A dietary transition from refined to whole grains would optimize grain processing, reduce food loss and emissions, and increase food nutritional contents. The results of systematical analysis and calculations in our study show that the average processing loss rate of grains including rice, wheat, and maize is approximately 4.1% in China due to the refinement, equivalent to an annual loss of around 13.3 Mt of grains. Furthermore, the refining process significantly reduces the nutritional contents of rice (51.6%), wheat flour (55.4%), and corn products (80.4%) mainly resulting from the removal of dietary fiber, minerals, and vitamins in refined grains. Replacing refined grains with whole grains in diets would lower agricultural carbon emissions by 2.7%, reducing agricultural water use by 4.3%, and saving arable land by 1,972,607 ha. Total environmental footprint could be reduced by 35% to 79% under three proposed scenarios. These findings indicate that shifting toward whole grain-based diets by Chinese consumers could reduce food losses, enhance human health, and improve environmental sustainability. This approach offers a promising strategy for transitioning towards more resilient and sustainable agri-food systems, benefiting human and planetary health.

Benzoxazinoids (BXDs) are a class of plant secondary metabolites that play pivotal roles in plant defense against pathogens and pests, as well as in allelopathy. This review synthesizes recent advances in our understanding of the structural and functional diversity of BXDs, the independent evolutionary trajectories of their biosynthetic pathways across different plant species, their metabolic transformations in target organisms, and the opportunities and challenges of optimizing BXD biosynthesis in crops through metabolic engineering. Compared with monocotyledons, dicotyledons employ a more diverse set of enzymes to catalyze the core reactions of BXD biosynthesis. This functional divergence—yet biochemical convergence—between monocotyledons and dicotyledons exemplifies the convergent evolution of BXD biosynthetic pathways in plants. BXDs act not only as potent antifeedants, insecticides, and antimicrobials but also function as signaling molecules that induce callose deposition and activate systemic immunity, thereby enhancing plant resistance to biotic stress. Furthermore, BXDs shape the rhizosphere by modulating microbial communities through species-specific antimicrobial activities and microbial detoxification mechanisms, ultimately exerting allelopathic effects that alter soil chemistry and nutrient dynamics. The translational potential of BXDs is increasingly recognized by synthetic biology approaches, including artificial intelligence-driven enzyme optimization, heterologous pathway engineering, and gene-editing to enhance crop resistance. Despite these promising prospects, challenges remain in balancing metabolic trade-offs and mitigating ecological risks associated with persistent accumulation of BXDs. Future research integrating multi-omics, evolutionary genomics, and microbiome studies will be essential to fully harness BXDs for sustainable crop improvement and reduced reliance on synthetic agrochemicals.

Artificial intelligence (AI) has transformed agricultural genetics, especially in the context of crop improvement strategies. Traditional breeding faces challenges such as polyploidy, high level of genomic heterogeneity, and complex gene-trait associations. By combining multi-omics data researchers learn more about the genetic and molecular basis of important agricultural traits. However, statistical methods are often insufficient to address the data complexity. By contrast, AI techniques, such as machine learning (ML) and deep learning (DL), are emerging as powerful tools to explore complexity. Algorithms such as random forests (RF) and support vector machines (SVM) can support genomic selection (GS) and trait value prediction. Furthermore, DL models such as convolutional neural networks (CNN) and long short-term memory networks (LSTM) dominate high-throughput phenotyping and time series analyses, providing accurate predictions for crop yield, disease resistance, and genotype adaptation. Large language models (LLMs) are able to integrate complex omics data. AI models can analyze large dataset, generated by genomics, transcriptomics, proteomics, metabolomics, and phenomic applications because algorithms can combine different inputs, such as DNA sequences, gene expression profiles, protein-protein interaction networks, metabolite concentrations, and phenotypic data under specific environmental conditions. The integration of individual models can improve prediction accuracy by reducing resource inputs and automating labor-intensive tasks involved in breeding programs. Some recent AI methods, such as gradient boosting machines (GBMs) and Transformer models, are increasingly being used to improve scalability and accuracy of predictive analytics. This review summarizes major advances in AI applications in agricultural genetics, highlighting the strengths and limitations of different ML and DL models and their role in integrating complex datasets. The study highlights the importance of artificial intelligence in understanding genomic complexity and promoting the development of innovative methods to improve crop performance.

The identification of haploid induction genes has promoted the advancement of several breeding technologies. Haploid induction genes in wheat, coupled with visual marker, have led to the establishment of a novel in vivo doubled-haploid (DH) technology. When combined with dominant male sterile genes, this innovative DH method presents a promising avenue for high-throughput production of DH lines. Furthermore, the application of haploid induction genes has facilitated the establishment of other innovative breeding technologies, such as HI-Edit and cyto-swapping in creating cytoplasmic male sterility lines, as well as synthetic apomixis. This review summarizes the progress of DH technology in wheat and presents examples of application of haploid induction genes in accelerating breeding practices, aiming to promote the development of these innovative technologies in wheat and enhancing wheat breeding efficiency.

Fusarium head blight (FHB) is a serious fungal disease that affect small grain cereals, causing significant wheat (Triticum aestivum L.) yield and quality losses globally. Breeding disease-resistant wheat varieties is key to address FHB-related challenges, but its progress is delayed by traditional methods due to the small-scale, laborious and relatively subjective nature of manual assessment. This study presents a new approach that combines ultralow-altitude drone phenotyping with an optimized You Only Look Once (YOLO) model to examine FHB in wheat, enabling us to perform large-scale and automated symptomatic analysis of this disease. We first established an Open FHB (OFHB) training dataset, consisting of 4867 diseased and 106,801 healthy spikes collected from 132 commercial breeding lines during FHB progression. Then, a deep learning model called YOLOv8-WFD was trained for detecting healthy and diseased spikes, followed by an adaptive Excess Green method to identify symptomatic regions and thus FHB-related traits on spikes. To study resistance levels, we employed an unsupervised SHapley Additive exPlanations (SHAP) method to pinpoint key traits between 10 and 20 d after inoculation (DAIs), resulting in the classification of 423 varieties trialed during the 2023-2024 growing seasons into four resistance levels (i.e., highly and moderately susceptible, and moderately and highly resistant), which were highly correlated with field specialists’ evaluations. Finally, we derived disease developmental curves based on measures of key traits during 10-20 DAI, quantifying varietal disease progression patterns over time. To our knowledge, this work represents a significant advancement in large-scale disease phenotyping and automated analysis of FHB in wheat, providing a valuable toolkit for breeders and plant researchers to assess resistance levels, select disease-resistant varieties, and understand dynamics of the fungal disease.

Chloroplasts are essential for normal plant growth and development. In plants, pentatricopeptide repeat (PPR) proteins mediate RNA processing in chloroplasts. Here, we characterized a rice albino leaf 5 (al5) mutant which exhibits albinism during early leaf development. The MutMap+ analysis and transformation experiments revealed that AL5 encodes a chloroplast-localized P-type PPR protein. The AL5 mutation resulted in the defective splicing of ribosomal protein L2 (rpl2) and ribosomal protein S12 (rps12), which are involved in the synthesis of chloroplast 50S and 30S ribosomal subunits, respectively. The RNA-electrophoretic mobility shift assay (REMSA) further demonstrated that AL5 directly binds to rpl2 transcripts. Finally, disruption of AL5 led to reduced expression of plastid-encoded polymerase (PEP)-dependent plastid genes and nuclear-encoded photosynthetic genes. Notably, the albino al5 mutant phenotype was regulated by low temperature. These results suggest that AL5 participates in plastid RNA splicing and plays an important role in chloroplast development in rice.

Rice seed germination marks the start of cultivation and influences subsequent seedling growth, and is affected by hormones and environmental factors. Ubiquitination plays a critical role in this process by regulating hormonal homeostasis. In the ubiquitination cascade, ubiquitin-conjugating enzymes (UBCs) function as ubiquitin carriers to determine linkage specificity of ubiquitin chains. In rice (Oryza sativa), 39 UBC genes are identified, but only one gene OsUBC12 has been functionally studied to promote seed germination under low-temperatures in japonica rice. To elucidate the role of UBCs in seed germination, we generated CRISPR-Cas9 mutants for 23 UBC genes and overexpressed 20 members in rice. Among them, seven UBC genes (OsUBC4/6/7/12/25/27/48) were found to regulate seed germination, with OsUBC27 and OsUBC48 acting through the ABA pathway. Exogenous ABA inhibitors restored the germination rate of osubc27^CR. RT-qPCR analysis revealed that the ABA synthesis genes OsNCED1-5 were significantly upregulated in the mutants. Further differential ubiquitination proteomics in knockout mutants and wild-type plants showed that OsUBC27 regulates ABA homeostasis by modulating ubiquitination of the ABA-degrading protein OsABA8ox1, thereby balancing seed dormancy and germination. Sequence analysis identified distinct haplotypes of the seven OsUBCs that showed differential distribution between japonica and indica subspecies. Our study provides valuable molecular targets for developing rice varieties resistant to seed vivipary.

Abiotic stresses, particularly salinity, pose a major threat to rice productivity, highlighting the need to identify novel genetic resources to improve stress tolerance. Gamma irradiation remains one of the most widely used tools breeding stress-tolerant plant varieties. In this study, we identified a salt-tolerant rice mutant, salt-insensitive TILLING line 4 (sitl4), generated via gamma irradiation and linked its enhanced tolerance to a loss-of-function mutation in Oryza sativa protein acyltransferase for ABA response 1 (OsPATA1), which encodes a DHHC-type palmitoyl acyltransferase. Functional analyses using both sitl4 and a CRISPR/Cas9-mediated OsPATA1-knockout line (ospata1) revealed that disruption of OsPATA1 leads to increased abscisic acid (ABA) accumulation and upregulation of ABA-responsive genes under salt stress conditions. We identified OsEULD1b, a previously uncharacterized Euonymus lectin (EUL) domain-containing protein, as an interactor of OsPATA1. In sitl4 and ospata1, OsEULD1b displayed cytosolic retention, suggesting that its subcellular redistribution enhances its role in ABA-mediated stress signaling. Taken together, our findings demonstrate that OsPATA1 and OsEULD1b form a regulatory module that modulates the ABA-dependent salt stress responses in rice. These results provide new insights into the molecular mechanisms underlying abiotic stress tolerance and will help to identify potential genetic targets for developing stress-tolerant rice cultivars through molecular breeding or genome editing.

Gama-aminobutyric acid (GABA) plays an important role in regulating plant growth and response to various stresses. Here, we studied the natural variation of GABA transporter gene OsGAT3 in rice germplasm and found four primary promoter haplotypes. OsGAT3 was highly expressed in roots, culms, and leaf blades and was strongly induced in roots by GABA, salt, drought, and low temperature. OsGAT3 expression level was positively correlated with tiller number and nitrogen utilization efficiency (NUtE). OsGAT3 was localized in the plasma membrane. Overexpression of OsGAT3 significantly promoted GABA accumulation in basal parts suggesting it boosted axillary bud formation, tillering, and grain yield. OsGAT3 overexpression also enhanced tolerance to drought and salt stress. Transcriptome analysis revealed enriched phenylpropanoid and pentose phosphate pathways, and MAPK signaling underlining tolerance to salt stress, whereas drought tolerance was attributed to enhanced photosynthesis, glyoxylate and dicarboxylate metabolism, and carotenoid biosynthesis. Taken together, our data support the potential application of the gene for increasing yield under abiotic tolerance.

Posttranslational modifications (PTMs) are essential regulatory mechanisms that play a critical role in plant immunity. Previously, we demonstrated that OsBBI1, a RING finger type E3 ligase, contributes to rice resistance against blast disease. In this study, we identified two Eps15 homology domain (EHD)-containing proteins, OsEHD1 and OsEHD2, as substrates of OsBBI1 and investigated their roles in rice immunity against Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae (Xoo). We found that OsBBI1 ubiquitinated and promoted the degradation of OsEHD1 and OsEHD2 via ubiquitin/26S proteasome system (UPS) pathway. CRISPR/Cas9-mediated knockout of OsEHD1 and OsEHD2 led to enhanced immunity against M. oryzae and Xoo, improved expression of pathogen-induced immunity-associated genes, and strengthened pattern-triggered immunity (PTI), while overexpression of OsEHD1 resulted in opposite phenotypes. Additionally, OsEHD1 and OsEHD2 interacted with three SUMO proteins, OsSUMO3, OsSUMO5, or OsSUMO6, with SUMOylation sites in OsEHD1 and OsEHD2 being critical for these interactions. OsSUMO6 enhanced the stability of OsEHD1 and OsEHD2 to promote their negative immune regulation, whereas OsBBI1 reversed these negative immune functions. This study delineates a regulatory network of OsEHD1 and OsEHD2 proteins in rice immunity, highlighting the balance between OssBBI1-mediated ubiquitination and SUMOylation.

Grain size is a crucial factor influencing both rice yield and appearance quality. In this study, we identified GL6.1 as a gene associated with rice grain size by map-based cloning. The GL6.1 encodes a protein with CC-NB-LRR domain, a structural motif related to rice disease resistance. Genetic transformation experiments and the construction of gene pyramiding lines indicate that GL6.1 functions as a negative regulatory factor for rice grain length. By the analysis of SSSLs with diverse donor parents, a total of 11 single nucleotide polymorphisms (SNPs) are identified that are closely associated with the phenotype variations. A yeast one-hybrid library screening revealed that GL6.1 interacts with OsWRKY53, a transcription factor associated with rice disease resistance. Furthermore, RNA-seq assay also revealed the involvement of pathways associated with disease resistance, hinting at a multifaceted role for GL6.1 in both yield and stress tolerance traits in rice. These results indicate that the cloning and in-depth studies of GL6.1 would provide valuable insights into the interplay among high yield, superior quality, and stress tolerance, which are critical goals for rice breeding.

High molecular weight glutenin subunits (HMW-GS), major components of seed storage proteins in wheat, have large effects on processing quality. GLU-1 genes encode HMW-GS and their expression is mainly controlled at the transcriptional level by interactions between cis-regulatory elements and transcription factors. We previously identified an Aux/IAA transcription factor TaIAA10-6D that bound to a conserved cis-regulatory module CCRM1-1, the most essential conserved cis-regulatory module in GLU-1. Here, we confirmed the binding of TaIAA10-6D to CCRM1-1 using yeast one hybrid and dual-luciferase reporter assays. The enhanced expression of TaIAA10-6D suppressed glutenin accumulation and increased gliadin content. Dynamic transcriptome analyses revealed that TaIAA10-6D overexpression down-regulated glutenin and gliadin genes during an early stage of grain filling, but up-regulated gliadin genes during a late stage probably by endoplasmic reticulum stress, accounting for its effect on the trade-off between glutenin and gliadin. Rheological property and processing quality assays showed that TaIAA10-6D overproduction reduced stabilization time and bread quality, but enhanced cookie quality. Overexpression of TaIAA10-6D also reduced plant height, leaf size, kernel number and grain yield. We identified two major haplotypes of TaIAA10-6D, Hap I and Hap II, and developed a breeding-friendly diagnostic marker. Hap I conferred higher expression of TaIAA10-6D and concomitantly reduced plant height and kernel number, but had little effect on grain yield, contributing to lodging resistance without yield penalty. Hap I was subjected to positive selection in breeding. The findings provide a useful gene for wheat improvement and broaden insights into the regulatory machinery underpinning auxin-mediated quality formation, plant morphogenesis and yield gain.

Iron (Fe) is a micronutrient for living organisms, and maintenance of Fe homeostasis is required for normal physiological functions. In this study, we report the function of a plasma membrane localized transporter (Polyol transporter 8, TaPLT8) in wheat, which is regarded as a novel regulator for Fe transport. TaPLT8 is specifically expressed in wheat roots and is induced by environmental Fe. Knockout of TaPLT8 increased Fe accumulation in roots but resulted in decreased Fe levels in shoots and grain. The change was caused by an altered tolerance or increased susceptibility to excessive environmental Fe in the vicinity of wheat roots, and inhibited root growth. Overexpression of TaPLT8A improved Fe transport from roots to shoots and grains, and increased grain Fe levels by up to 14.46%. Compared to wild type (WT) plants, the levels of Citrate and Fe levels in xylem sap were significantly decreased in taplt8 mutants but significantly increased in TaPLT8 OE lines. Transcriptome analysis of taplt8 mutants indicated that TaPLT8 affected citrate levels by influencing glycolysis and the citrate cycle pathway in roots, thus impacting Fe translocation. The findings demonstrated that TaPLT8 mediates Fe distribution in wheat roots and shoots, contributing to greater understanding of the contribution of TaPLT8 to Fe accumulation in grains.

Pre-harvest sprouting (PHS) or vivipary is a major problem affecting cereal quality and grain quantity and is primarily linked to the dysregulation of abscisic acid (ABA) biosynthesis in plants. Therefore, elucidating the molecular mechanisms governing seed dormancy is crucial for developing strategies to improve crop productivity. In this study, we identified a novel viviparous maize mutant, viviparous-like 5 (vp-like5), which exhibits precocious germination in developing seeds. Through map-based cloning, we discovered that ZmCNX6, which encodes a small subunit of molybdopterin synthase essential for molybdenum cofactor (MoCo) biosynthesis, is the causal gene responsible for the vp-like5 phenotype. Biochemical assays have demonstrated significantly reduced activities of MoCo-dependent enzymes, including aldehyde oxidase (AO), xanthine dehydrogenase (XDH), and nitrate reductase (NR), in vp-like5. AO is essential for the ABA biosynthesis, and the observed ABA deficiency in vp-like5 likely drives the viviparous phenotype. Expression analysis showed that ZmCNX6 was stably expressed during seed development, indicating its significant role in seed development. Furthermore, overexpression of ZmCNX6 not only enhanced the activities of MoCo-dependent enzymes but also improved drought tolerance in maize. Collectively, our study revealed ZmCNX6 as a multifunctional hub coordinating MoCo metabolism, ABA-dependent dormancy regulation, and abiotic stress responses, offering a potential target for simultaneously mitigating vivipary and improving drought resistance in maize.

Soybean mosaic virus (SMV) poses a substantial threat to the yield and quality of soybean (Glycine max (L.) Merr.), leading to significant economic losses in soybean production. However, the mining of SMV-resistance loci and the exploration of the underlying disease resistance mechanisms remain relatively limited. MicroRNAs (miRNAs) are a class of post-transcriptional regulators that play a pivotal role in modulating plant growth, development and responding to various stresses. In this study, we demonstrated the function of the “miR398c/d-GmCSDs” module between soybean resistant and susceptible varieties, focusing on its differential regulatory roles in SMV infection. Specifically, SMV infection downregulated gma-miR398c/d expression in the resistant variety (Qihuang 1, QH), while upregulated them in the susceptible variety (Nannong 1138-2, NN). Transient expression assay in N. benthamiana confirmed that gma-miR398c/d can target six superoxide dismutase (SOD) family genes, which responded to SMV infection in both varieties. Stable overexpression of Gma-MIR398c/d in soybean or inhibition of the corresponding target genes’ expression via Bean pod mottle virus (BPMV)-induced gene silencing (VIGS) led to reduced H₂O₂ content and thereby promoted SMV infection. Conversely, plants overexpressing the target genes exhibited the opposite phenotypes. The functions of gma-miR398c/d and their target genes were further validated in N. benthamiana through transient co-expression with SMV infectious clone (pSC7-GFP), indicating that gma-miR398c/d negatively regulated soybean resistance to SMV, while the target genes positively contributed to disease resistance. Collectively, our findings provide novel insights into the regulatory mechanisms underlying soybean resistance to SMV.

Peanut seedlings develop from seeds by hypocotyl elongation and differentiation. However, the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown. In this study, a single-nucleus gene expression landscape in peanut seedlings was initially developed from diverse tissues, including stems, roots, leaves, and hypocotyls. Core transcription factor interaction networks driving developmental trajectories were identified to decipher hypocotyl cell heterogeneity. Jasmonic acid and cytokinin regulate peanut hypocotyl expansion and differentiation based on the number and size of cortex cells and hormone levels between the hypocotyl at 3 and 7 d after germination. We further demonstrated that AhBHLH143 potentially represses hypocotyl elongation by promoting the JA pathway and inhibiting the cytokinin pathway. The single-nucleus transcriptomic atlas of peanut seedlings reveals new insights into hypocotyl development and provides a valuable resource for future investigations of seedling development.

Cytoplasmic male sterility (CMS) caused by mitogenomic variation underlies CMS lines essential for hybrid crop production. However, the role of CMS in pearl millet remains unclear. To clarify the function of CMS in pearl millet (Pennisetum glaucum), the mitochondrial genomes of the CMS line ‘23A’ (L23A) and its maintainer ‘23B’ (L23B) were sequenced and further assembled. With a mitochondrial genomic comparison, an rpl16 (ribosomal protein L16-like protein) gene in L23A that was absent in L23B was successfully identified. An analysis of RT-PCR and qRT-PCR validated that rpl16 was specifically expressed in the inflorescences of L23A. Overexpression of the rpl16 gene in rice truly induced pollen abortion, further leading to a reduced grain number. When compared to L23B at earlier stages of millet anther development, a higher ROS level and premature tapetal degradation (PCD) in L23A were observed through a reactive oxygen species (ROS) staining and anther paraffin section. The protein interaction between RPL16 and NADH dehydrogenase subunit 1 (NDUFV1) may indicate a potential role for the rpl16 gene in disrupting anther ROS homeostasis in the CMS line, suggesting an important role of CMS in hybrid millet breeding.

Base editors are essential tools for precise genome editing in plants. However, achieving high efficiency in C-to-G editing while minimizing byproduct and offtarget mutations remains challenging. In this study, we present the development and evaluation of a novel glycosylase-based cytosine base editor (gCBE) for efficient C-to-G editing in rice. Unlike traditional cytosine base editors, which rely on cytosine deamination, gCBE directly excises cytosine to generate an apurinic/apyrimidinic (AP) site, thus circumventing the deamination step and reducing the production of C-to-T byproducts. We constructed several gCBE variants, including N-gCBE, M-gCBE, and C-gCBE, by fusing engineered human UDG2 (UNG*) to SpCas9 nickase (nSpCas9, D10A) and tested their editing efficiency and specificity in rice. Our results demonstrate that M-gCBE achieved efficient C-to-G editing (6.3% to 37.5%) similar to OsCGBE (9.4% to 28.1%) at most targets, though with site-dependent variations. Notably, gCBE tools showed a marked reduction in C-to-T byproducts, with average C-to-T mutation rates of 12.5% for N-gCBE and 16.7% for M-gCBE, compared to 53.1% for OsCGBE. Notably, both N-gCBE and M-gCBE were capable of generating homozygous C-to-G mutations in the T₀ generation, a key advantage over OsCGBE, which predominantly generated C-to-T mutations. Off-target analysis revealed minimal off-target effects with M-gCBE, highlighting its potential for high-precision genome editing. These findings suggest that gCBE tools, particularly M-gCBE, are highly efficient and precise, providing an advanced solution for C-to-G editing in plants and offering promising applications for crop improvement.

The environment has an important impact on maize (Zea mays L.) production, making it necessary to identify plant adaptation regions that are suitable for different maize varieties. Traditional methods using field trials are costly and restricted to a limited number of areas. Identifying adaptation regions based on climate data has great potential, but a basic understanding and a prediction approach for diverse maize varieties are lacking. Here, we collected a representative dataset comprising 32,840 data points from the National Maize Variety Trial Data Management Platform. We employed three traits to characterize the adaptability of different maize varieties: PH (plant height), DTS (days to silking), and yield. First, we quantified the contributions of variety (V), environment (E), and V × E to variance in the three adaptation-related traits. The mean contributions of E to variance in PH, DTS, and yield were 54.50%, 82.87%, and 75.92%, respectively, suggesting that environmental effects are crucial for phenotype construction. Second, we analyzed correlations between the three traits and three environmental indices: GDD (growing degree days), PRE (precipitation), and SSD (sunshine duration). The highest absolute correlation coefficients between phenotypes and environmental indices were 0.15-0.69 at the whole-data level. To predict variety adaptation on a national scale, we modeled the three traits using environmental indices and best linear unbiased predictors (BLUPs) via the random forest algorithm. The predictive abilities of our models for PH, DTS, and yield were 0.90 (MAE = 9.95 cm), 0.99 (MAE = 1.09 d), and 0.95 (MAE = 0.55 t ha⁻¹), respectively, indicating that our proposed framework can predict adaptation-related traits for diverse maize varieties in China.

Flag leaf angle (FLANG) is one of the key traits in wheat breeding due to its impact on plant architecture, light interception, and yield potential. An image-based method of measuring FLANG in wheat would reduce the labor and error of manual measurement of this trait. We describe a method for acquiring in-field FLANG images and a lightweight deep learning model named LeafPoseNet that incorporates a spatial attention mechanism for FLANG estimation. In a test dataset with wheat varieties exhibiting diverse FLANG, LeafPoseNet achieved high accuracy in predicting the FLANG, with a mean absolute error (MAE) of 1.75°, a root mean square error (RMSE) of 2.17°, and a coefficient of determination (R²) of 0.998, significantly outperforming established models such as YOLO12x-pose, YOLO11x-pose, HigherHRNet, Lightweight-OpenPose, and LitePose. We performed phenotyping and genome-wide association study to identify the genomic regions associated with FLANG in a panel of 221 diverse bread wheat genotypes, and identified 10 quantitative trait loci. Among them, qFLANG2B.2 was found to harbor a potential causal gene, TraesCS2B01G313700, which may regulate FLANG formation by modulating brassinosteroid levels. This method provides a low-cost, high-accuracy solution for in-field phenotyping of wheat FLANG, facilitating both wheat FLANG genetic studies and ideal plant type breeding.

African cultivated rice (Oryza glaberrima) was domesticated from its wild progenitor, Oryza barthii. The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication. A QTL analysis of 331 recombinant inbred lines (RILs) using 194 InDel markers identified five quantitative trait loci (QTL) associated with awn length. Locus qObAwn5 made the highest contribution in regulating awn length and was fine-mapped to a 260-kb genomic interval. RNA-seq and RT-qPCR analyses, combined with CRISPR/Cas9-mediated knockout that disruption of gene G12 caused a significant reduction in awn length indicating that G12 was ObAwn5. Genomic analysis revealed a large structural variation (SV) between W1411 and IRGC104165 within this region, characterized by an inversion and two large deletions. Population genomic analyses revealed that all the cultivated African accessions exhibit a domestication-like (Dom-like) pattern, whereas non-cultivated accessions consisted of two distinct types: W1050-like and W1411-like. The W1411-like type was exclusively found in the AA genome of African wild rice. This discovery of ObAwn5 newly substantiates the independent origin of African cultivated rice.

Leaf rust, caused by the fungus Puccinia triticina, is one of the most destructive diseases affecting global wheat production. Developing disease-resistant wheat varieties is the most cost-effective and environmentally friendly approach to managing this disease. We phenotyped a collection of 559 wheat accessions from five continents for resistance to leaf rust in field trials at three locations in China (Zhoukou, Henan; Wuhan, Hubei; and Xinxiang, Henan) during the 2020-2021, 2021-2022, and 2022-2023 cropping seasons, followed by best-linear-unbiased-estimation analysis across environments. These accessions were genotyped using the MGISEQ-2000 re-sequencing platform, and a genome-wide association analysis was subsequently performed. Twenty-four stable leaf rust resistance loci across 15 chromosomes were identified. Among these, 11 loci may represent new sources of resistance. Notably, Lr.hzau-2BS.1 and Lr.hzau-7AL were consistently detected across all three environments and BLUE. Lr.hzau-2BS.1 has the highest frequency in European wheat accessions, whereas Lr.hzau-7AL is most prevalent in South American accessions. Gene-expression analysis identified 101 candidate genes associated with these loci. Closely linked Kompetitive Allele Specific PCR (KASP) markers, 2B-209172 and 7A-348992, were developed for Lr.hzau-2BS.1 and Lr.hzau-7AL, respectively. Chinese wheat varieties Mianmai 45 and Liaomai 16, which carry resistance alleles at both loci and exhibit < 5% leaf rust severity, represent valuable sources of leaf rust resistance for wheat breeding programs. These newly identified resistance loci and their KASP markers provide valuable resource for their exploitation in wheat breeding.

Soybean (Glycine max) is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals. Cultivated soybean varieties exhibit considerable genetic diversity depending on their geographical origin. Heinong 531 (HN531) is an elite cultivar that was released in China in June 2021 with 22.34% seed oil, high resistance to soybean cyst nematode (SCN) race 3, and enhanced yield. However, the genetic basis for these desirable agronomic traits is unclear. In this study, we generated a high-quality genome assembly for HN531 and used it to systematically analyze genes related to agronomic traits such as resistance to SCN. The assembled genome spans 981.20 Mb, featuring a contig N50 of 19.47 Mb, and contains 58,151 predicted gene models. Pan-genomic comparison with 27 previously reported soybean genomes revealed 95,071 structural variants (SVs) of > 50 bp, of which 602 were HN531-specific. Furthermore, we identified a copy number variation at rhg1 that underlies resistance to SCN, and we found elite alleles of functional genes underlying important agronomic traits such as seed oil content, adaptability, and yield. This high-quality HN531 genome can be used to explore the genetic basis for the excellent agronomic traits of this cultivar, and is a valuable resource for breeders aiming to improve HN531 and related cultivars.

Peanut is a globally significant oil crop and economic resource, notable for its kernel containing over 50% oil content. White testa peanuts are highly valued for their superior nutritional profile, minimal pigmentation, and superior oil clarity. Identification of genes controlling white testa color is crucial for advancing breeding programs and understanding the genetic mechanisms involved. A genetic mapping study was performed in peanut to identify genes controlling white testa color, a trait associated with desirable end-use quality traits in this oilseed crop. In an F₂ population generated from a cross of a white-testa with a pink-testa cultivar, two recessive quantitative-trait loci controlling white testa were identified and fine-mapped to A02 and B02 chromosomes. Two homologous genes, Arahy.MP3D3D and Arahy.26781N, encoding bHLH transcriptional factors, were identified as candidates for the two loci. Reduced expression of these two genes likely suppresses anthocyanin biosynthesis.

Inferior grains exhibit delayed developmental processes and reduced metabolic activities compared to superior grains, leading to unstable rice yield and quality. While significant advancements have been achieved in elucidating the physiology of endosperm filling in inferior grains, the role of the embryo remains underexplored and warrants comprehensive investigation. Two Wuyujing 3 mutants, DW024 (relatively synchronous; syn-DW024) and DW179 (significantly asynchronous; asyn-DW179), with different grain-filling patterns were used in this study. Samples of superior and inferior grains were collected at intervals from 5 to 60 d after fertilization and subsequently dissected into subsamples of the embryo and endosperm. Histochemical staining, biochemical analysis, and RNA sequencing (RNA-seq) were combined to systematically compare developmental and physiological traits between superior and inferior grains. Combining hierarchical clustering of mRNA datasets revealed three developmental phases of the endosperm and embryo: morphogenesis, endosperm filling/embryo enlargement, and maturation. In both syn-DW024 and asyn-DW179, the duration of the endosperm/embryo morphogenesis phase was identical in superior and inferior grains. The inferior grains of asyn-DW179 exhibited a 10-day prolongation in the endosperm filling phase and a 20-day extension in the embryo enlargement phase compared to the superior grains. The endosperm of inferior grains exhibited higher contents of sugars and free amino acids, along with slower accumulation of storage compounds, which was associated with the down-regulation of genes for starch synthesis and ABA signaling. In addition, transporters for nutrient exchanges between endosperm and embryo were down-regulated, suggesting a potential role of the embryo in adjusting the endosperm filling process. Collectively, our results reveal that the prolonged phases of endosperm filling and embryo enlargement may underlie the impaired development of inferior grains, offering a new perspective for breeding or cultivating rice with uniform grain quality.

This study aimed to identify the physiological mechanisms enabling low-N-tolerant maize cultivar to maintain higher photosynthesis and yield under low-N, low-light, and combined stress. In a three-year field trial of low-N-tolerant and low-N-sensitive maize cultivars under two N fertilization (normal N: 240 kg N ha⁻¹; low-N: 150 kg N ha⁻¹) and two light conditions (normal light; low-light: 35% light reduction), the tolerant cultivar showed higher net photosynthetic rate than the sensitive one. Random Forest analysis and Structural Equation Modeling identified PSI donor-side limitation (elevated Y_ND) as the key photosynthetic constraint. The tolerant cultivar maintained higher D1 and PsaA protein levels and preferentially allocated photosynthetic N to electron transport. This strategy reduced Y_ND and sustained photosystem stability, thus improving carboxylation efficiency and resulting in higher photosynthesis.

Increasing soil phosphorus (P) availability and plant P uptake are potential approaches to alleviate low P stress in plants and mitigate P resource shortages. Application of fulvic acid (FA) in soil is observed to increase plant growth and P uptake. However, the biological mechanisms underlying these effects remain largely unknown. In this study, based on a three-year field experiment, multi-omics analyses were performed to reveal the effects of FA on rice growth and P uptake, the expression of P transporter genes, root exudates, and rhizosphere bacterial communities in a P-deficient soil. The results showed that FA application significantly promoted rice growth and P absorption under P deficiency, in association with the upregulation of P transporter genes expression and increased rhizosphere P mobilization. FA increased the transformation of non-labile to labile P in the rhizosphere by increasing the secretion of P-dissolving exudates and changing a rhizosphere bacterial community with high P-mobilization capacity, and the variations in the rhizosphere bacterial community were coupled with those of the root exudates, especially glutamylproline, tryptophanamide, 5-chloro-2′-deoxyuridine, L-menthyl (R,S)-3-hydroxybutyrate, and 2,7-diamino-7-iminoheptanoic acid. These findings reveal the multiple positive effects of FA on rice P uptake and indicate the potential utilization of FA in increasing P utilization in rice production.

The plant cell wall serves as a barrier in defense against pathogen invasion. However, the specific contribution of cell walls in vascular tissues to plant immunity remains largely unexplored. In this study, we demonstrate that OsCSLC3, a member of the rice cellulose synthase-like (CSL) gene family, is predominantly expressed in vascular tissues and that its overexpression promotes hemicellulose biosynthesis. This enhancement of hemicellulose accumulation is associated with improved disease resistance. Targeted editing of conserved cis-regulatory elements in the OsCSLC3 5′ untranslated region (UTR) showed that deletion of the specific fragment (−575 to −824 bp) elevated OsCSLC3 transcript levels, promoted hemicellulose accumulation, enhanced disease resistance, and improved agronomic traits. Our findings highlight a previously underappreciated role for hemicellulose in plant immunity and demonstrate that precise 5′ UTR editing is a promising strategy for improving disease resistance and agronomic traits.

Broad-spectrum resistance (BSR) reduces pathogen-related yield losses in crops such as rice (Oryza sativa). To achieve BSR, traditional breeding has focused on the time-intensive process of incorporating resistance (R) genes into elite germplasm. Now, CRISPR/Cas9-mediated genome editing makes it possible to modify susceptibility (S) genes to rapidly achieve BSR in rice. However, identifying S genes remains challenging. Here, we analyzed transcriptome data and determined that OsJAC1, encoding a mannose-binding jacalin-related lectin, is significantly induced upon infection by the rice blast fungus Magnaporthe oryzae. To explore the role of OsJAC1 in BSR in rice, we generated OsJAC1 overexpression and knockout mutant lines in the rice ZH11 (Zhonghua 11) background and performed pathogen inoculation assays, revealing that OsJAC1 negatively regulates resistance against M. oryzae and the bacterial blight pathogen Xanthomonas oryzae pv. oryzae. Further evidence of defense responses, such as a reactive oxygen species burst, defense-related gene expression, and MAPK phosphorylation, also supports the role of OsJAC1 as a negative regulator of plant immunity. To further validate the function of OsJAC1, we knocked out OsJAC1 in the Nipponbare (NPB) background. The resulting NPB-osjac1^cas9 plants showed enhanced defense responses and resistance against M. oryzae. Notably, the osjac1 mutants did not compromise agronomic traits in the ZH11 or NPB background. Hence, OsJAC1 could be regarded as an S gene and could serve as a potential target in rice breeding programs, providing valuable insights for crop improvement.

Rice (Oryza sativa L.) root characteristics are closely associated with nitrogen (N) uptake, root growth and development are greatly influenced by ethylene. In this study, a hydroponic experiment was conducted using four rice genotypes [Shanyou 63 (SY63) and Zhonghua 11 (ZH11) with well-developed aerenchyma; Yangdao 6 (YD6) and mutant rcn1 from ZH11 with less-developed aerenchyma] to investigate the effects of exogenous ethephon (Eth) on root characteristics, N uptake, dry matter distribution, and clarify the underlying relationship. Compared with YD6 and rcn1, SY63 and ZH11 had higher N accumulation, higher root aerenchyma area to cortex area ratio (ACR), higher NH₄⁺ uptake via the apoplasmic pathway and root-to-shoot NH₄⁺ translocation under no ethephon application (NEth) and Eth treatment, and elevated expression of the three genes (OsAMT1;2, OsAMT2;2, and OsAMT4;1) for ammonium transporters under Eth treatment. Eth treatment increased shoot N and dry matter accumulation, decreased the total root length and root diameter, and increased ACR and the expression of OsAMT genes in four genotypes. In summary, Eth could increase N accumulation via modifying root characteristics in rice, particularly by enlarging root aerenchyma and thinning the roots. The findings provide implications for development of elite rice varieties and green rice production with higher N efficiency.

Achieving a sustainable cropping system requires the efficient use of resources, particularly nitrogen (N). Nitrogen fertiliser is applied in most irrigated cotton fields to maximise yield potential, but plant fertiliser recovery can be low. Identifying the crucial pathways of fertiliser remobilisation internally within cotton plants will lead to greater awareness of the plants’ ability to match the N demands of the developing fruiting matter. This study investigated the fate of N fertiliser when applied to cotton at various dates, with the goal to improve N fertiliser recovery in a modern transgenic cotton cultivar. ¹⁵N-labelled urea (10 atom%) was applied at multiple times and harvested at four key cotton growth stages (first square, early bolls, cut-out and maturity). Remobilised N was determined as the difference in the proportion of N fertiliser in individual plant components against the fertiliser utilised by the whole plant. The application of fertiliser N at first square resulted in 23% greater fertiliser N recovery at plant maturity compared to fertiliser N applied 100% pre-plant (P < 0.001). The improvement was in-part due to higher N derived from the fertiliser (Ndff%) in the cotton seed (3%). Conversely, the Ndff% was higher in the stem (4%) and petioles (1%) when the fertiliser was applied pre-plant. In total, 73% of plant N was remobilised to another plant organ, predominantly the seed (67%). Applying N fertiliser post-planting improved N recovery and lint yield compared to applying all fertiliser pre-plant.