The breakthrough in super hybrid rice yield has significantly contributed to China's and global food security. However, the inherent conflict between high productivity and environmentally sustainable agriculture poses substantial challenges. Issues such as water scarcity, energy crises, escalating greenhouse gas emissions, and diminishing farm profitability threaten longterm agricultural sustainability. In response, we applied a holistic food-carbon-nitrogen-water-energy-profit (FCNWEP) nexus framework to comprehensively assess the sustainability of distinct crop management strategies across three sub-sites in Central China. Field experiments were conducted in Hubei and Hunan provinces from 2017 to 2021 using a widely adopted elite super hybrid rice cultivar (Y-liangyou 900). Four crop management treatments were implemented: a control (CK, 0 kg N ha-1), conventional crop management (CCM, 210-250 kg N ha-1, 7:3 basal:mid-tiller fertilizer ratio), and two integrated crop management (ICM) treatments (ICM1, 180-210 kg N ha-1, 5:2:3 basal:mid-tiller:panicle initiation fertilizer ratio; ICM2, 240-270 kg N ha-1, 5:2:2:1 basal:mid-tiller:panicle initiation:flowering fertilizer ratio). Variables assessed included grain yield, carbon footprint, nitrogen footprint, water footprint, energy footprint, nitrogen use efficiency, and economic benefits. Our results showed significant yield variations, with ICM2 consistently outperforming CCM and ICM1 across all three sites. In Jingzhou, Suizhou, and Changsha, ICM2's grain yield was 30.2, 24.7, and 13.3% higher than CCM, respectively. Net profits under ICM2 exceeded those of CCM and ICM1 by 31.8 and 115.2% in Jingzhou, 32.2 and 109.9% in Suizhou, and 15.4 and 34.0% in Changsha, respectively. Integrated crop management, particularly ICM2, demonstrated improved nitrogen and energy use efficiency, leading to reduced carbon, nitrogen, water, and energy footprints. Overall, composite sustainability scores derived from the FCNWEP framework indicated that both ICM2 and ICM1 exhibited higher sustainability levels compared to CCM. This study provides valuable insights into practical management methodologies and offers recommendations for enhancing agricultural sustainability.

Plant viruses cause substantial yield and quality losses worldwide, and their rapid evolution can erode deployed host resistance. This review synthesizes current knowledge of antiviral resistance and tolerance mechanisms, using barley yellow dwarf virus (BYDV) in cereals as an illustrative case study. We first summarize key layers of plant antiviral immunity, including pre-formed physical and chemical barriers, dominant and recessive resistance genes, RNA silencing, hormone-regulated defense signaling, and degradation pathways such as the ubiquitin-proteasome system and selective autophagy. We then discuss how these mechanisms are exploited in breeding and biotechnology, covering conventional introgression, marker-assisted selection, QTL mapping and pyramiding, induced variation (mutation breeding and TILLING/ecoTILLING), transgenic strategies (pathogen-derived resistance and plantibodies), RNA interference-based approaches, and CRISPR-enabled editing of susceptibility factors. Finally, we highlight emerging nano-enabled tools and propose integrated strategies that combine genetic resistance with surveillance and vector management to improve durability under climate change and ongoing viral diversification.

Aluminium toxicity in acid soils is a major constraint to global crop production, particularly for cereal crops like barley, which are vital to food security. Although the HvAACT1 gene within the Alp QTL has been recognized as a key factor in aluminium tolerance through citrate secretion, its direct impact on barley yield under dynamic, real-world acidic conditions remains poorly understood. Most existing studies have focused on fixed pH levels, limiting insights into crop performance across the broader pH spectrum typical of acidic field conditions. In this study, we evaluated barley yield and agronomic traits across eight soil pH levels (4.0-4.8), using two near-isogenic lines (NILs): RGT Planet (acid soil susceptible) and P33-1 (acid soil tolerant, introgressed with Alp). Our results demonstrate that P33-1 consistently outperformed RGT Planet, maintaining higher yield and better agronomic traits. Notably, yield reductions under acidic conditions were primarily driven by decreases in fertile tiller number and kernels per spike (P < 0.01), rather than changes in grain size or 1000-kernel weight, providing new insights into the physiological basis underpinning yield loss. By quantifying the complex relationship between soil pH and agronomic trait losses, our study delivers essential data that will inform crop modeling and advance breeding efforts for acid soil-tolerant varieties, contributing to more resilient and sustainable crop production in marginal soils worldwide.

Salinity stress has become an increasingly critical challenge for agricultural production, especially for rice, a staple crop that feeds over 50% of the world population but is extremely sensitive to salt stress. In this study, ten rice genotypes were treated with three salinity levels (0, 50, and 100 mM NaCl) to investigate the effects of salt stress on rice, and this data was then used to build regression models that describe plant growth responses as a function of stomatal conductance (Gs), chlorophyll content (SPAD), and shoot K+ and Na+ contents—parameters that can be used for high-throughput screening of rice plants for salinity stress tolerance. In silico modeling results showed that the best model for predicting shoot dry weight (SDW) was based on Gs, SPAD, and shoot K+ content, while shoot Na+ content had no significant influence on biomass accumulation. These findings challenge the traditional focus on Na+ exclusion from the shoot as a breeding target and suggest that enhancing K+ retention and optimizing stomatal development and operation may be a more effective strategy for improving rice growth under salinity. Overall, this study highlights the need to reconsider key genetic targets involved in the regulation of Gs, K+ homeostasis, and chlorophyll maintenance to better face the challenges caused by salinity in future climate scenarios.

Abiotic stresses such as heat waves significantly reduce wheat productivity by altering leaf anatomy and physiology, leading to reduced photosynthetic carbon assimilation and crop yield. Despite the advancement in various imaging technologies at the field, canopy, plant, tissue, cellular, and subcellular levels, phenotyping of imaging-based leaf structural traits (e.g. vein density, stomatal density, and stomatal aperture) for abiotic stresses is still time-consuming and expensive without the aid of artificial intelligence (AI) and machine learning (ML). This review consolidates current knowledge of wheat leaf structural and functional adaptations to heat stress and highlights key advancements in imaging technologies for studying these important phenotypic traits. Recent high-resolution, non-destructive imaging technologies, including confocal laser scanning microscopy, X-ray computed tomography, and optical coherence tomography, have enabled in vivo visualization of plants. Integrating these imaging techniques with AI/ML facilitates high-throughput phenotyping and the modelling of stress responses. We emphasize the potential for future research to leverage these technological advancements in imaging and AI, combining imaging data with physiological and multi-omics studies to deepen the understanding of plant heat tolerance mechanisms. Such multidisciplinary integration in leaf structure phenotyping will accelerate the development of resilient wheat varieties, offering critical insights for crop improvement in the face of climate change.

Climate change-driven heat and drought stresses during reproductive stages significantly threaten wheat productivity. To investigate the genetic and physiological basis of combined heat-drought (HD) tolerance, we evaluated 345 wheat genotypes under three environments of HD stresses, non-stress glasshouse conditions and a late-sowing field trial. HD stresses caused significant reductions in chlorophyll content, flag leaf area, biomass, seed-setting rate and grain weight-related traits. Notably, HD-tolerant lines maintained higher grain weight, grain number and chlorophyll retention, with less than half the reductions observed in sensitive genotypes. A genome-wide association study using a 40K single-nucleotide polymorphism (SNP) array identified 124 candidate SNPs (cSNPs) associated with 51 traits across three environments with 78 cSNPs associated with HD tolerance. In total, 24 cSNP blocks exhibited pleiotropic associations with multiple traits under those three environments. Tight genomic co-localisations were detected between chlorophyll content (SPAD or CCM200 values), flag leaf width, seed-setting rate and grain yield components (thousand grain weight, grain number per spike), with superior haplotypes identified, supporting their utility in selections. Stay-green traits appeared to contribute significantly to yield stability under HD stresses. Those results provide valuable genomic and physiological insights into wheat HD tolerance for future targeted wheat breeding.

Winter wheat (Triticum aestivum L.) productivity in intensive rice–wheat systems of the Jianghan Plain is constrained by sub-optimal nitrogen (N) management and residue handling. Straw residue return (SRR) can increase soil organic carbon and improve soil structure but may also immobilize N and alter the temporal pattern of soil mineral N (SMN). Although straw return and N fertilization have been widely studied, the combined effects on SRR and N applications on wheat yield and soil N dynamics in this region remain insufficiently resolved. In this study, we evaluated three SRR levels (0, 50, and 100% of approximately 3.5 t rice straw ha−1) combined with four N application treatments over three years of field trials in the Jianghan Plain of Yangtze River Basin. Treatments were arranged in a randomized complete block design. Our results show that wheat performance is closely associated with SMN (NO3−-N, NH4+-N, total N) at 0–20 soil layers from booting to maturity. Grain yield increased sharply with N application, with SRR further enhancing yield. The combination of a 100% SRR and 70/30 basal-to-overwinter N split with a total N rate of 180 kg ha−1 (T11) achieved the highest three-year mean grain yield. This superior performance was driven by optimized yield components, including a maximum of 55 grains per spike and a 1000-grain weight of 42.4 g under T11. Soil total N, nitrate-N, ammonium-N, and SOC were all significantly influenced by both N application timing and SRR. Across the three-year experiment, we concluded that 50–100% SRR combined with 70–100% basal N application represents an optimal agronomic practice for rice–wheat rotations in the Jianghan Plain.

Salt stress disrupts ion homeostasis, leading to toxic sodium accumulation and reduced potassium uptake. The Calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) network plays pivotal roles in response to abiotic stresses. Here, the root preferentially expressed OsCIPK7 with significantly salt-induced transcription was identified and functional characterized. Knockout of OsCIPK7 increased sensitivity to salt stress and a pronounced reduction of potassium content in their tissues under salt stress was observed compared to wild type. Decreased allocation of potassium was observed in the root and the youngest leaf of the knockout seedlings, accompanied by an increased distribution in older leaves relative to the wild type. However, the disruption of OsCIPK7 hardly affected the accumulation and the distribution of sodium across different organs. Notably, these phenotypic differences were completely mitigated by the addition of tetraethylammonium chloride, a non-specific inhibitor of potassium channels. Transcriptomic profiling revealed that OsCIPK7 modulates differentially expressed genes involved in ion transport, redox homeostasis, cell wall integrity and hormonal signaling. Collectively, we propose that OsCIPK7 function as a potentially salt-induced calcium-signaling component essential for maintaining sodium/potassium homeostasis and supporting certain physiological response. These findings underscore the potential for enhancing salt tolerance through precise manipulation of OsCIPK7 in plants.

Oryza coarctata is the only halophytic relative in the genus Oryza (Oryza sp.) that is tolerant to high salinity levels lethal to cultivated rice varieties. An excessive accumulation of reactive oxygen species (ROS) caused by salinity leads to oxidative stress, although certain ROS also play important signaling roles. This work investigated differences in root redox and ionic homeostasis between cultivated (O. sativa) and wild (O. coarctata) rice species. Root treatment with 10mM H2O2 decreased cell viability in cultivated but not wild rice, and histochemical staining showed greater H2O2 accumulation in wild rice roots under non-saline conditions, suggesting a signaling role. Wild rice showed higher superoxide dismutase (SOD) activity that lowers superoxide (O2-) accumulation. Cultivated rice showed greater K+ loss from the root mature zone through ROS-activated cation channels accompanied by stronger Ca2+ uptake in response to H2O2 application, while wild rice possessed better Ca2+ homeostasis with less H2O2-induced K+ leakage. Cultivated rice also demonstrated much higher sensitivity to hydroxyl radicals (●OH). Wild rice effectively controlled cytosolic Ca2+ homeostasis by Ca2+ efflux systems such as Ca2+-ATPase and CAX, while cultivated rice downregulated RBOH expression that may affect operation of the “ROS-Ca2+ hub” and signaling cascades under salinity.

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 lmol 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 lmol 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. (c) 2026 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NCND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Phosphorus (P) deficiency is one of the most widespread constraints on global crop productivity. Root hairs are widely regarded as a pivotal tissue for P acquisition, yet their quantitative contribution to P uptake and subsequent plant performance remains unclear. We examined 12 cultivated and 12 wild barley genotypes, classified as tolerant or sensitive to low P based on relative total biomass, and quantified root hair number and length in relation to plant performance. While P deficiency generally stimulated root hair proliferation, contrasting strategies emerged: tolerant genotypes have maintained growth and P status with minimal changes in root hair traits, whereas sensitive genotypes depended strongly on root hair proliferation and elongation, which correlated positively with root and shoot biomass as well as shoot P status. In tolerant genotypes, negative correlations between shoot performance and root hair traits indicated that enhanced root hair development often represents a compensatory response or even a trade-off, where carbon allocation to epidermal traits does not yield proportional benefits. These results suggest that metabolically inexpensive traits aid stress adaptation in sensitive backgrounds. Crucially, root hair traits are not a reliable proxy for P efficiency, as their functional value varies across genetic backgrounds. Our findings challenge the prevailing view that longer or denser root hairs universally improve P uptake and call for a reappraisal of how visible morphological responses are interpreted. These insights emphasize that breeders should integrate root hair plasticity into broader root system ideotypes, rather than targeting it in isolation, to enhance P efficiency in cereal crops.

Wheat is a major staple food in the human diet, but its production under current climate scenarios is problematic given the predicted extent of land salinization and the fact that wheat is highly sensitive to soil salinity. This work aims to critically assess previous breeding efforts and the pros and cons of targeting Salt Overly Sensitive 1 (SOS1) and High-affinity K+  Transporter 1 (HKT1) genes to improve salinity stress tolerance in wheat. We argue that overexpressing SOS1 genes encoding Na+/H+ exchangers for Na+ removal from root to the rhizosphere may come with the caveat of increased loading of Na+ into the xylem and its delivery to the shoot, as well as numerous pleiotropic effects. Similarly, targeting HKT1 transporters for removing Na+ from the shoot comes with significant yield penalties due to the high carbon cost of osmotic adjustment; this strategy is also limited by the relatively small capacity of the root to store excessive Na+ without experiencing toxicity symptoms. We suggest that targeting tissue tolerance traits such as K+ retention in mesophyll and vacuolar Na+ sequestration in the shoot will be able to deliver better outcomes. We also call for a better understanding of the structure-function relationships of various isoforms of key proteins involved in maintenance of Na+ and K+ homeostasis and a need for more in-depth physiological studies of wheat species with the DD genome, a key contributor to tissue tolerance traits. Our arguments are supported by a bioinformatic analysis of the number of orthologs for some key genes between hexaploid (AABBDD) and tetraploid (AABB) wheats and their structural differences.

Waterlogging and salinity stresses significantly affect crop productivity and often coincide in nature. While adaptive responses to each of the individual stresses have been studied in detail, the traits conferring tolerance to combined stresses (and thus the most appropriate targets for breeding) remain poorly understood. In the present work, we studied the morphological and ionic responses of 11 barley varieties contrasting in salinity (NaCl) stress tolerance under waterlogging (WL) and combined waterlogging and salinity (WL + NaCl) stresses. Stress damage responses were much higher in plants under combined WL + NaCl stress than those under either stress alone. The adverse effect of combined stress was much greater in salt-sensitive varieties than in more tolerant varieties. As shown by PCA analysis, growth traits such as shoot and root biomass, number and length of adventitious roots, and K+ concentration contributed strongly to PC1. Under NaCl stress, PC1 (47%) and PC2 (24.2%) accounted for 71.2% of the variance, with growth-related traits strongly correlated with PC1, while Na+ concentration and salt damage index contributed positively to PC2. A significant negative correlation (r = -0.86 and -0.96, respectively) was found between aerenchyma score and salt damage index under WL and combined stress, respectively. Overall, PCA, membership function value analysis, and correlation matrix analysis consistently identified the number of adventitious roots, percentage formation of aerenchyma, and shoot K+ content as the traits most strongly associated with the stress damage index, highlighting their suitability as key phenotyping proxies for selection in breeding programmes.

Wheat is a major staple crop for over one-third of the world's population, crucial for global food security, economic stability and cultural traditions. Recently, single-cell and spatial omics approaches have transformed biological discovery, primarily in medical and animal sciences, and they are now beginning to be applied in plant research. Here we summarize the technical innovations and feasibility of spatial omics applications in wheat research, particularly for understanding developmental and environmental responses, thereby potentially enhancing wheat breeding. We highlight how these tools can reveal spatial and temporal patterns in gene expression, cellular heterogeneity and tissue organization in wheat. Furthermore, we propose developing a spatially resolved single-cell atlas of wheat across its life cycle to facilitate breakthroughs in basic research and potential applications in breeding. To achieve these goals, we advocate for a Wheat Spatial Omics Consortium to foster worldwide collaboration for overcoming barriers and developing sustainable and climate-resilient wheat.

Heat stress during the reproductive stage significantly reduces wheat (Triticum aestivum L.) productivity, primarily by impairing pollen viability and grain filling rate. This study employed genome-wide association study (GWAS) using 5,171 high-quality single nucleotide polymorphisms (SNPs) across 319 diverse wheat lines to identify genomic regions associated with pollen viability and spikelet fertility under reproductive-stage heat stress. Pollen viability was assessed from field-grown plants subjected to high temperature in a controlled setup using a thermal cycler. Spikelet fertility was evaluated in two years with heat treatment applied at the four different ear emergence stages. The wheat population showed significant genotypic and phenotypic variation. Chinese landraces formed a distinct cluster from other groups and generally exhibited lower pollen viability and spikelet fertility compared to Chinese commercial varieties. Pollen viability score exhibited moderate correlation with spikelet fertility after two weeks’ heat treatment at early-ear emergence stage. GWAS identified 15 significant SNPs associated with these two traits. Notably, AVRIG15341 on chromosome 1B and AVRIG21657 on chromosome 3A explained 20.31

Heat stress accelerates leaf senescence, reduces photosynthetic efficiency, and limits the translocation of photosynthates to developing reproductive organs, thereby posing a major constraint to wheat production. The ability of plants to remain stay-green with sustained photosynthesis ability is considered an important adaptive mechanism. This two-year study aimed to determine the genomic regions associated with stay-green trait in a panel of 319 diverse natural wheat lines using a simple visual phenotyping method based on leaf greenness after heat stress. The method clearly captured the variation among genotypes, with lower mean stay-green scores in Australian and Chinese landraces and improved stay-green scores in modern wheat varieties. Stay-green scores exhibited moderate but significant correlation with both pollen viability scores (r=37**) and seed weight per spike (r=0.57**), indicating its role in reproductive success under heat stress. Genome-wide association study revealed two marker-trait associations, AVRIG14898 on chromosome 1A and IWA7725 on chromosome 6B, which explained 12.55% and 6.61% of phenotypic variation, respectively. Wheat lines carrying favorable allele combinations exhibited enhanced stay-green performance under heat stress conditions. Several candidate genes located near significant SNPs are associated with stress responses, hormone signaling, protein degradation, membrane transport and enzymatic activity. In-silico expression of two candidate genes showed higher expression during booting and grain-filling stage under stress conditions, suggesting their roles in stay-green regulations. Overall, this study demonstrated the usefulness of the simple method for stay-green phenotyping, provided insights into the genetic architecture of the stay-green trait, identified potential candidate genes, and offered genetic resources for breeding stay-green and high-yielding wheat varieties under the future climatic conditions.

Abiotic stress tolerance has been significantly weakened in modern crops during the domestication process. Regaining tolerance has become a critical task in light of current climate trends and their impact on global food security. Abiotic stress tolerance is an extremely complex trait and is conferred at various levels of plant functional organization and developmental stages, with regulatory mechanisms operating across multiple scales, from individual cells to tissues and the entire plant. The emergence of advanced molecular tools such as single-cell RNA sequencing and spatial omics technologies has revolutionized the field, advancing our understanding of plant responses to hostile environments. However, the implementation of this knowledge in crop breeding programmes is handicapped by the lack of appropriate phenotyping platforms. Here, we argue that current phenotyping methods may be excellent tools for functional validation of previously discovered traits but have limited predictive value in stress biology. We also propose that bridging the mismatch between omics technologies and phenotyping is the only way to account for cell-specific operation of key genes conferring stress tolerance and implementing them in breeding programmes. Some practical examples using cell-based phenotyping tools such as fluorescence dyes or electrophysiological methods are given, and current limitations and prospects of cell-based phenotyping are discussed.

Genomic selection (GS) can accelerate crop breeding and enhance selection efficiency. However, accurately predicting genomic estimated breeding values (GEBVs) for complex traits and applying GS in diverse environments remains challenging. To address these issues, we developed a novel hybrid method capable of modelling gene-gene and gene-environment interactions. This method offers precise predictions of phenotypic performance for complex traits, identifies haplotypes associated with desirable phenotypes, and enables prediction of optimal haplotypes tailored to specific environments. We evaluated the approach using a dataset of 855 barley lines, with phenotypic data for grain yield and flowering time collected across multiple environments. The model incorporated 30,543 SNPs, nine soil parameters, and six daily environmental variables, achieving high prediction accuracies, with correlation coefficients of 0.93 for flowering time and 0.82 for grain yield. Our method identified 10 haplotype blocks significantly associated with flowering time and 13 blocks with grain yield, collectively accounting for over 90% of the total genetic variance. Additionally, we predicted the phenotypic effects of each haplotype and identified elite varieties carrying the most favourable haplotypes for crossing design and selection. The method also allows prediction of untested genotype × environment combinations, enabling selection of optimal genotypes for targeted environments. To facilitate its application, we developed a web-based interface (accessible at [https://penghaowang.shinyapps.io/shinygui/]), which enables breeders to identify optimal haplotypes and the varieties that carry them, streamlining the process of haplotype-based, environment-informed breeding. We note that the reverse prediction framework is currently applied on a single-trait basis and does not resolve multi-trait trade-offs such as between flowering time and yield, which remains a topic for future extensions.

Phosphorus (P) deficiency constrains cereal production, yet improving low-P performance remains challenging because P efficiency depends on rhizosphere mobilisation and internal utilisation. Wild relatives may provide insights into traits weakened during domestication. Here, we compared cultivated barley (Hordeum vulgare; CB) and wild barley (H. spontaneum; WB) to identify traits underpinning low-P tolerance. Twenty barley genotypes (10 CB and 10 WB) were grown under low (P5) and moderate (P20) P supply, and twelve low-P response physiological traits were integrated into a composite tolerance index (D-value) to assess the multidimensional basis of low-P tolerance. Under both P5 and P20, WB showed consistently higher physiological P-use efficiency (PPUE) than CB, while root morphological traits were broadly similar between CB and WB. This decoupling of biomass production from tissue P status indicates more efficient internal utilisation of absorbed P in WB. Under P5, the amount of rhizosheath citrate per plant was strongly stimulated and showed a pronounced species effect with WB exhibiting significantly higher rhizosheath citrate than CB. By contrast, increasing P supply shifted carboxylate composition towards malate dominance (85% at P20). The D value showed strong and consistent associations with key growth, PPUE, root morphology and rhizosphere functional traits in both CB and WB, validating its effectiveness as an integrative metric of low-P tolerance. Overall, WB's superior low-P performance is primarily driven by higher PPUE and elevated citrate exudation under acute P limitation, highlighting the value of targeting internal P utilisation and rhizosphere mobilisation efficiency to improve P-use efficiency in barley.