%, with stable transgene heritability. We targeted GsDELLA and successfully generated homozygous mutants, which displayed reduced plant height and branch number. We extended this approach to 19 elite soybean cultivars, obtaining positive transformants, with higher transformation efficiencies for late-maturing (MG I–VI; typically?>?10%) than early-maturing (MG 00–I; 2%–10%) varieties. Our versatile transformation platform should accelerate the genetic improvement of both wild and cultivated soybean germplasm.

Plant height is a key agronomic trait in soybean (Glycine max L.), as it directly influences the number of nodes on the main stem, pod number per plant, yield, and lodging resistance. Identifying genes that regulate plant height is therefore essential for optimizing plant architecture and enhancing soybean productivity. Through a genome-wide association study (GWAS), we identified qGPH3 as a region associated with soybean plant height that co-located with qBPH16, a quantitative trait locus (QTL) derived from a bulked segregant analysis by sequencing (BSA-seq) and mapping to chromosome 17. RT-qPCR analysis revealed that Glyma.17?g082100 expression levels are significantly higher in the dwarf parent Wandou 15 than in the tall parent Xudou 18 used for the QTL mapping. We detected four haplotypes for this gene, with soybean accessions carrying Glyma.17g082100^Hap3 being the shortest, whereas those with Glyma.17g082100^Hap4 were the tallest. Functional validation using gene editing and overexpression in transgenic lines confirmed Glyma.17?g082100 as the causal gene regulating soybean height underlying qGPH3 and qBPH6. This bHLH transcription factor gene, designated GmBIM1, is highly expressed in developing stems and leaf buds and encodes a nucleus-localized protein. Our findings identify useful genetic resources for improving soybean yield potential through targeted breeding of plant architecture.