Sexual transfer of the CRISPR/Cas genome-editing system to targeted cotton cultivars could bypass their recalcitrance to regeneration from tissue culture. We used sexual hybridization to transmit a CRISPR/LbCas12a system from a regenerable Gossypium hirsutum donor to a nonregenerable G. barbadense recipient. We knocked out the GbCLA and GbPGF genes in the recipient, generating respectively albino and glandless phenotypes. Focusing on GbPGF, we detected novel mutations in the progeny across generations, and developed a set of nearly isogenic lines. The average editing efficiency of the target gene at crRNA1 exceeded 70% in the BC₃F₁ generation, yielding plants with agronomic traits or fiber quality nearly identical to those of the recurrent parent but lacking glands or gossypol. We introduced the CRISPR/LbCas12a system into three other nonregenerable G. hirsutum genotypes and one diploid cotton by hybridization and edited three more genes in two recipients.

Fructokinases (FRKs) are key regulators in carbohydrate metabolism and plant development. However, their specific functions in crop photosynthesis and sugar metabolism remain unclear. In this study, we identified three rice FRKs (OsFRK1, OsFRK2, and OsFRK3), investigating their catalytic activities, expression pattern, and subcellular localization. OsFRK1 and OsFRK2 localized to the cytosol, whereas OsFRK3 localized to chloroplasts, indicating spatially distinct functions. Using CRISPR/Cas9, we generated single mutants (osfrk1, osfrk2, osfrk3) and a double mutant osfrk1×osfrk2 deficient in both cytosolic OsFRKs. All mutants showed significantly reduced plant height, biomass, and grain yield under field conditions. At the physiological level, OsFRK mutants displayed markedly reduced OsFRK enzyme activity, accompanied by impaired photosynthetic efficiency, excessive starch and fructose accumulation in leaves, and elevated sucrose and fructose levels in grains. Loss function of OsFRKs also triggered metabolic compensation in source leaves, including elevated activities of sucrose-degradation enzymes and hexokinase. Additionally, haplotype analysis identified elite alleles of OsFRKs: FRK1^C (higher panicle number), FRK2^C (greater 1000-grain weight), and FRK3^A (higher panicle number). Cultivars carrying the combined haplotypes (FRK1^C–FRK2^C–FRK3^A) exhibited higher grain yields than other genotype combinations. Together, these findings revealed cytosolic and chloroplastic OsFRKs in regulating rice photosynthesis, sugar allocation, and yield formation, and highlighted the elite OsFRK haplotypes as valuable genetic resources for future rice improvement.

Optimizing rice (Oryza sativa L.) plant architecture and seed germination is critical for improving agronomic performance. Here, we investigated the role of OsARF9, a class B auxin response factor, in regulating these traits. Through analysis of OsARF9 transgenic lines, combined with phenotypic characterization, hormone response assays, and promoter binding studies, we demonstrate that OsARF9 functions as a transcriptional repressor. OsARF9 transgenic lines display clear differences in architecture traits and genotype-dependent responses to auxin, brassinosteroid (BR), and abscisic acid (ABA) treatments. OsARF9 directly binds promoter elements beyond the canonical auxin response element (AuxRE) and represses expression of OsGH3-5 and OsRLA1. Furthermore, it binds the promoters of OsABI3 and OsEm1, reduces their transcription, and thereby modulates ABA-mediated inhibition of seed germination. Collectively, our results establish OsARF9 as an integrative transcriptional repressor that coordinates auxin, BR, and ABA signaling to shape rice architecture and seed germination.

High-salt stress severely inhibits plant growth and development, leading to a significant reduction in rice yield. Although significant progress has been made in understanding the functions of plant MAP4Ks in stress responses, the role of rice MAP4Ks in abiotic stress, particularly salt tolerance, remains largely unexplored, highlighting a critical knowledge gap. Here, we identify OsMAP4K6 as a positive regulator of salt stress tolerance in rice, a role previously unreported for this gene family in monocot plants. We demonstrate that OsMAP4K6 modulates root Na⁺ flux and maintains Na⁺/K⁺ homeostasis under salt stress. Furthermore, we uncover a unique regulatory mechanism by which OsMAP4K6 directly interacts with and phosphorylates OsMKK6 at Ser13, and this Ser13 phosphorylation is essential for enhancing the activation of OsMKK6 under salt stress. Our genetic evidence reveals that OsMKK6 and OsMAP4K6 play similar roles in salt stress tolerance in rice. Our findings not only establish OsMAP4K6 as a key player in rice salt tolerance but also reveal a novel, direct regulatory pathway linking a MAP4K to a component of the MAPK cascade, providing new mechanistic insight into salt stress adaptation in plants.

Chromatin remodeling plays an essential role in plant reproductive development. Our previous studies demonstrated that CHR721, a SWI/SNF-family chromatin remodeler, is essential for reproductive development in rice, as evidenced by a chr721 mutant exhibiting unrepaired DNA lesions during late meiosis and subsequent cell cycle arrest, ultimately causing sterility. Here, we observed defective pollen exine, anther epidermis, tapetal degeneration, and aberrant nutrient metabolism in the chr721 mutant, particularly in lipid mobilization. Lipid species essential for anther development, including phosphatidylcholine (PC), lysophosphatidylcholine (LPC), and phosphatidylethanolamine (PE), exhibited reduced accumulation in the mutant compared to the WT. We established the central regulatory role of CHR721-mediated transcription during anther development. RNA-seq profiling of the mutant uncovered many differentially expressed genes (DEGs) at the late-meiotic, uninucleate, and binucleate stages, revealing progressive transcriptional perturbations. Functional enrichment analysis (GO and KEGG) revealed significant associations with lipid metabolism-related pathways and biological processes necessary for anther development, including tapetal development and regulation of programmed cell death (PCD). These transcriptional regulations were consistent with the morphological characterization and lipidomic analysis of the anthers in the WT and mutant. All these results and previous studies suggest that CHR721 regulates transcription by influencing the chromatin status and provide novel insight into the transcriptional function of CHR721 in anther development in rice.

Grain size and weight contribute to wheat (Triticum aestivum L.) yield, yet how Glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinase signaling interfaces with carbohydrate metabolism during grain development remains poorly understood. In this study, we characterized four wheat TaSK41 gene copies (TaSK41-1A, ?4A, ?5B, and ?5D), which were preferentially expressed in young spikes and developing grains, particularly in the pericarp during early development. TaSK41-5B localizes to both the cytoplasm and nucleus. Using CRISPR/Cas9-mediated multiplex genome editing, we generated two independent quadruple mutant lines (task41-cr1 and task41-cr2) in the wheat cultivar ‘Fielder’ with all four TaSK41 copies simultaneously disrupted. The quadruple mutants exhibited a greater number of grains per spike, increased thousand-grain weight, larger grain size, and enhanced starch accumulation. The larger grains in the mutant lines were associated with increased cell proliferation in the outer pericarp and higher levels of auxin (IAA and IBA) in developing grains. TaSK41 physically interacted with TaSnRK1β1, the β regulatory subunit of SNF1-related protein kinase 1 (SnRK1) and promoted its phosphorylation in vivo, supporting that the TaSK41–TaSnRK1β1 module is associated with carbohydrate metabolism. Transcriptomic profiling revealed coordinated changes in genes related to phytohormone signaling, cell-wall remodeling, and starch/sucrose metabolism in developing grains of task41 mutants. Moreover, haplotype association analysis revealed that TaSK41-5B-HapI was significantly associated with higher thousand-grain weight across 233 hexaploid wheat accessions. These results demonstrate that TaSK41 acts as a negative regulator of wheat grain size and weight and provide genetic and haplotype resources for yield improvement.

Heading date (HD) in wheat determines geographic adaptation, seasonal performance, and ultimately affects yield and quality. However, the genetic regulation of HD remains unclear. Here, we identified an Ethyl Methane Sulfonate (EMS)-induced wheat mutant, je0072, which headed two days earlier than the wild-type (WT) cultivar Jing411 without significant changes in yield components. Bulked segregant analysis (BSA) using an F₂ population of 618 individuals identified the early-heading locus to the long arm of chromosome 5D. Genetic fine mapping further narrowed the locus to a 460-kb interval containing 10 high-confidence genes based on the Chinese Spring v2.1 reference genome. Sequence variation analysis identified a candidate gene, TaBGLU1-5D, encoding β-glycosyl hydrolase 1, which harbored a T-to-C substitution at position 31. Functional validation using independent mutants confirmed the role of TaBGLU1-5D in regulating HD. Transcriptome sequencing revealed that differentially expressed genes (DEGs) between WT and je0072 spikes at the heading stage were significantly enriched in starch and sucrose metabolism pathways. Weighted Gene Co-expression Network Analysis (WGCNA) further identified MADS-box transcription factor TaMADS26 as a regulatory hub associated with TaBGLU1-5D. We also found that TaBGLU1-5D modulates expression of key heading date-related genes, including VRN1, VRN3, and VRT2, thereby influencing HD. These results provide new insights into the genetic control of HD in wheat, and offer valuable resources for HD optimization in breeding programs.

Aluminium (Al) toxicity in acidic soils limits cereal productivity, yet the stomatal activities linking Al exposure to reduced growth performance remain poorly defined. Here, we investigated stomatal responses to long-term (acidic soil condition, pH 4.3) and transient Al exposure (250?μmol L^?1 Al³⁺, hydroponic, pH 4.3) using two barley near isogenic lines (NILs): RGT Planet (acid soil-sensitive) and P33-1 (acid soil-tolerant, introgressed with Al exclusion gene, HvAACT1). In RGT Planet, excessive Al accumulation in shoots reduced stomatal size but increased stomatal sensitivity and closure to exogenous abscisic acid (ABA). Physiological observations revealed rapid stomatal closure in RGT Planet under transient 250?μmol L^?1 Al exposure. Conversely, P33-1 exhibited less Al accumulation in leaves, epidermis and stomata, along with enhanced stomatal opening during light transitions, thus facilitating optimal photosynthetic performance. Molecular investigations indicated that Al induced stomatal closure involves ABA signaling pathways, reactive oxygen species (ROS), cytosolic Ca²⁺ signals, and ion channel activities in guard cells. We propose that Al susceptibility in RGT Planet is associated with excessive Al accumulation in shoots which caused reductions in stomatal size and conductance, ultimately compromising photosynthetic efficiency despite rapid stomatal responsiveness.

Waterlogging stress severely hampers plant growth and represents a major challenge to agricultural productivity. Therefore, identifying key genes involved in plant waterlogging responses and elucidating the underlying regulatory mechanisms are essential for sustaining modern agriculture. In this study, we unraveled a specific role of the maize WRKY transcription factor ZmWRKY122, which was significantly induced by waterlogging stress, in improving tolerance to waterlogging stress. ZmWRKY122 was localized to the nucleus and functioned as a transcriptional activator in vivo. Functional and physiological analyses revealed that ZmWRKY122 improved maize tolerance to waterlogging by enhancing the antioxidant defense system, thereby alleviating oxidative damage. Transcriptome and qRT-PCR analyses further demonstrated that ZmWRKY122 upregulated ZmPRX101 expression in maize roots under waterlogged conditions. A combination of yeast one-hybrid, chromatin immunoprecipitation qPCR, and electrophoretic mobility shift assays confirmed that ZmWRKY122 directly bound to the W-box motif in the ZmPRX101 promoter. Furthermore, functional analyses indicated that ZmPRX101 knockout significantly decreased maize tolerance to waterlogging by exacerbating oxidative damage. Collectively, these results demonstrate that ZmWRKY122 positively regulates ZmPRX101 to alleviate waterlogging-induced oxidative stress, thereby improving waterlogging stress tolerance in maize.

Post-transcriptional modification of organellar RNA is critical for organellar gene expression, biogenesis, and function in plants. This process involves RNA splicing, editing, maturation, and stabilization. However, the underlying mechanism of these events is not fully understood. In this study, we report an E-type PPR protein EMP14 that is required for RNA editing and intron splicing in maize (Zea mays) mitochondria. Loss of EMP14 function arrested embryogenesis and endosperm development, leaving an empty pericarp phenotype in maize. Positional cloning identified that Emp14 encodes an E-subclass PPR protein localized to mitochondria. The emp14 mutants were impaired in the C-to-U editing at nad4-i3-2687, nad4-819, and ccmF_C-966 sites and the splicing of nad4 intron 3, resulting in substantially decreased nad4 transcript level and severely reduced assembly and activity of mitochondrial complex I. EMP14 interacts with PCW1 but not bCCP1 in the yeast two-hybrid assay and luciferase complementation imaging analysis, suggesting it recruits PCW1 as the trans deaminase but not facilitated by bCCP1. In vitro splicing assay showed that neither the edited nad4-i3-2687U nor the unedited nad4-i3-2687C could enable the splicing of nad4-i3. These results indicate that EMP14 is required for the C-to-U editing and intron splicing in mitochondria and is essential for seed development in maize.

To determine how high temperature (HT) impairs cotton fiber elongation, greenhouse experiments compared two temperature regimes (CT, 28?°C; HT, 38?°C) for 12 d. The findings indicated that compared with CT, the fiber elongation rate initially increased during HT (0–8 d), but subsequently decreased, resulting in a significant decrease in cotton fiber length at harvest. At 3 and 6 d under HT, cell turgor pressure increased; additionally, the auxin and ethylene content in fiber significantly increased, promoting cell wall loosening and increasing elongation rate through regulating xyloglucan endoglycosyltransferases/hydrolases and expansin. At 12 d under HT, cellulose and hemicellulose decomposition were inhibited in fiber, which hindered cell wall loosening and restricted fiber elongation. Meanwhile, the lipid and callose content in fiber was increased, and the enhanced abscisic acid and H₂O₂ content promoted lignin synthesis by up-regulating the expression of WLIM1a gene. Both changes accelerated the initiation of secondary wall synthesis. Consequently, the transition stage that coincides with fiber elongation and secondary wall thickening was reduced by 0.3–0.5 d, leading to a decrease in fiber length. In summary, fiber length was reduced under HT, accompanied by restricted cell wall loosening and accelerated secondary wall synthesis.

Arginine decarboxylase (ADC), a rate-limiting enzyme in the polyamine biosynthesis pathway, plays a critical role in plant growth and development. Our previous study revealed that cotton GhADC2 has potential to regulate fiber initiation. In this study, we further elucidate the molecular mechanism by which GhADC2 regulates fiber development. Overexpression of GhADC2 significantly enhanced fiber elongation, whereas RNAi-mediated suppression of GhADC2 resulted in shorter fibers. Further analysis demonstrated that the promoter of GhADC2 is transcriptionally regulated by transcription factor GhMYB2. Subcellular localization assays using Arabidopsis protoplasts and tobacco leaves revealed that GhADC2 localizes to the cell nucleus, differing from the usual chloroplast localization of ADCs. Yeast library screening identified GhBCCP1, a nuclear-targeted protein in cotton fibers, as an interacting partner of GhADC2. GhBCCP1 directly regulates plant physiological processes by catalyzing the conversion of acetyl-CoA to malonyl-CoA. Metabolomic sequencing of GhADC2 overexpression and RNAi plants highlighted significant enrichment in the tryptophan metabolism and flavonoid biosynthesis pathways. Collectively, our data demonstrate that GhADC2 is a positive regulator of cotton fiber development, and that it is transcriptionally activated by GhMYB2 and physically interacts with GhBCCP1, suggesting that these three components form a regulatory module associated with fiber growth. These findings provide valuable information for improving cotton fiber quality.

The plant intracellular Ras-group related leucine-rich repeat proteins (PIRLs) play important roles in pollen tube growth and development. However, the role of PIRLs in modulating defense responses against fungal diseases has not been reported. In this study, the IbPIRL8 gene was isolated from the resistant variety Nongdabai. Its expression was strongly induced by salicylic acid (SA) and methyl jasmonate. The IbPIRL8 protein was localized to the nucleus and cell membrane. Overexpression of IbPIRL8 conferred resistance to soft rot and root rot in sweet potato. Key SA-responsive genes, cellulose biosynthesis-related genes and callose biosynthesis-related genes were upregulated in IbPIRL8-OE plants compared with wild type (WT). Consistently, the storage roots of IbPIRL8-OE plants accumulated more endogenous SA, cellulose and callose than WT plants. Yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays demonstrated that IbDEAR2, induced by Rhizopus stolonifer, binds to the IbPIRL8 promoter to repress its expression. These findings provide insights into the genetic basis for improving disease-resistant sweet potato varieties.

This work presents a comprehensive biochemical landscape of pea seeds captured by untargeted LC-MS-based metabolomics of ten pea cultivars grown at three Danish field sites following different agricultural practices. More than 1200 metabolite features were detected in methanolic extracts of pea seed flours. Of these, nearly 300 features were identified using mass spectral libraries and advanced computational tools. Approximately 40 metabolites were found to be associated with location effect, independent of cultivar type. Organically grown pea samples showed lower levels of the main pea triterpene glycoside soyasaponin I and higher levels of nitrogen-abundant amino acids, indicating increased nitrogen availability in soil. More than 100 metabolites were associated with the location-independent cultivar effect. Akooma and Greenway cultivars showed the most distinct metabolome with greater levels of polyunsaturated fatty acids and lipid oxidation products known to give ‘beany’ off-flavors. The commonly cultivated pea variety, Ingrid, was devoid of compounds derived from the phenylpropanoid pathway including hydroxycinnamic acid amides such as caffeoyl, feruloyl, and coumaroyl aspartates that were present in all other cultivars. Three chloroauxin metabolites, reported here for the first time, were identified through molecular networking within GNPS platform and propagation of annotation from a computationally predicted indole-3-acetic acid catabolite. Overall, the results indicate biochemical adaptation of pea plants to location or agricultural practices as reflected in their seed metabolome.

Intensifying heat stress resulting from global warming threatens both the yield and quality of rice (Oryza sativa L.). Identifying pleiotropic genes that coordinately regulate yield, quality, and thermotolerance and applying them to rice breeding represents a promising strategy to mitigate the effects of high-temperature stress. Here, we identified Small Grain 9 (SMG9), which regulates grain size, grain chalkiness, and thermotolerance in rice. Map-based cloning indicated that SMG9 encodes a vernalization insensitive 4-like protein that is a component of Polycomb Repressive Complex 2. The smg9 mutant exhibited reduced grain size and chalkiness without compromised yield, and had improved thermotolerance during the flowering and seedling stages. By contrast, overexpressing SMG9 led to significantly larger grains, but resulted in inferior grain quality and increased thermosensitivity. Further study revealed that SMG9 positively regulates grain size by enhancing cell proliferation and cell expansion, and negatively regulates grain chalkiness by reducing reactive oxygen species (ROS) accumulation and delaying programmed cell death (PCD) in endosperm. Under natural high-temperature conditions, the loss of SMG9 function increased thermotolerance, thereby preserving both yield and grain quality. This enhanced thermotolerance at the seedling stage was also attributed to an improved ROS-scavenging capacity. Our study reveals the potential roles of SMG9 in maintaining yield and quality in rice under high-temperature conditions, offering a novel target gene for breeding thermotolerant rice.

Directional selection within elite breeding pools has narrowed the genetic base, yet phenotypic diversity persists among modern cultivars. Here, we analyzed 257 Korean japonica rice cultivars to dissect the genetic and environmental determinants of heading date. A genome-wide association study (GWAS) identified Hd1, Ghd7, OsPRR37, and Hd16 as major-effect genes in the population. Given the central role of Hd1 in variation of heading date, subpopulation-specific GWAS based on Hd1 functionality was performed to uncover minor-effect variants. Regression models using alleles identified in GWAS explained a substantial portion of phenotypic variance and achieved higher predictive accuracy than genome-wide SNP-based prediction within this population. Allele-specific genomic prediction with the additive linear model LASSO closely matched the nonparametric machine learning model XGBoost, indicating that additive effects largely accounted for variation in heading date. A redefined accumulated temperature index (ATI) model further enabled estimation of cultivar-specific thermal requirements within an optimized developmental window. We also discuss how the Hd1-Type14 allele was preferentially utilized for developing early maturing cultivars in Korean breeding programs. These findings demonstrate that integrating allele-based and environment-based prediction provides an effective framework for improving breeding precision for regional adaptation.

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

Fusarium crown rot (FCR), caused by the fungal genus Fusarium, is a severe soil-borne disease of wheat (Triticum aestivum) worldwide. In this study, we identified five quantitative trait loci (QTL) associated with FCR resistance on chromosomes 3A, 3B, 4B (two QTL), and 6A using a population of 128 F₇ recombinant inbred lines (RILs) derived from a cross between the two Chinese cultivars 04zhong 36 and Jinxiu 21. Of these QTL, two major QTL, QFcr.cau-3A and QFcr.cau-4B.1, were stably detected across multiple trials and explained 14.06% and 18.09%, respectively, of the phenotypic variance based on best linear unbiased prediction (BLUP) data. The resistance alleles at these two loci were derived from the parental lines 04zhong36 (QFcr.cau-3A) and Jinxiu 21 (QFcr.cau-4B.1), respectively. We confirmed the effects and stability of QFcr.cau-3A and QFcr.cau-4B.1 in an independent RIL population and in a collection of wheat accessions, respectively. Additionally, we detected a major and stable QTL for plant height, QPh.cau-4B, that overlapped with QFcr.cau-4B.1. The allele of QPh.cau-4B conferring tallness was from Jinxiu 21. Conditional QTL mapping indicated that although QFcr.cau-4B.1 and QPh.cau-4B showed significant interactions, the effect of QFcr.cau-4B.1 remained significant after the effects of plant height were removed. Field inoculation experiments with the 60 RILs showing the greatest sensitivity or resistance to FCR at the seedling stage detected a significant and positive correlation between seedling and adult plant resistance (correlation coefficient?=?0.71). The confidence intervals for QFcr.cau-3A and QFcr.cau-4B.1 contain 264 and 240 high-confidence genes, respectively. Based on gene annotation, sequence variation, and expression patterns, three genes (TraesCS3A02G373300, TraesCS3A02G376500, and TraesCS4B02G222600) were considered as potential candidates for QFcr.cau-3A and QFcr.cau-4B.1. Our results provide valuable resources for the cloning of FCR resistance loci that can be utilized in FCR resistance breeding programs.

Rye (Secale cereale L.) contains numerous disease resistance genes that can be utilized for wheat (Triticum aestivum) improvement. For example, rye chromosome 6 carries powdery mildew resistance genes. Wheat-rye 6R translocation lines are highly useful, but more wheat-rye 6R translocation lines with potential breeding value are needed. In this study, we identified a new wheat-rye T6BS.6BL-6RL^Ku translocation chromosome, conferring powdery mildew resistance, from the progeny of the irradiated wheat-rye 6RL^Ku ditelosomic addition line. Genotyping using the wheat GBW16K array and specific markers revealed that approximately 104.03?Mb of the distal segment of 6RL^Ku replaced approximately 6.1?Mb of the distal segment of the long arm of 6B (6BL) to form the translocation chromosome. Oligo-FISH painting indicated that the 104.03?Mb segment of 6RL^Ku is homologous to homoeologous group 7 chromosomes. Using wheat cultivars Chuanmai 62 (CM62) and Chuannong 32 (CN32) as backcross parents, we transferred the T6BS.6BL-6RL^Ku chromosome into the two wheat backgrounds. We selected two translocation lines: CM62-6RL and CN32-6RL. Genotyping analysis indicated that the CM62-6RL and CN32-6RL genomes are highly similar to those of CM62 and CN32, respectively. The grains of CM62-6RL were shriveled, whereas those of CN32-6RL were full. The effect of the T6BS.6BL-6RL^Ku chromosome on grain width also depended on the genetic background of the wheat. The improved grain lengths of both CM62-6RL and CN32-6RL contributed to the improvement in their thousand-kernel weight. The translocation chromosome had no negative effects on other important agronomic traits. These findings highlight the potential breeding value of the wheat-rye 6R translocation chromosome T6BS.6BL-6RL^Ku. The compensation mechanisms of this translocation chromosome in different wheat backgrounds deserve further study.

Flowering time is a crucial agronomic trait that affects the adaptability and yield of soybeans. Despite extensive research aimed at uncovering the genetic basis of flowering time in soybean germplasm, investigations involving the soybean germplasm from Northeast China have been limited. Here, we elucidated the genetic basis of days to flowering (DTF) in the soybean germplasm grown in Northeast China by employing an integrated strategy, including association mapping, quantitative trait locus (QTL) analysis, haplotype analysis, and candidate gene analysis. Overall, the genome-wide association study (GWAS) revealed 15 single-nucleotide polymorphisms (SNPs) significantly linked with DTF across six GWAS models and four individual environments plus a combined environment (CE). Five stable QTL were identified, among which four (viz., qDTF8, qDTF12, qDTF15.1, and qDTF15.2) are reported for the first time, and the remaining one (qDTF19) was detected in previous studies. On the basis of the findings of expression and haplotype analysis, fourteen putative candidate genes were detected across the genomic intervals of these five QTL. Among these genes, Glyma.19?g197600 and Glyma.19?g200700 were confirmed through both expression and haplotype analysis. Moreover, the relationship of the haplotypes with gene expression indicates that Glyma.19?g197600 is a negative regulator of early flowering, thereby providing evidence of its role in flowering. This study reveals potential genetic loci and genes that could facilitate the expansion of soybean cultivation into regions with short growing seasons and long photoperiodic conditions across the globe.

Pods are unevenly distributed on soybean (Glycine max L. Merr.) plants, with significantly fewer pods in the lower regions, which limits overall yield. Elucidating the genetic basis of pod formation in the lower part of the plant holds substantial theoretical and practical significance for breeding efforts aimed at increasing seed yield. In this study, we evaluated a four-way recombinant inbred line (FW-RIL) population and a germplasm population (GP) of soybean across seven and five environments, respectively, to assess pod number in the lower part (PNL) of the soybean plant. We identified quantitative trait loci (QTL) and quantitative trait nucleotides (QTN) associated with PNL. We systematically screened candidate genes potentially involved in regulating PNL within linkage disequilibrium (LD) blocks of QTN that colocalized with QTL. Finally, we developed a molecular-assisted selection (MAS) model based on QTN derived from the GP and identified the optimal breeding schemes using the B4L (breeding for pure lines) ISB (in silico breeding) model. We identified 25 QTL in the FW-RIL population and 93 QTN in the GP, including 5 QTN that colocalized with the QTL. In LD blocks surrounding the QTN AX-90477863, we identified Glyma.09G040000 as a candidate gene associated with PNL. Using a MAS model, the 93 QTN accounted for 52.5% of the standing phenotypic variation in PNL in the GP. Using this model, we selected 16 hybrid combinations with PNL genotypic values exceeding the breeding target of 16. Our findings enhance our understanding of the genetic basis of soybean pod number and provide technical support for the molecular breeding of high-yielding soybean varieties.

The oil yield of Brassica napus is determined by both seed yield and oil content. A previous study showed that strong RNA interference, designed to simultaneously knock down all four BnAP2 paralogs, reduced seed yield due to abnormal floral development in B. napus. However, the function of individual, specific BnAP2 paralogs in seed oil production and the underlying mechanisms remain unclear. Here, we found that all four BnAP2 paralogs present in the genome of the B. napus ‘K407’ inbred line were highly expressed in flowers and developing seeds; however, BnaA01.AP2 was minimally expressed in floral tissues. Interestingly, BnaA01.AP2 knockout mediated by CRISPR/Cas9 resulted in significant increases in both seed yield and oil content, thereby increasing overall seed oil yield without detectable negative effects on the other examined agronomic traits. Furthermore, we demonstrated that BnaA01.AP2 repressed oil accumulation by directly downregulating BnaA09.WRI1, BnaA03.BCCP1, BnaA09.L1L, and BnaC09.L1L and indirectly regulating a series of key genes involved in glycolysis, fatty acid biosynthesis, and triacylglycerol assembly during B. napus seed development. Our research not only provides insights into the regulatory mechanisms of seed oil accumulation but also provides promising genetic resources and germplasm for breeding cultivars with higher seed oil yield in B. napus.

Centella asiatica is a medicinal plant containing various ursane-type saponins that serve as a model system for studying triterpenoid accumulation. We assembled a haplotype-resolved genome for C. asiatica, and it showed allelic imbalance between haplotypes. The genome underwent one whole-genome duplication event followed by chromosomal fusion resulting in the current karyotype. We also constructed the metabolic regulatory network of triterpenoid saponins and found that triterpenoid biosynthesis was accompanied by gene duplication. These findings may assist in mining genes for the metabolism of C. asiatica and improving the understanding of the genetic basis for the diversity of triterpenoid biosynthesis.

Planting density and grain filling are important cultivation practices and physiological processes that affect the yield and quality of indica-japonica hybrid rice. Elucidating how planting density influences the yield and quality of indica-japonica hybrid rice by regulating physiological processes such as grain filling, and revealing the relationships between grain filling characteristics and yield as well as quality, is of great significance. This study selected two indica-japonica hybrid rice varieties with different yield levels as experimental materials and conducted a two-year field experiment under four planting densities. The results showed that increasing the planting density of two indica-japonica hybrids affected photosynthesis, enzyme activities, and grain filling rate, reducing the brown rice rate, milled rice rate, head rice rate, protein content, and amylose content, while increasing chalkiness. However, the increase in tiller number enlarged the population and extended the grain filling duration. Consequently, the yield of the two hybrids increased significantly by 5.47%–11.38% and 4.76%–10.93%, respectively, and the taste values of superior grains (SG) and inferior grains (IG) increased by 0.83%–5.35%, 0.54%–2.45% and 0.96%–2.24%, 0.73%–2.65%, respectively. Analysis of the relationships between grain filling characteristics and yield as well as quality in indica-japonica hybrid rice revealed that a higher grain filling rate contributed to increases in brown rice rate, milled rice rate, head rice rate, protein content, and amylose content, while reducing chalkiness degree and chalky grain percentage. In contrast, a longer grain filling duration not only helped improve rice taste value but was also one of the main reasons for high yield.

In our previous research, we firstly demonstrated blocking the light to the juvenile spike directly and qualitatively affected floret fertility by affecting anther greening and inducing pollen sterility in wheat. However, the underlying mechanisms remain unclear. Here, we integrated morphology, cytology, physiology and transcriptome to investigate the differences in spike fertility under control (CT) and light blocking (LB) treatments from jointing to either anthesis (LB_J-A) or booting (LB_J-B). Our results revealed that LB affected anther greening by disturbing chloroplast development and chlorophyll synthesis, suggesting that light received by the juvenile spike is essential for anther greening. The downregulation of genes involved in photosynthesis and chlorophyll biosynthesis suppressed the expression of enzymes in fatty acid, lignin, and starch metabolism, and combined with tapetum degradation resulted in abnormal pollen exine formation and pollen sterility. Collectively, this study elucidates the possible mechanism by which light blocking inhibits anther greening and leads to pollen sterility. These findings provide novel insights into light blocking regulating spike fertility, advancing the understanding of the regulation mechanism of reproductive development in wheat.

Layered nitrogen (N) application to wheat is intended to avert nutrient retention in the topsoil, which limits deep root development and grain yield. In a two-year field experiment on the Loess Plateau comparing two N treatments: 240?kg N ha^?1 applied at the 8-cm soil depth or in a 1:2:1 ratio to the 8-, 16-, and 24-cm soil layers, the layered treatment increased grain yield, post-anthesis N accumulation, phosphorus (P) accumulation, root biomass, and soil organic carbon and available P in the 8?24 cm layers. It also upregulated N and P transporter genes in roots across different soil layers. Layered N application optimized the vertical nutrient distribution in the wheat root zone, induced adaptive root architectural development, and activated the transcriptional regulatory network of nutrient uptake, which peomoted post-anthesis nutrient assimilation and ultimately improving grain yield.

Nitrogen (N) fertilizer deep placement has been widely adopted to improve nutrient use efficiency and maize yield in the semiarid regions of northwest China. However, previous studies on optimal fertilization depth have yielded inconsistent results across climate conditions, limiting its practical application. This study aims to determine the site-specific optimal N fertilization depth for spring maize by evaluating photosynthetic growth dynamics, yield formation, and N utilization in two contrasting semiarid regions. A two-year (2021–2022) field experiment was conducted in Dingxi (semiarid drought-prone region) and Jingning (typical semiarid region), with five fertilization depths: 0?cm (D0), 5?cm (D5), 15?cm (D15), 25?cm (D25), and 35?cm (D35). A ¹⁵N-labeled urea micro-plot experiment was additionally conducted to trace N fate. The results demonstrated that, compared with the conventional N placement treatment (D15), D25 increased soil total N storage, net photosynthetic rate, root bleeding rate, and the concentrations of NO₃^?-N and NH₄⁺-N in the bleeding sap. PLS-PM analysis revealed that fertilization depths that are excessively deep (D35) or shallow (D0, D5, D15) adversely affect the photosynthetic parameters and root activity of maize, thereby inhibiting dry matter accumulation and grain N uptake, which ultimately reduces both yield and nitrogen use efficiency (NUE). Compared with D15, D25 increased grain yield, and NUE by 8.79% and 33.19% at Dingxi, and by 7.11% and 11.25% at Jingning. ¹⁵N isotope tracing revealed that D25 improved maize N uptake while reducing residual soil N and N losses. Regression analysis indicates regional differences in the optimal N application depth. To achieve the lowest N residual loss and the highest yield and NUE, Dingxi (23.49?cm) requires a deeper fertilization depth compared to Jingning (21.64?cm). In conclusion, N fertilizer deep placement is a viable strategy for enhancing agricultural productivity and efficiency in semiarid regions, but the appropriate depth should be selected based on local conditions.

This study aimed to develop a nitrogen fertilization strategy for rainfed maize systems on the Loess Plateau, based on an optimal available nitrogen supply, to meet soil N availability with crop demand while minimizing groundwater quality damage from nitrate leaching. A three-year field experiment was conducted with varying planting density and N rate. The optimal relative yield was achieved at an integrated nitrogen nutrition index of 1.0 with an available N supply (ANS, mineral N fertilizer plus initial soil nitrate N) around 300 kg ha^?1, which represented the optimal level for minimizing soil nitrate residues without yield penalty. This ANS-based framework offers a practical strategy for sustainable N management in rainfed maize production under variable climatic conditions.

The objective of this study was to identify a boron (B) application strategy maximizing cotton yield. In a two-year experiment across two soil types with three B application rates, B availability significantly regulated boll biomass accumulation rate in a 12–19-d post-anthesis window; B concentrations of 41–74?mg B kg^?1 in leaves subtending bolls maximized boll weight; and moderate B application increased source–sink carbon flux by increasing net photosynthetic rate, sucrose biosynthesis, and phloem loading efficiency. Integrating these three findings will increase photoassimilate partitioning to reproductive sinks, boosting cotton yield and B-use efficiency.

Climate change and the drawbacks of traditional monitoring techniques pose challenges to efficient crop phenology management, making accurate winter wheat sowing date estimation crucial for agricultural optimization. We present a machine learning framework for estimation of winter wheat sowing dates using high-resolution early-season remote sensing. It uses the Normalized Difference Greenness Index (NDGI) from Sentinel-2 data to detect crop emergence. A dynamic climate window extracts pre- and post-emergence environmental variables, and machine learning models estimate sowing dates. Evaluated for Henan province, China, during the 2024 growing season, the framework achieved an R² of 0.82, supporting high-resolution spatial mapping. This approach provides a reliable and scalable tool for large-scale sowing date monitoring, supporting climate-resilient agricultural management and data-driven farming decisions.

Training software models for crop disease diagnosis requires large image datasets to achieve high accuracy. We describe a lesion information transfer diffusion model, LesionDiff, for generating image data that augments a real-world disease lesion image dataset. An information preprocessing module identifies lesion areas on leaves, an enhancement module captures diverse visual and semantic lesion features, and a generation module fills missing regions in masked disease images by synthesizing lesion phenotypes. This augmentation increased the average diagnostic accuracy of a test dataset by more than 3%.

Fusarium head blight (FHB) threatens global wheat (Triticum aestivum L.) production and food security. Fhb1 confers stable, broad-spectrum resistance to FHB, but the underlying molecular mechanisms are not fully understood. In this study, integrated transcriptomic and proteomic analyses of near-isogenic lines for the Fhb1 locus revealed that Fhb1 coordinates a multi-layered defense network characterized by extensive transcriptome reprogramming and post-transcriptional regulation. The phenylpropanoid pathway emerged as a central downstream module, as Fhb1 coordinately upregulates the expression of genes encoding key enzymes in this pathway, including PHENYLALANINE AMMONIA LYASE (PAL), CINNAMATE 4-HYDROXYLASE (C4H), and 4-COUMARATE-CoA LIGASE (4CL). Gene regulatory network analysis identified the R2R3-MYB transcription factor TaMYB30-B1 as a key regulatory hub. A single nucleotide polymorphism (SNP) in TaMYB30-B1 was significantly associated with FHB resistance across natural wheat populations. This association was more pronounced in the absence of Fhb1. Our findings elucidate the mechanistic basis for Fhb1-mediated resistance and highlight TaMYB30-B1 as a valuable target for improving FHB resistance in wheat breeding programs.

A key objective of wheat (Triticum aestivum) breeding is the simultaneous improvement of disease resistance and bread?making quality. The Glu-V1 locus encoding the high-molecular-weight glutenin subunit (HMW-GS) V71 and the powdery mildew resistance gene Pm67 were previously identified on chromosome arm 1VS of the wild wheat species Dasypyrum villosum. Here, we generated the T1DL·1V#4S translocation line NAU195, which carried the V71 subunit for improved bread-making quality but was susceptible to all 18 isolates of the powdery mildew fungus Bgt examined. By contrast, the previously developed T1DL·1V#5S line NAU196 harbors the Pm67 gene conferring broad-spectrum powdery mildew resistance but lacks the V71 subunit. Genetic analysis of F₁ and F₂ progenies from a cross between NAU195 and NAU196 confirmed that Pm67 is a single dominant gene. By screening 2954 F₂ plants, we fine?mapped Pm67 to an approximately 2.1??Mb interval on chromosome arm 1VS in the reference genome. We identified 35 high–confidence protein–coding genes in this region, including eight candidate genes encoding nucleotide?binding site leucine?rich repeat (NLR) proteins. We identified 12 recombinant T1DL·1VS translocation lines harboring both the V71 subunit and Pm67 genes, and introgressed one of the corresponding translocations into the high-yielding cultivar NMZ119. Plant development in the resulting T1DL·1VS translocation lines harboring the V71 subunit and Pm67 genes was comparable to that of NMZ119, with no significant yield penalty but with markedly improved powdery mildew resistance and gluten strength. Overall, our strategy for mapping and pyramiding alien genes in the common wheat background allowed us to generate a valuable genetic resource and molecular tool for accelerating the concurrent improvement of powdery mildew resistance and bread?making quality.

The heading date is an important trait that affects crop adaptability and significantly affects crop yield. The discovery and functional understanding of genes related to heading are crucial for wheat breeding in various environments. Aegilops tauschii, the D-genome donor of wheat, serves as an important model for exploring genetic regulatory mechanisms in common wheat. In this study, extremely early heading mutants were identified after treatment with 0.4% ethyl methanesulfonate (EMS) and compared with the wild type. Genetic analysis revealed that a single recessive gene was responsible for early heading, and gene mapping revealed a mutation in a 10.3-Mb region on the short arm of chromosome 6D. Bulked segregant exon capture sequencing revealed a missense mutation within the highly conserved nucleotide-binding domain of AET6Gv20469900, which encodes a protein phosphatase 2C (PP2C). This gene was in the mapping interval and associated with early heading. Transcriptomic profiling and quantitative validation analyses suggest that PP2C likely modulates vernalization pathways, thereby affecting heading date. This work provides a novel genetic resource for breeding early heading wheat cultivars.

The objective of this study was to determine whether leaf color change in rice plants predicts ammonia (NH₃) volatilization during the late grain-filling period. In a pot study of indica and indica–japonica hybrid cultivars, the leaf color-changing rate was highly significantly positively correlated with NH₃ volatilization during the grain-filling stage. Cultivars with fast leaf color-changing had higher NH₃ volatilization loss due to their higher apoplastic NH₄⁺ concentration and NH₃ compensation point, along with lower glutamine synthetase (GS) activity. N application, although it delayed leaf color change, led to increased NH₃ volatilization. Selecting cultivars with slow leaf color-changing characteristics and managing fertilization to delay the leaf color change process could reduce N gas loss and increase N use efficiency.

Although controlled-release urea (CRU) has demonstrated higher nitrogen use efficiency compared to conventional urea, comprehensive evaluations of its multi-year continuous application on yield stability and environmental sustainability remain limited. A field experiment initiated in 2013 in the Huang-Huai-Hai Plain compared the effects of two coated ureas and conventional urea on sustainable yield, soil quality, and carbon footprint. Sulfur-coated urea achieved optimal balance among productivity, economic benefits, and environmental performance, while polymer-coated urea excelled in soil quality. The findings emphasize the importance of multi-criteria evaluation in fertilizer selection and provide scientific evidence for sustainable fertilizer management in intensive maize production systems.