A predictive model of meiotic crossover engineering would increase precision in crop breeding. We review the biological principles underlying crossover formation and chromosomal distribution, hierarchical control mechanisms enforcing crossover assurance, and an emerging phase-separation model determining crossover interference patterning.

Global climate change seriously threatens food security. To address this challenge, breeders have achieved remarkable results using multiple breeding strategies and technologies. In recent years, the application of biomolecular condensates to crop improvement has remained in its early stages. Nevertheless, growing evidence indicates their crucial roles in regulating crop development and stress adaptation. This review synthesizes recent advances in understanding biomolecular condensate functions across key plant developmental phases and their regulatory roles in abiotic and biotic stress responses. The regulatory mechanisms associated with these condensates primarily encompass transcriptional regulation, RNA processing and metabolism, translational control, and membrane organelle biogenesis, collectively establishing a solid theoretical foundation for agricultural molecular breeding. In the final section, we discuss the potential applications and challenges of biomolecular condensates in crop improvement.

Because cereal kernel texture is a determinant of maize end-use properties, it is desirable to elucidate the genetic control of kernel formation and thereby to optimize maize kernel texture for breeding. Basically, maize kernel texture is determined by the ratio of vitreous endosperm in the peripheral region to the floury endosperm in the center of the kernel. In contrast to the puroindoline proteins (Pins) as the major determinants of grain texture specific to wheat, maize kernel texture is a quantitative trait that is controlled by many minor-effect genes. Nonetheless, substantial progresses have been made in unravelling gene regulatory networks underlying maize kernel formation that is related to its texture. Here, we review the current knowledge on maize endosperm development, focusing on vitreous and floury endosperm formation, and summarize the potential transcription regulatory mechanisms for starch and zein biosynthesis. The integration of the information will potentially provide valuable candidate genes for breeding maize varieties with improved kernel texture and quality.

Direct seeding of rice (DS) has been widely adopted due to reduced labor cost and simpler cultivation practices. However, anaerobic flooding conditions reduce seed germination and seedling establishment. Here, a genome-wide association study (GWAS) of four coleoptile traits using 572 rice accessions subjected to 3 d of anaerobic conditions was conducted. The traits were coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD). Ninety-two QTL were identified, with 59 overlapping with previously reported loci. Two rice varieties (C126 and C261) with contrasting coleoptile lengths were selected for multi-omics analyses. A specific anaerobic-responsive blue module was identified by weighted gene co-expression network analysis (WGCNA). Thirty-six candidate genes were screened, including OsMYB48 that was predominantly localized in the nucleus. Loss-of-function OsMYB48 mutants exhibited significantly increased coleoptile length relative to the control under 4 d of anaerobic conditions. Endogenous hormone measurements revealed that the content of 1aminocyclopropanecarboxylic acid (ACC), the ethylene precursor, was significantly increased in the ko-osmyb48-1 mutants. Ethylene-related genes OsACS1 and OsACO2 were also upregulated in the mutants. OsMYB48 DAP-seq identified 31 potential target genes, including WB1 and OsBURP16. Hence, anaerobic-responsive gene OsMYB48 likely acts as a transcriptional repressor of coleoptile elongation under anaerobic germination conditions, probably via the ethylene signaling pathway. This work provides a theoretical basis and genetic resources for breeding rice lines with high germination when directly sown.

Salt stress severely limits rice growth and productivity. Auxin signaling has a well-documented role in development, but its role in rice salt stress responses is far from clear. In this study, we identified OsARF12, an auxin response factor, as a critical positive regulator of salt tolerance in rice. Transcript analysis revealed salt-induced upregulation of OsARF12. More importantly, OsARF12 overexpression (OsARF12-OX) induced significantly increased survival rates and reduced biomass loss under 200 mmol $L^(-1)$ NaCl treatment compared with wild-type (WT) plants, and OsARF12 knockout (OsARF12-KO) using CRISPR-Cas9 showed the opposite tendency. Physiological analyses revealed that OsARF12-OX plants mitigated salt-induced oxidative damage by enhancing ROS scavenging capacity and promoting $Na^+/K^+$ homeostasis as well as through their superior photosynthetic efficiency under 200mmol$L^(-1)$ NaCl treatment, which was consistent with the upregulation of differentially expressed genes involved in ROS scavenging, photosynthesis and ion transport pathways. Furthermore, auxin receptor genes or transcription inhibitor genes were upregulated or downregulated in OsARF12-OX lines compared with WT plants under salt stress, respectively. Biochemical assays indicated that OsARF12 acts as a transcriptional activator, directly binding to TGTC-box motifs in the promoters of the key ion transporters OsSOS1 and OsHKT1;5 to reduce shoot $Na^+$ content and the $Na^+/K^+$ ratio, thereby increasing salt tolerance. These findings revealed the potential role of OsARF12 in increasing salt tolerance by integrating auxin signaling with ROS scavenging, ionic homeostasis and photosynthetic networks, offering valuable targets for breeding resilient rice varieties.

Salinity is a major hazard to crop plant growth and significantly reduces grain yield. When subjected to high salinity, plants maintain ion homeostasis through $Na^+$ compartmentalization and exclusion, enabling them to mitigate salt stress. In this study, we revealed the role of rice (Oryza sativa) MYB9 (OsMYB9) in regulating salt stress tolerance. OsMYB9 was expressed in the vascular bundles of roots and leaves, particularly in the parenchyma cells. The null mutation of OsMYB9 resulted in increased sodium ion accumulation in shoot tissues under salt stress, leading to salt-sensitive phenotypes. Real Time Quantitative Reverse Transcription PCR analysis indicated the OsMYB9 mutation led to decreased expression of several genes associated with vacuolar $Na^+$ antiporters (OsNHX1, OsNHX2, OsNHX3, OsNHX4, and OsNHX5), high-$Na^+$ affinity transporters (OsHKT1;5), and SALT OVERLY SENSITIVE proteins (OsSOS2 and OsSOS3). Among these, OsMYB9 upregulated the expression of OsNHX1 and OsNHX2 by directly binding to their promoter regions. Furthermore, GIGANTEA (OsGI) interacted with OsMYB9, suggesting that OsGI negatively acts upstream of OsMYB9 and regulates the expression levels of OsNHX1. Collectively, OsMYB9 alleviates the excess accumulation of $Na^+$ ions in the xylem by retrieving $Na^+$ ions from xylem parenchyma cells and compartmentalizing them into vacuoles. These regulatory mechanisms mediated by OsMYB9 are crucial for minimizing $Na^+$ toxicity in photosynthetic tissues and enhancing salt stress tolerance in rice.

Jasmonate ZIM-domain (JAZ) proteins are key repressors of the jasmonate signaling pathway and are involved in plant stress responses. However, their roles in starch biosynthesis in cereal crops remain unclear. In this study, we identified a locus associated with starch content on chromosome 5A by a genome-wide association study (GWAS). At this locus, a gene (TraesCS5A02G204900) encoding a JAZ protein (TaJAZ1) was found to be highly expressed in grains. CRISPR/Cas9-induced mutants were generated to investigate the role of TaJAZ1 in starch biosynthesis. Phenotypic characterization revealed significant alterations in starch granule size, crystallinity, and digestibility. Specifically, the two mutant lines (tajaz1abd#1 and tajaz1-abd#2) exhibited increased total starch (12.5% and 17.6%, respectively), amylose (79.3% and 72.1%, respectively), resistant starch (88.5% and 96.8%, respectively), and grain yield per plant (103.8% and 58.8%, respectively). Furthermore, the mutation of TaJAZ1 significantly increased the expression levels of TaSBEI, TaAGPS1, TaAGPL1 and TaGBSSI, but decreased the expression levels of TaSSIIa, TaSSIIb and TaSBEIIa by binding to their promoters. Taken together, our results demonstrate that TaJAZ1 is a negative regulator of starch biosynthesis and grain yield. These findings not only provide novel insights into wheat starch biosynthesis regulation, but also contribute to potential genes for breeding wheat varieties of better quality and higher yield.

Soil salinity severely affects wheat (Triticum aestivum) yield and quality. Identifying salt-tolerance genes and elucidating their mechanisms are essential for improving salt tolerance in this crop. Previously, the wheat microRNA tae-miR9668 was found to be significantly downregulated by salt stress. Tae-miR9668 was predicted to target TaRPM1-1A, but how these two genes are involved in wheat salt tolerance is unclear. Here, we demonstrated that tae-miR9668 negatively regulates TaRPM1-1A expression, as overexpressing tae-miR9668 in transgenic lines suppressed TaRPM1-1A expression, leading to enhanced sensitivity to salt stress. Conversely, transgenic lines overexpressing TaRPM1-1A exhibited significantly enhanced salt tolerance. Under salt stress, TaRPM1-1A-overexpressing plants exhibited reduced oxidative damage, as shown by reduced MDA content and reactive oxygen species levels. Accordingly, the activities of antioxidant enzymes such as SOD, POD, CAT, and APX increased, together with increased accumulation of osmoprotectants such as proline, soluble sugars, and soluble proteins relative to the control. By contrast, tae-miR9668 overexpression had opposite effects in transgenic plants. Additional molecular studies showed that tae-miR9668 can cleave TaRPM1-1A mRNA, whereas TaRPM1-1A can interact with TaSnRK1.3-D, supporting its role in salt tolerance. Therefore, the tae-miR9668-TaRPM1-1A module might play important roles in salt tolerance in wheat, providing valuable targets for breeding salt-resilient wheat varieties.

Nitrogen (N) is crucial for maize (Zea mays L.) growth, development and yield. Dysfunction of the maize NIN-like protein 5 (ZmNLP5) reduces N assimilation, but the precise mechanism by which ZmNLP5 modulates N metabolism and its contribution to agricultural applications are not well understood. In this study, our transcriptomic profiling and chromatin immunoprecipitation followed by sequencing (ChIPseq) analyses reveal 581ZmNLP5-modulated target genes. We confirmed that ZmNLP5 physically interacted and transactivated contributors to N assimilation, including ZmNRT1.1D, ZmNIR1.1, ZmNR2.1, ZmGS4, ZmAS1, and ZmLBD6. Overexpression of ZmNLP5 upregulated N metabolism genes, and enhanced the enzymatic activities of nitrate reductase and glutamine synthase. Furthermore, overexpressing ZmNLP5 increased grain yield under both normal-N and low-N conditions. Introgression of the overexpressed ZmNLP5 allele into Zhengdan 958 resulted in comparable yield increases in field trials. Our study unveiled that ZmNLP5 is a potential genetic target for increasing nitrogen use efficiency and grain yield in maize.

Wheat grains contain various bioactive substances, of which, condensed tannins (CT) are polymeric flavan-3-ols that accumulate in wheat seed coat influencing the end-use quality and nutritional value. However, the genetic architecture underlying CT biosynthesis in wheat grain remains unclear. Here, we studied the deposition and genetic regulation of CT in wheat grains, and found that CT deposited specifically in the testa layer of red-grained wheat as catechin- and epicatechin-formed polymers. Genome-wide association study identified 22 genetic loci affecting CT content, one of which, TaTAN, a single dominant gene controlling CT presence, was mapped to chromosome 3A in a segregation population. Further pan-genome analysis, transcriptome profiling and ethyl methanesulfonate induced mutants sequencing revealed a R2R3-MYB transcription factor, TaMYB10-3A, as the causal gene. Three loss-of-function alleles in TaMYB10-3A caused by large fragment inversion-deletion and insertion were identified which abolish both CT deposition and red pigmentation, demonstrating the pleiotropic effect of TaMYB10-3A on CT presence and grain color. TaMYB10-3A directly trans-activates core flavonoid genes such as chalcone synthase and dihydroflavonol 4-reductase to initiate CT biosynthesis. Our investigation provides a comprehensive understanding of CT presence in wheat grains and lays a solid foundation for manipulating CT metabolites to improve wheat grain end-use quality and nutrition values in wheat.

To investigate the effect of structural variation of rye 6RL arms on their meiotic behavior and to locate powdery mildew resistance gene(s), we developed a wheat-rye T6BS.6RL^Ar translocation chromosome and its deleted translocations, T6BS.6RL ^Ar -2 and T6BS.6RL ^Ar -4. Some 6RL-specific markers were used to determine that the segments from 733.91 to 849.52 Mb and from 832.72 Mb to the telomere of 6RL ^Ar arms were deleted from T6BS.6RL ^Ar -2 and T6BS.6RL ^Ar -4, respectively. Translocations T6BS.6RL ^Ar and T6BS.6RL ^Ar -4 were resistant to powdery mildew and T6BS.6RL ^Ar -2 was susceptible. The segment of 6RL ^Ar with powdery mildew resistance was about 100 Mb. Deletion of the 6RL ^Ar telomeric region inhibited the pairing and recombination of T6BS.6RL ^Ar -4. Compared with T6BS.6RL ^Ar and T6BS.6RL ^Ar -4, T6BS.6RL ^Ar -2 showed a normal meiotic behavior. Immunolocalization using anti-ZYP1, anti-DMC1 and anti-MLH1 proteins indicated that more DSBs (DNA double-strand breaks) and crossovers formed on the 6RLL^Ar arm in T6BS.6RL ^Ar, and this might be related to the formation of anaphase I bridges of 6RL ^Ar. Although the 6RL ^Ar deletions were used to physically locate powdery mildew resistance gene(s), more accurate location through meiotic recombination was needed. The results in this study indicated that altering the structure of the 6RL ^Ar arm promoted normal meiotic behavior, and this might facilitate the localization of resistance genes through meiotic homologous recombination.

Fusarium graminearum is the causal agent of Gibberella ear rot (GER) in maize, a devastating fungal disease leading to yield reduction and contamination of grains with type B trichothecene mycotoxins (TCTB). Reducing GER damage requires the implementation of an integrated strategy in which the use of resistant maize genotypes is a key pillar. F. graminearum infects maize ears most often by the silk channel, which represents the first plant tissue encountered by the pathogen. The present study aimed at providing new phenotyping tools to improve breeding pipelines by investing the importance of maize silk composition in GER resistance. Here we used targeted and untargeted metabolomics approaches to characterize differences between genotypes reported as susceptible or tolerant to GER. Promising results were obtained with the LC-HRMS/MS analysis that led to outline $25m/z$ signals, among which 14 were assigned to a unique compound, that could distinguish tolerant and susceptible genotypes. We notably evidenced that a metabolite putatively identified as feruloyl-hexose could contribute to GER tolerance, while two others putatively identified compounds (chlorogenic acid and eupatilin) could be susceptibility-associated biomarkers. The present study paves the avenue for the use of new approaches based on silk composition to improve the breeding programs aiming at increasing maize resistance.

Stem strength is an important indicator of lodging that significantly influences yield and quality in soybean. Therefore, understanding the regulatory mechanisms underlying stem strength is critical for ensuring soybean production. However, the genetic basis underlying this trait remains largely elusive. Here, we explored the key loci and regulators of stem strength by integrating quantitative trait locus (QTL) mapping with genome-wide association study (GWAS) using the recombinant inbred line (RIL) population and natural accessions. Finally, a major QTL covering an interval containing 15 genes was identified. One of these genes encodes a transcription factor related to WUSCHEL-related homeobox 4 (GmWOX4-like), a high-confidence candidate for regulating stem strength based on bulk transcriptome deep sequencing and single-cell sequencing. Anatomical analysis of residual heterozygous lines (RHLs) suggested that GmWOX4-like may influence stem strength by modulating cambium differentiation through various pathways. Natural variations in the GmWOX4-like promoter region showed significant correlation with stem strength and lodging ratio across the natural population. These findings provide valuable insights into the molecular mechanisms of stem strength and will contribute to markerassisted selection for stem strength in soybean breeding.

Faba bean, with its high protein yield and low nitrogen inputs, is a promising crop, but it suffers from low yield stability due to poor heat and drought adaptation. To improve yield performance, faba beans can be produced as synthetic cultivars, where multiple lines are advanced through open pollination resulting in offsprings, which are a mixture of $F_1$-hybrids and self-pollinated offsprings. This leads to an enhanced performance due to per se performance of the components and heterotic effects of $F_1$-hybrids. While distinct genetic pools have shown high heterotic effects in hybrid breeding programs, they have not been systematically established in faba bean breeding. To promote establishment of heterotic pools, we employed a cost-effective chain-crossing scheme accompanied with only 58 genome-wide KASPmarkers and generated diverse genetically distinct pools within one generation. However, artificial crossing methods in faba bean result in low crossing efficiency and seed set. To overcome this, we introduced bumblebee-assisted intercrossing in greenhouse chambers, achieving an increased seed set and further enhancing genetic distance between gene pools. Genotyping was conducted with an Illumina 10 K SNP-chip, which enabled the identification of $F_1 × F_1$ double-cross combinations and $F_2$ self-pollinated offsprings from open pollinated offsprings with a custom pipeline. In contrast to standard crossing and recombinant inbred line (RIL) production in faba bean, which results in small families with limited recombination, the chain-crossing scheme and within-pool open pollination allows us to rapidly generate large and diverse base populations for future breeding, genetic studies and with that to increase genetic gain in faba bean.

Cadmium ($CD^{2+}$) exhibits pronounced phytotoxicity and poses significant risks to human health through bioaccumulation in agricultural products. This study investigates the mitigative effects of foliar-applied nano-molybdenum particles (MoNPs) on Cd accumulation and growth rates in rice (Oryza sativa). Our findings demonstrate that MoNPs application effectively alleviates Cd-induced root growth suppression and reduces Cd deposition in root cell walls, through MoNPs-mediated attenuation of Cd-induced elevation of pectin content. Through cross-sectional analysis combined with ROS-specific fluorescent probes revealed a spatial pattern of Cd-induced H₂O₂ accumulation, with strongest signals observed in the apoplastic regions of root elongation and maturation zones, with minimal accumulation in meristematic regions. This oxidative burst was significantly mitigated by MoNPs treatment, which enhanced plasma membrane (PM)-localized respiratory burst oxidase homolog (RBOH) activity via transcriptional upregulation of $OsRBOH$ genes. Furthermore, foliar MoNPs application activated the ascorbate-glutathione (ASAGSH) cycle through selective upregulation of OsAPXs and OsGRs, enhancing cellular capacity for $H_2 O_2$ detoxification. These coordinated mechanisms collectively suggest that MoNPs treatment offers dual protection against Cd toxicity by 1) reducing Cd bioavailability in plant tissues and 2) counteracting Cd induced oxidative damage, thereby effectively ameliorating root growth inhibition under Cd stress.

Alkaline stress in saline soil limits cotton production that may be improved by using emerging nanobiotechnology approaches. Here, we applied poly acrylic acid coated $Mn_3 O_4$ nanoparticles (PMO) on cotton leaves which showed higher chlorophyll content (up to 100.0%) and fresh weight (46.9%) and lower electrolyte leakage rate (up to 6.8%) and cell death rate (up to 84.8%) than controls. Further investigation showed that PMO can maintain reactive oxygen species (ROS) homeostasis, increase the stability of actin filament (AF), and reduce $Na^+$ content. Confocal imaging and ROS content measurement showed that PMO foliar application effectively alleviated ROS over-accumulation (up to 16.4% decrease for $H_2 O_2$ and 45.3% decrease for $O_2^{*-}$) in cotton leaves. Moreover, under alkaline stress, genes for AF depolymerization such as GhADF1/8 and GhADF6 and for AF polymerization such as GhADF5 were significantly down-regulated in PMO treated cotton lines relative to those in the control, consistent with the fluorescence intensities of AFs. Furthermore, our results showed that PMO mitigated $Na^+$ toxicity under alkaline stress, as indicated by the reduced $Na^+$ fluorescence intensity and $Na^+$ content. Furthermore, relative to those of the control, PMO treatment increased seed yield and lint yield by 65.0% and 66.3% respectively. Together, our work demonstrates that ROS scavenging PMO alleviated alkaline stress by stabilizing actin filaments and reducing Na^+toxicity.

Rhizosheath development benefits drought resistance in many upland crops. Although water-saving irrigation techniques induce rice rhizosheath formation, how and whether root hairs and different root types influence rice rhizosheath development and shoot water relations at seedling stage in drying soil are unclear. Wild-type (WT) seedlings with root hairs and its root hairless mutant rth2 were watered every 2 or 4 d, with root hair, whole root and shoot traits determined. Less frequent irrigation significantly increased rhizosheath of both genotypes by 14% during the seedling stage. Although root exudates from rth2 adhered 54% more soil than WT, facilitating rhizosheath development, root hairs and 25% greater lateral root proliferation of WT seedlings allowed 48% more rhizosheath especially in older seedlings. Greater root hair length, root hair length density and root hair number/root surface area on lateral than axial roots especially enhanced WT rhizosheath development. Soil water deficit increased root and leaf ABA concentrations especially in WT seedlings, causing stomatal closure that contributed to increased leaf water potential. In 36-d-old seedlings, 10% greater shoot biomass of WT plants than rth2 accompanied 15% higher root and 36% higher foliar ABA concentrations and ultimately lower stomatal conductance. Higher ABA concentrations of WT plants at the same soil moisture suggested root hairs may be important in mediating shoot water status of rice seedlings.

To study the relationship between rice leaf color change and grain filling, two indica-japonica hybrids with distinct leaf colors were grown under three N fertilizer dosages (LN, 0" " $kgha^(-1)$; MN, $150" " kgha^(-1)$; HN, $300" " kgha^(-1)$). The leaf color change features of flag leaf, 2nd leaf and 3rd leaf, as well as grain filling traits of superior and inferior grains were compared. Compared to cultivar CY167 (normal green leaves) under the same N level, cultivar CY927 (dark green leaves) exhibited delayed leaf color change onset time ($T_0$) by 0-3.6 d, reduced mean leaf color change rate ($R_m$) by 1.98%-9.45%, and increased leaf color index at maturity ($CI_f$) by 3.77%-53.48%. Additionally, CY927 prolonged the grain filling period ($D$) of inferior grains by $0.6-2.0d$, resulting in a yield increase of 8.13%-25.46%. N supply significantly increased rice yield, primarily by delaying $T_0$ and reducing $R_m$ of flag leaf, improving initial grain filling potential ($R_0$) and maximum grain weight (A), delaying the time to reach the maximum grain filling rate ($T_max$), and prolonging the grain filling activity period ($D$) of inferior grains. The time interval ($T_(L-G)$) between the $T_0$ of the flag leaf and $T_max$ of inferior grains was negatively correlated with yield ($-0.780,P<0.01$). Suggesting that rice yield can be improved by optimizing N fertilizer management to shorten the $T_(L-G)$. These findings provide valuable knowledge about the relationship between leaf senescence and grain filling, and benefit the understanding of the physiological mechanisms underlying high-yield rice production.

In the rice-rapeseed cropping system in the Yangtze River Basin, late rapeseed sowing increases lodging. To identify the mechanisms of reduced lodging resistance, a two-year field experiment compared four rapeseed cultivars with differing lodging resistances under normal and late sowing. Rapid stem elongation during bolting in late-sown rapeseed reduced stem plumpness, vascular bundle development, and lignin accumulation, weakening lodging resistance. Slowing stem elongation and promoting vascular bundle formation and lignin synthesis could increase lodging resistance in late-sown rapeseed.

Improving crop yield and N utilization while mitigating environmental pollution is a key goal in sustainable agriculture. Integrating green manure with reduced chemical N application is a promising strategy to enhance N utilization efficiency and minimize reactive N losses. However, the agronomic mechanisms through which green manure incorporation affects soil N retention and N loss under reduced N application remain unclear. This study aimed to uncover the compensatory mechanisms of green manure in improving wheat yield and N utilization under reduced N application, and to identify the principles behind reduced N loss in wheat fields. We conducted a split-plot experiment in the Hexi Oasis irrigation area of Northwest China from 2019 to 2024, using two cropping systems (W, fallow after wheat; W-G, green manure returning after wheat) combined with three N application levels (N1, local conventional N application rate; N₂, N-reduction 15%; N₃, N-reduction 30%). Our results demonstrated that green manure returning improved soil quality and compensated for the yield and N use efficiency losses caused by 15% chemical N reduction. Specifically, compared to the W-N₁, W-GN₂ increased soil organic matter content and soil water content by 6.5% and 9.4%, respectively, while reducing soil bulk density and pH by 8.9% and 6.7%. Meanwhile, W-GN₂ increased soil nitrate N and total N content in the 0-40cm soil layer by 8.4% and 8.7%, respectively. Moreover, W-GN₂ reduced NH₃ volatilization by 13.8%,N₂O emissions by 8.8%, and N leaching by 9.4%. It also enhanced microbial biomass N by 50.7%, urease activity by 10.2%, and decreased nitrate and nitrite reductase activities by 19.9% and 32.6%, respectively. Additionally, W-GN₂ improved soil bacterial α-diversity and increased the abundance of functional bacteria. Green manure can sustain wheat yield and improve N utilization efficiency under reduced chemical N input by improving the soil environment, enhancing soil N retention and minimizing N losses, which presents a sustainable, yield-stabilizing strategy for Oasis agroecosystems in northwestern China.

Rice productivity faces critical sustainability challenges from stagnating yields and inefficient fertilizer use, particularly in intensive agricultural regions like the Yangtze River Delta (YRD) of China. Controlled-release blended fertilizers (CRBF), which synchronize nutrient release with crop demand, represent a promising strategy to enhance rice productivity. Here, we conducted an eight-year (2017-2024) field study across 25 representative sites in the YRD to evaluate CRBF's effects, complemented by a regional extrapolation analysis. Our findings showed that, relative to conventional fertilization, CRBF increased rice yield by 4.9%, primarily by increasing the number of effective panicles (5%) and plant biomass (5.2% 11.3%). Notably, this yield benefit rose to 5.3% when CRBF was applied via deep placement, which was attributed to greater root biomass (13.1%-29.2%) and higher soil $NH_{4}^{+}-N$ availability (24.3%-43.6%), thereby enhancing N uptake. Furthermore, initial soil organic matter was identified as the predominant modulator of CRBF effectiveness. Regional extrapolation projected that applying CRBF could enhance rice yield by 4.0% across the YRD, with deep placement providing an additional 2.1% gain. In conclusion, our study demonstrates that adopting CRBF, particularly with deep placement, is a robust and effective strategy to sustainably boost rice productivity in intensive rice cultivation systems.

With the aim of maximizing nitrogen use efficiency (NUE) of wheat in the North China Plain by optimizing irrigation and nitrogen application, a field experiment with a split-plot design was conducted. The main plots were subjected to three irrigation levels: bringing soil water content in the 0-40cm profile to 65% (I₁), 75% (I₂) and 85% (I₃) of field water capacity. The subplots were subjected to three nitrogen application rates: 150 (N150), 210 (N210) and 270 (N270) kg N $ha^(-1)$. Compared with the N270, N210 treatment enhanced grain yield, NUE, and net income by 4.5%,6.2%, and 5.8%, respectively (two-year averages). Additionally, it reduced soil nitrate reductase activity, the abundance of denitrificationrelated bacteria, and loss rate of fertilizer nitrogen by 12.9%,53.3%, and 16.3%, respectively. Compared with the N150, N210 treatment increased grain yield, grain nitrogen accumulation, and net income by 15.9%,14.2%, and 26.3%. Relative to I₁ and I₃, I₂ treatment increased root length density in the 2060 cm soil layer, uptake rate of fertilizer nitrogen, grain yield, and net income. Overall, the combination of irrigation to 75% of field capacity with nitrogen application at 210 kg $Nhaa^(-1)$ increased wheat's capacity for nitrogen uptake and remobilization and thereby grain nitrogen accumulation, and increased NUE by reducing nitrogen loss rate.

Optimizing root system architecture (RSA) is essential for plants because of its critical role in acquiring water and nutrients from the soil. However, the subterranean nature of roots complicates the measurement of RSA traits. Recently developed rhizobox methods allow for the rapid acquisition of root images. Nevertheless, effective and precise approaches for extracting RSA features from these images remain underdeveloped. Deep learning (DL) technology can enhance image segmentation and facilitate RSA trait extraction. However, comprehensive pipelines that integrate DL technologies into image-based root phenotyping techniques are still scarce, hampering their implementation. To address this challenge, we present a reproducible pipeline (faCRSA) for automated RSA traits analysis, consisting of three modules: (1) the RSA traits extraction module functions to segment soil-root images and calculate RSA traits. A lightweight convolutional neural network (CNN) named RootSeg was proposed for efficient and accurate segmentation; (2) the data storage module, which stores image and text data from other modules; and (3) the web application module, which allows researchers to analyze data online in a user-friendly manner. The correlation coefficients ($R^2$) of total root length, root surface area, and root volume calculated from faCRSA and manually measured results were $0.96^(**)$, $0.97^(**)$, and $0.93^(**)$, respectively, with root mean square errors (RMSE) of 0.05cm³, and, processed at a rate of 9.74 s per image, indicating satisfying accuracy. faCRSA has also demonstrated satisfactory performance in dynamically monitoring root system changes under various stress conditions, such as drought or waterlogging. The detailed code and deployable package of faCRSA are provided for researchers with the potential to replace manual and semi-automated methods.

For fast in-situ assessment of tiller phenotypes in rice breeding, we introduce the TillerPET model, an improved transformer-based deep learning solution that permits phenotyping the number and compactness of rice tillers in images of post-harvest rice stubble. A rice tiller phenotype dataset covering three years of field data and four experimental sites across China was constructed to train and validate the model. TillerPET reports an $R^2$ of 0.941 for counting tiller number, demonstrating state-of-the-art performance on the proposed RTP dataset. Beyond its minimal errors in estimating tiller number, TillerPET also achieves an $R^2$ of 0.978 for characterizing tiller compactness. The two phenotypic parameters exhibit a high degree of consistency with expert breeders, offering reliable phenotypic indicators to guide further breeding.

Staple crops are the cornerstone of the food supply but are frequently threatened by plant diseases. Effective disease management, including disease identification and severity assessment, helps to better address these challenges. Currently, methods for disease severity assessment typically rely on calculating the area proportion of disease segmentation regions or using classification networks for severity assessment. However, these methods require large amounts of labeled data and fail to quantify lesion proportions when using classification networks, leading to inaccurate evaluations. To address these issues, we propose an automated framework for disease severity assessment that combines multi-task learning and knowledge-driven large-model segmentation techniques. This framework includes an image information processor, a lesion and leaf segmentation module, and a disease severity assessment module. First, the image information processor utilizes a multi-task learning strategy to analyze input images comprehensively, ensuring a deep understanding of disease characteristics. Second, the lesion and leaf segmentation module employ prompt-driven large-model technology to accurately segment diseased areas and entire leaves, providing detailed visual analysis. Finally, the disease severity assessment module objectively evaluates the severity of the disease based on professional grading standards by calculating lesion area proportions. Additionally, we have developed a comprehensive database of diseased leaf images from major crops, including several task-specific datasets. Experimental results demonstrate that our framework can accurately identify and assess the types and severity of crop diseases, even without extensive labeled data. Codes and data are available at http://dkp-ads.samlab.cn/.

Northern wild rice (NWR; Zizania palustris L.), an annual aquatic plant in the Poaceae family, has high economic importance due to its nutrient-rich grains. However, the existing NWR genome assembly for this species has severe fragmentation and incomplete gene representation. A near-complete genome was assembled in this study to provide a high-quality genomic reference for NWR-associated research. The assembled genome exhibited a total contig length of 1.41 Gb and a contig N 50 of 109.22 Mb. Overall, a 73.60% repetitive sequence content was identified and 47,804 genes predicted. Phylogenetic analysis indicated that Z. palustris was most closely related to Zizania latifolia, with an estimated divergence time of 4.57-8.15 Mya. Meanwhile, Z. palustris underwent a recent, species-specific long terminal repeat (LTR) expansion, associated with its larger genome size. We identified two genomic blocks in the Z. palustris and Z. latifolia genomes that exhibit strong synteny with the rice phytocassane biosynthetic gene cluster. The centromeric satellite repeats in Z. palustris identified in this study primarily comprised a 145 bp repetitive unit. The findings also revealed centromere homogenisation and rearrangement accompanied by LTR invasion in NWR. Among the genes missing in the previous NWR genome, we observed LTR insertion events that resulted in expanded gene lengths in our updated NWR genome. The present updated NWR genome provides a valuable resource for crop genetic improvement, functional gene discovery, and research on critical biological processes.

Sclerotinia sclerotiorum, a fungus that causes a devastating fungal disease of rapeseed (Brassica napus), causes significant yield losses globally. Carbon dots (CDs), a class of carbon-based nanomaterials, have emerged as promising agents for plant disease management owing to low toxicity and biocompatibility. This study demonstrates the antifungal potential of Salvia miltiorrhiza-derived CDs in enhancing resistance to S. sclerotiorum in rapeseed. In vitro assays revealed concentration-dependent suppression of fungal growth by CDs. In planta applications triggered multifaceted defense responses evidenced by: (1) increased glucosinolate accumulation and redox homeostasis through ROS modulation and elevated superoxide dismutase/catalase activities; (2) transcriptional activation of ROS-scavenging systems and biosynthesis pathways for defensive metabolites (flavonoids and phenylpropanes); and (3) restoration of pathogen-impaired physiological processes, including photosynthetic recovery via Calvin cycle reactivation, energy metabolism through TCA cycle enhancement, and stress-responsive hormone signaling. Integrated multi-omics analyses further indicated that CDs establish a coordinated defense network by simultaneously optimizing metabolic homeostasis and amplifying disease resistance mechanisms. These findings position CDs as a novel eco-friendly strategy for biotic stress management, providing a sustainable approach to mitigate crop losses caused by fungal pathogens.

With the aim of adapting agricultural practices to climate warming, this study projected sowing dates for summer maize in the 2030s (2031-2040) across the Huanghuaihai Plain by analyzing key photo-thermal variables derived from field experiments and projected future climate data under Shared Socioeconomic Pathway 2-4.5 within a restricted planting season. Results showed that growing degree days (GDD) during the active dry matter accumulation period (AP), killing degree days (KDD) during AP, and GDD during the late dry matter accumulation period (LP) explained most yield variation and were used for determining suitable sowing windows. Thresholds of them were 571 ∘Cd, 21∘Cd and 411∘Cd, respectively. In the 2030s, postponing sowing dates and shifting planting regions northward resulted in gradual declines in KDD during AP and GDD during LP. The proportion of regions limited by KDD and GDD changed from 66% to 0% and from 3% to 100% when sowing dates were postponed from June 1 to July 15. Suitable sowing dates for maize were determined as follows: June 25 to July 10 in regions south of 34∘N, June 5 to June 30 between 34∘N and 39∘N, and before June 20 in regions north of 39∘N.