The United Nations Sustainable Development Goal (SDG) 2 aims to achieve Zero Hunger by 2030. However, global hunger and food insecurity have continued to rise at an alarming rate (UN 2023). Subtropical regions are home to more than 30% of the world’s population, predominantly in developing countries where per capita farmland and food supply are only 40% of those in developed nations (FAO 2018). Meeting the Zero Hunger target amid ongoing population growth in these regions requires a substantial increase in agricultural production while minimizing soil degradation and adverse ecological impacts. This challenge is shared by many countries across South Asia, Africa, and Central and South America.
Against this background, the 4th International Symposium on Sustainable Agriculture for Subtropical Regions (ISSASR-4) was held from June 21 to 24, 2024, in Changsha, China, hosted by the Institute of Subtropical Agriculture, Chinese Academy of Sciences. The symposium brought together over 300 experts and scholars from nearly 30 countries. Under the theme “Ecosystem Management and Agricultural Green Development in Subtropical Regions”, discussions focused on four key topics: (i) regional resources and ecosystem management for enhancing agricultural productivity, (ii) green crop and animal production, (iii) minimizing adverse environmental impacts of agricultural production, and (iv) the growing role of big data, artificial intelligence(AI), and smart farming. Participants exchanged the latest research advances, identified major challenges, and explored countermeasures for agriculture and ecological sustainability in subtropical regions worldwide.
This Special Focus of the JournalofIntegrativeAgriculture(JIA) addresses these pressing issues by presenting empirical evidence and innovative solutions for agricultural green development. It comprises 13 papers covering a wide range of topics related to carbon, nitrogen, and phosphorus pathways in natural and agricultural ecosystems, with attention to microbial processes, land-use change, production management, and their effects on nutrient cycling and grain yield. We hope this collection enhances understanding of ecosystem management and green agricultural development, offering actionable insights for policymakers, researchers, and practitioners.
Section 1: Regional resources and ecosystem management
This section examines three key areas: agricultural bio-resources, soil carbon and nutrient dynamics across ecosystems, and regional grain supply–demand matching. Studies provide insights into bioinput-based agricultural frameworks, soil nutrient responses to climate change and anthropogenic influences, and the dynamic, heterogeneous patterns of grain matching. Vermelho etal.(2026) reviewed microbial bioinputs, outlining their categories, mechanisms, global challenges, and Brazil’s production infrastructure and regulatory context. Wang M M etal.(2026) reported moderate spatial variation with positive autocorrelation in soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), and total potassium (TK), noting greater vulnerability to phosphorus and potassium limitation than to nitrogen, with soil properties outweighing spatial or environmental factors in explaining nutrient variation. Another study by Wang L Y etal.(2026) identified climate and hydrological changes as key drivers of SOC loss in Dongting Lake, with accelerated loss occurring above 21.4 m elevation, suggestingthatmanaged water levels during droughts could enhance carbon sequestration. Wan etal.(2026) showed that plantations can mitigate climate change by increasing carbon storage at the aggregate scale in alpine regions. Miao etal.(2026) demonstrated a scale-dependent mismatch in grain supply and demand, highlighting how interregional flows from 1980 to 2020 reduced deficit areas. Together, these studies advance frameworks for sustainable ecosystem management.
Section 2: Green crop production in subtropical regions
Enhancing green crop production in subtropical regions requires practices that improve soil health and carbon sequestration while sustaining yields. Given the vulnerability of subtropical croplands, effective strategies for maintaining SOC are critical. Hua etal.(2026) found that long-term livestock manure substitution improves soil aggregate stability and reduces water erosion but increases lateral loss of labile organic carbon, revealing a trade-off. Kautsar etal.(2026) reported that terrace reconstruction altered rice yields between field sides and modified SOC, TN, and decomposition dynamics in the 15–30 cm layer, with subsoil fertility determining productivity. Wang J etal.(2026) demonstrated that massive granulated straw incorporation boosts SOC and crop yield in infertile soils, with accumulation efficiency ranging from 30.8 to 60.0%, primarily from plant residues. These studies highlight practical pathways for sustainable soil management.
Section 3: Environmental impacts of agricultural production
Assessing and mitigating agriculture’s environmental footprint requires a multiscale understanding of soil ecological processes. Pan etal.(2026) found that natural restoration enhances karst soil phosphorus-cycle multifunctionality more than artificial restoration or cropping, driven by increased SOC and bacterial network complexity, with rare phoD-harboring taxa playing a critical role. Wang Y etal.(2026) reported that niche outweighs genotype in shaping pea fungal communities, with β-diversity driven by species replacement and deterministic assembly in niche-based groups. Zhu etal.(2026) showed that SOC is higher in brown and yellow-brown soils and that spring irrigation significantly increases farmland SOC, supporting carbon sequestration. Zheng etal.(2026) demonstrated that spatial factors govern carbon-cycling gene abundances in uplands, while biotic and substrate factors dominate in paddy soils, revealing an integrated “microbial carbon pump” in trace-gas cycling at a continental scale. Collectively, these studies advance understanding of the mechanisms underlying soil functionality and greenhouse gas modulation.
Section 4: Big data, artificial intelligence and smart farming in agriculture
The integration of big data, AI, and smart technologies is pivotal for the digital transformation of agriculture. This section presents a study on their practical application to environmental challenges. Wang M H etal.(2026) developed an Android-based decision support system (CNPDSS) to control non-point source nitrogen (N) and phosphorus (P) pollution. Integrating GIS, a Bayesian predictive model, an optimization algorithm, and a smartphone interface, the system identified solutions that minimize both pollutant loadings and engineering costs in the Tuojia catchment, China. Its adaptive design demonstrates potential for broader application, offering a scalable tool for sustainable water quality management.
This Special Focus underscores the critical intersection of ecosystem management and agricultural development in subtropical regions. Through 13 studies organized across four themes-resource management, green production, environmental impact mitigation, and smart technology-the collection provides a science-based framework for enhancing productivity while preserving ecological integrity. It offers concrete insights for achieving sustainable food systems and advancing the UN Zero Hunger goal in some of the world’s most vulnerable and vital agricultural landscapes.

Brazil maintains a leading position in agricultural exports and stands as the world’s foremost producer and user of bioinputs in agriculture. These bioinputs generate annual savings of billions of dollars that would otherwise be allocated to chemical fertilizers and pesticides. The nation’s regulatory framework enables bioinput agriculture and serves as a model for countries transitioning toward regenerative agriculture. Brazilian legislationcategorizes bioinputs into: 1) biofertilizers (extracts); 2) biostimulants (plant growth-promoting and biocontrol agents); and 3)inoculants (active ingredient comprises one or more living microorganisms). The inoculation of soybeans with Bradyrhizobiumstrains provides approximately 90% of the nitrogen accumulated by this crop. Brazil has registered over six hundred inoculants, with at least 60% specifically designated for soybean cultivation. The annual sales of inoculants in Brazil reach approximately 120 million doses. Although beans (Phaseolusvulgaris and Vignaunguiculata) represent an essential food crop in Brazil’s staple diet and benefit from inoculation, inoculant supply remains insufficient. Regarding biocontrol,soy, corn, sugarcane, and coffee rank among the most protected crops, employing biocontrol agents against bacteria, fungi, nematodes, and insects. Bacillus, Pseudomonas, Streptomyces, Rhizobium, Azotobacter, and Paenibacillusstrains were predominantly cited in the 5,000+ bioproduct patents filed between 2022 and 2024. Among fungal genera, Trichoderma, and Penicilliumreceived the most citations. EMBRAPA's biobanks maintain over 10,000 strains of bacteria, fungi, and viruses for biocontrol, and 14,000 strains of nutrient-fixing and plant-growth promoters. Production challenges include quality control,particularly as on-farm production of inoculants becomes prevalent on larger farms, alongside product availability and supplylimitations. Brazilian farmers maintain global competitiveness partly through reduced chemical fertilizer and pesticide costs enabled by bioinput usage. As components of regenerative agriculture, bioinputs enhance soil quality, decrease carbon footprints, and support Sustainable Development Goals. Brazil's leadership in microbial bioinput utilization stems from its extensive agricultural sector, rich microbial biodiversity, and progressive regulatory framework.

Understanding the spatial distributions and corresponding variation mechanisms of key soil nutrients in fragile karst ecosystems can assist in promoting sustainable development. However, due to the implementation of ecological restoration initiatives such as land-use conversions, novel changes in the spatial characteristics of soil nutrients remain unknown. To address this gap, we explored nutrient variations and the drivers of the variation in the 0–15 cm topsoil layer using a regional-scale sampling method in a typical karst area in northwest Guangxi Zhuang Autonomous Region, Southwest China. Descriptive statistics, geostatistics, and spatial analysis were used to assess the soil nutrient variability. The results indicated that soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), and total potassium (TK) concentrations showed moderate variations, with coefficients of variance being 0.60, 0.60, 0.71, and 0.72, respectively. Moreover, they demonstrated positive spatial autocorrelations, with global Moran’s indices being 0.68, 0.77, 0.64, and 0.68, respectively. However, local Moran’s index values were low, indicating large spatial variations in soil nutrients. The best-fitting semi-variogram models for SOC, TN, TP, and TK concentrations were spherical, Gaussian, exponential, and exponential, respectively. According to the classification criteria of the Second National Soil Census in China, SOC and TN concentrations were relatively sufficient, with the proportions of rich and very rich levels being up to 90.9 and 96.0%, respectively. TP concentration was in the medium-deficient level, with the areas of medium and deficient levels accounting for 33.7 and 30.1% of the total, respectively. TK concentration was deficient, with the cumulative area of extremely deficient, very deficient, and deficient levels accounting for 87.6% of the total area. Consequently, the terrestrial ecosystems in the study area were more vulnerable to soil P and K than soil N deficiencies. Furthermore, variance partitioning analysis of the influencing factors showed that, except for the interactions, the single effect of other soil properties accounted more for soil nutrient variations than spatial and environmental variables. These results will aid in the future management of terrestrial ecosystems.

In floodplain wetlands, alterations in hydrological patterns resulting from climate change and human activities could potentially diminish the carbon sequestration capacity of the soils, thereby having a negative impact onglobal climate change. However, the magnitude of the influence of hydrological regime change on soil carbon remains inadequately monitored. To address this research gap, we collected 306 upper layer (0–20cm) soil samples from the Dongting Lake floodplain between 2013 and 2022. The random forest (RF) algorithm was used to analyze the spatial distribution of soil organic carbon (SOC) in the upper soil layer of Dongting Lake floodplain and the impact of climate and hydrological changes in the past decade on surface SOC in the East Dongting Lake area was studied. In 2022, the SOC concentration of the Dongting Lake floodplain upper layer soil ranged from 3.34 to 17.67g kg^–1, averaging 10.43g kg^–1, with a corresponding SOC density of (2.65±0.49)kg m^–2and total SOC stock of 6.82Tg C (2.87–13.48Tg C). From 2013 to 2022, the SOC concentration of the upper soil layer of the East Dongting Lake area decreased from 18.37 to 10.82g kg^–1. This reduction could be attributed to climate and hydrological changes which reduce SOC input by reducing vegetation growth and accelerating SOC decomposition. Above 21.4m elevation, the amount of SOC loss increased with elevation, the loss being related to the decline in Miscanthuscommunity biomass and greater susceptibility of higher altitude areas to climate and hydrological changes. Our results highlight the need for strengthening wetland SOC management to increase SOC in the soils to helpcombat climate change.

Insight into the carbon turnover in soil aggregates and density fractions is essential for reducing the uncertainty in estimating carbon pools on the Tibetan Plateau, and how they vary with land use type is unclear. In this study, the effect of land use type on carbon storage and fractionation was quantified based on organic carbon and its ¹³C abundance at the microscale of soil aggregates and density fractions in Tibetan alpine ecosystems. The sequence of soil aggregate destruction in the land use types of plantation (13.1%)<shrubland (32.7%)<grassland (47.9%)<farmland (61.8%) shows that plantations strengthen the soil structure. Plantation land had a greater contribution of light fraction organic carbon (28.3%) but a lower contribution of mineral-associated organic carbon (40.6%) to the carbon stock compared to farmland (13.5 and 70.3%). Interestingly, plantation land enhanced the aggregational differentiation of organic carbon and ¹³C in each density fraction, whereas no such phenomenon existed in the soil organic carbon. Carbon isotope analyses revealed that carbon transfer in the plantation land occurred from the light fraction in macroaggregates (–24.9‰) to the mineral-associated fraction in microaggregates (–19.9‰). When compared to the other three land use types, the low transferability of carbon in aggregates and density fractions in plantation land provides a stable carbon pool for the Tibetan Plateau. This study shows that plantations can mitigate global climate change by slowing carbon transfer and increasing carbon storage at the microscale of aggregates and density fractions in alpine regions.

A comprehensive assessment of grain supply, demand, and ecosystem service flows is essential for identifying grain movement pathways, ensuring regional grain security, and guiding sustainable management strategies. However, current studies primarily focus on short-term grain provision services while neglecting the spatiotemporal variations in grain flows across different scales. This gap limits the identification of dynamic matching relationships and the formulation of optimization strategies for balancing grain flows. This study examined the spatiotemporal evolution of grain supply and demand in the Beijing-Tianjin-Hebei (BTH) region from 1980 to 2020. Using the Enhanced Two-Step Floating Catchment Area method, the grain provision ecosystem service flows were quantified, the changes in supply–demand matching under different grain flow scenarios were analyzed and the optimal distance threshold for grain flows was investigated. The results revealed that grain production follows a spatial distribution pattern characterized by high levels in the southeast and low levels in the northwest. A significant mismatch exists between supply and demand, and it shows a scale effect. Deficit areas are mainly concentrated in the northwest, while surplus areas are mainly located in the central and southern regions. As the spatial scale increases, the ecosystem service supply–demand ratio (SDR) classification becomes more clustered, while it exhibits greater spatial SDR heterogeneity at smaller scales. This study examined two distinct scenarios of grain provision ecosystem service flow dynamics based on 100 and 200 km distance thresholds. The flow increased significantly, from 2.17 to 11.81 million tons in the first scenario and from 2.41 to 12.37 million tons in the second scenario over nearly 40 years, forming a spatial movement pattern from the central and southern regions to the surrounding areas. Large flows were mainly concentrated in the interior of urban centers, with significant outflows between cities such as Baoding, Shijiazhuang, Xingtai, and Hengshui. At the county scale, supply–demand matching patterns remained consistent between the grain flows in the two scenarios. Notably, incorporating grain flow dynamics significantly reduced the number of grain-deficit areas compared to scenarios without grain flow. In 2020, grain-deficit counties decreased by 28.79 and 37.88%, and cities by 12.50 and 25.0% under the two scenarios, respectively. Furthermore, the distance threshold for achieving optimal supply and demand matching at the county scale was longer than at the city scale in both grain flow scenarios. This study provides valuable insights into the dynamic relationships and heterogeneous patterns of grain matching, and expands the research perspective on grain and ecosystem service flows across various spatiotemporal scales.

The lateral transport of labile organic carbon represents a critical pathway for soil organic carbon (SOC) loss, reducing organic carbon sequestration and increasing the risk of waterbody pollution. Livestock manureapplication on croplands serves as a common fertilizer reduction practice to sustain crop yields, enhance SOC sequestration, and reduce water erosion. However, limited quantitative assessments have examined the effects of livestock manure substitution on labile organic carbon lateral loss and fluxes in long-term experiments. This study conducted a three-year field investigation on subtropical sloping croplands to assess the impact of livestock manure substitution on dissolved organic carbon (DOC) and particulate organic carbon (POC) loss viasurface runoff, interflow and eroded sediments. There are four treatments: no fertilization (CK); chemical nitrogen fertilizer (SF),40% nitrogensubstitution with pig manure (PMF), and 100% nitrogensubstitution from pig manure (PM). Compared to SF treatment, long-term livestock manure substitution in PMF and PM treatments significantly (P<0.05) reduced annual cumulative surface runofffluxes by 13.5 and 21.6%, respectively. Manure applications decreased annual sediment fluxes by 12.9 and 19.1%, respectively. Soil water stable aggregates for mean weight diameter (MWD) increased significantly by 37.7 and 73.6%. Annual cumulative POC lossflux viaeroded sediment under PMF and PM treatments increased significantly (P<0.05) by 61.1 and 47.9%, respectively. The labile organic carbon loss fluxes, including DOC and POC losses, under PMF and PM treatmentsincreased significantly (P<0.05) by 11.9 and 31.4%, respectively. These results demonstrate that while water erosion intensity decreases due to enhanced soil aggregate stability, the risk of labile organic carbon loss increases after long-term livestock manure substitution in subtropical sloping croplands. Future research should examine labile organic carbon lateral migration under various soil types and slope gradients for livestock manure application in subtropical agricultural ecosystem croplands to better understand extreme rainfalleffects.

To examine the impact of anthropogenic land reconstruction, particularly the consolidation of small terraces into larger fields, on soil organic carbon (SOC), total nitrogen (TN) dynamics, rice yield, and its components, soil and plant samples were collected from seven newly reconstructed fields in Japanese Andosols in Tochigi, Japan. Samples were obtained from both the former low- and high-elevation sides within each field plot. During harvest season, nine rice plants were randomly selected from each plot (0.675 m2, comprising 3 rows and 3 hills per row), collected from a 3-m stretch along both the east (former low side) and west (former high side) ridges. Soil cores were collected from identical plots at two depths (0–15 and 15–30 cm) and combined into one composite sample per layer. Rice plant samples were air-dried for two weeks until reaching constant moisture content, after which stems and ears were separated and weighed to determine biomass, yield, yield components, and nitrogen uptake. This indicated that land reconstruction significantly affected rice yield and its components between the two sides of all field plots. SOC, TN, and their decomposition following land reconstruction showed notable changes, especially in the 15–30 cm subsurface soil layer. Additionally, grain weight demonstrated significant correlation with SOC, TN, and carbon decomposition in both the 0–15 and 15–30 cm layers, indicating that soil fertility to a depth of 30 cm was crucial for rice productivity after land reconstruction.

Rapidly improving infertile croplands and enhancing their soil organic carbon (SOC) pool necessitate substantial organic materials incorporation. Converting loose crop straw into granulated form facilitates uniform incorporation within the plough soil layer. As an innovative soil amelioration approach, the efficiency and patterns of SOC accumulation remain unclear. Two field experiments were conducted in infertile subtropical upland and paddy soils with 0, 30, 60, and 90Mg ha⁻¹granulated straw incorporation. After one year, SOC accumulation efficiency from straw input remained stable in upland (30.8–37.5%) with increasing amounts of straw incorporation, while declined from 60.0 to 38.3% in paddy. In both croplands, the contributions of lignin phenols to SOC increased with increasing straw incorporation, while the contributions from amino sugars remained constant at higher straw input levels. Subsequently, the ratios of lignin phenols to amino sugars increased with increasing straw incorporation, indicating faster plant residue accumulation compared to microbial necromass, as the granulation approach limited microbial involvement in straw transformation. Thus, single-time incorporation of substantial granulated straw presents an effective agricultural strategy for rapid amelioration of infertile croplands.

Phosphorus (P) is an essential nutrient element that is critical for plant growth and ecosystem functionality. The soil P cycle plays multiple roles, such as sustaining plant growth and productivity, regulating nutrient balance within ecosystems, and enhancing ecosystem adaptability and resilience. This cycle is influenced by factors such as the restorationapproachand microbial community dynamics. However, the extent to which the restorationapproach alters the P cycle in karst ecosystems and the underlying microbial mechanisms remain poorly understood. The P-cycle multifunctionality index (P-cycle MFI) serves as a comprehensive indicator for evaluating soil P cycle function, and it provides insights into changes in the P cycle betweendifferentrestorationapproaches. To investigate the shifts in soil P-cycle MFI and microbial mechanisms betweendifferentrestorationapproaches, we analyzed soil available P (AP), total P (TP), microbial biomass P (MBP), and the activities of acid phosphatase (ACP) and alkaline phosphatase (ALP). These data were used to calculate the P-cycle MFI by averaging the Z-scores between tworestoration approaches(artificial restorationof forest(AF)and natural restoration offorest (NF))and a control(cropland, CP) at six subtropical karst ecosystem sites in China. We also determinedthe soil organic carbon (SOC), exchangeable calcium (Ca) and magnesium (Mg), pH, bulk density(BD), microbial biomass C(MBC), and microbial biomass nitrogen (MBN), as well as thecommunity structure,relative abundance, diversity indices, and co-occurrence networks of phoD-harboring bacteria. The results showed that the community structureofphoD-harboring bacteria variedsignificantly among AF, NF, and CPand across differenttemperature gradients. Thesebacteria exhibited increasingcomplexityandtightness in co-occurrence networks from CPto AFand then to NF, along with the ACP and ALP activities,but notthe TP and AP contents. The P-cycle MFI values were significantly higher in NF compared to AF and CP, and the variation was significantly explained byrestoration approach, temperature, MBC, MBN, SOC, exchangeable Ca, BD, community structure ofphoD-harboring bacteria, and exchangeable Mg. Furthermore, natural restoration had a more substantial impact on the P-cycle MFI than temperature by enhancing SOC, microbial biomass, the complexity and co-occurrence network tightness of the phoD-harboring bacterial community structure, and ACP and ALP activities, but it reduced soil BD. The rare genera of phoD-harboring bacteria significantly influenced the variation of soil P-cycle MFI compared to the dominant genera. This study highlights the importance of rare genera of phoD-harboring bacteriain driving soilP-cycle multifunctionality in karst ecosystems, with natural restoration being more effective than artificial methods forenhancing soil organic matter and microbial community complexity.

Fungi play crucial roles in nutrient acquisition, plant growth promotion, and the enhancement of resistance to both abiotic and biotic stresses. However, studies on the fungal communities associated with peas (PisumsativumL.) remain limited. In this study, we systematically investigated the ecological effects of host niches (soil, root, stem, leaf, and pod) and genotypes on the diversity and composition of fungal communities in peas using a multi-level approach that encompassed pattern recognition (β-diversity decomposition), mechanism validation (neutral community model testing), and dynamic tracking methods (migration pathway source-tracking). The results revealed that the dominant fungal phyla across niches and genotypes were Ascomycota, Basidiomycota, and Mortierellomycota, and the community structures of the soil–plant continuum were primarily determined by the pea niches rather than genotypes. β-diversity decomposition was largely attributed to species replacement rather than richness differences, indicating strong niche specificity and microbial replacement across microhabitats. Neutral model analysis revealed that stochastic processes influenced genotype-associated communities, while deterministic processes played a dominant role in niche-based community assembly. Source-tracking analysis identified niche-to-niche fungal migration, with Erysiphe, Fusarium, Cephaliophora, Ascobolus, Alternaria, and Aspergillusas the key genera. Migration rates from exogenous to endogenous niches were low (1.3–61.5%), whereas those within exogenous (64.4–83.7%) or endogenous (73.9–96.4%) compartments were much higher, suggesting that the pea epidermis acts as a selective barrier that filters and enriches microbial communities prior to internal colonization. This study provides comprehensive insights into the mechanisms of host filtering, enrichment and microbial sourcing, which increases our understanding of the assembly rules of the pea-associated fungal microbiome.

Soil organic carbon (SOC) dynamics significantly influence ecosystem carbon source-sink balance, particularly in agroecosystems. However, uncertainty remains regarding optimal land use types for maximizing farmland carbon storage across different soil types, and identifying effective land management practices for enhanced carbon accumulation is essential for reducing agricultural emissions and strengthening carbon sinks. This study examined SOC variations in eastern Yunnan’s subtropical highlands (2,132 sites), analyzing topsoil (0–20cm) across five land uses (dryland, irrigated land, forestland, grassland and plantation) of five soil types (red, yellow, yellow-brown, brown, purple). The investigation explored relationships between SOC and edaphic factors (26 elements) to determine SOC influencing factors. The study area demonstrated a mean SOC content of 27.78g kg^–1, with distinct spatial heterogeneity characterized by lower values in the southwestern sector and higher concentrations in the northeastern region. Brown soils displayed the highest SOC content (P<0.05), followed by yellow-brown then red, yellow, and purple soils. Irrigation significantly enhanced SOC storage, particularly in brown soils where irrigated land contained 2.2-, 2.4-, and 1.6-times higher SOC than forestland, grassland, and dryland, respectively. Similar irrigation benefits occurred in purple, yellow, and yellow-brown soils, indicating moisture limitation as the primary SOC constraint. Notably, SOC exhibited strong positive correlations with nitrogen, sulfur, and selenium. Nitrogen fertilization demonstrated dual benefits: enhancing SOC sequestration and promoting Se enrichment in crops, potentially supporting specialty agriculture. Although land use impacts on SOC varied across soil types (P>0.05), irrigation consistently emerged as the optimal management for carbon sink enhancement. These findings suggest that targeted water management could effectively reduce farmland carbon emissions in moisture-limited subtropical highlands. Strategic nitrogen application offers co-benefits for soil fertility and selenium biofortification, providing practical pathways for climate-smart agriculture in similar ecoregions.

Microorganisms carrying cbbL, pmoAand coxLgenes play crucial roles in regulating soil-atmosphere exchanges of carbon trace gases (CO₂, CH₄, and CO). However, the geographical distribution patterns of these functional genes in agricultural ecosystems and their environmental drivers remain poorly understood. Here, we surveyed agricultural soils across four climate zones (tropical, subtropical, warm temperate, and mid-temperate) in eastern China to quantify the abundances of CO₂-assimilating bacteria (cbbLgene), methanotrophs (pmoAgene), and CO-oxidizing bacteria (coxLgene). We found significant ecosystem-specific patterns: the cbbLgene was more abundant in upland soils (averaging 9.46×10⁹ copies g^–1) than in paddy soils (6.44×10⁹copies g^–1). In contrast, methanotrophs abundance was 1 to 3 orders of magnitude higher in paddy (averaging 1.17×10⁸copies g^–1) than in upland (5.78×10⁶ copies g^–1) soils. The coxLgene maintained similar abundance levels across both soil types (averaging 6.12×10⁸vs. 5.91×10⁸copies g^–1).Structuralequation models revealed that spatial factors primarily shaped cbbLand pmoAin uplands, whereas total bacterial abundance was the dominant predictor for all three genes in paddy soils. These results highlight distinct ecological controls on microbial functional groups and provide a predictive framework for how land use and climate change may regulate microbial mediation of carbon gas fluxes across a continental-scale transect in eastern China.

Intervention strategies to control non-point source nitrogen (N) and phosphorus (P) pollution in agriculture are expensive and there is a trade-off between engineering cost and treatment effectiveness. Implementing strategies often result in unsatisfactory outcomes and massive engineering costs when managing diffusive pollution in agricultural catchments. To address this issue, this paper proposes a robust, handy, catchment N&P decision support system (CNPDSS), an Android-based smartphone system integrated with a web-based geographic information system (GIS). The CNPDSS aims to provide artificial intelligence-driven decisions that minimize N&P loadings and engineering costs for mitigating pollution in agricultural catchments. It consists of four components: a general user interface (GUI), GIS, N&P pollution modeling (NPPM), and a DSS. The CNPDSS simplifies the GUI and integrates GIS modules to create a user-friendly interface, enabling non-professional users to operate the system easily through intuitive actions. The NPPM uses straightforward empirical models to predict N&P loadings, enhancing efficiency by avoiding excessive parameters. Taking into account the N&P movement pathway in the catchment, the DSS incorporates three control measures: source reduction in farmland (before migration stage), process retention by ecological ditch (midway transport stage), and down-end purification by constructed wetland (waterbody discharge stage), to formulate a comprehensive ternary controlling strategy. To optimize the cost-effectiveness of any proposed N&P control strategies for sub-catchments, a differential evolution algorithm (DEA) is employed in CNPDSS to carry out a dual-objective decision-making optimization computation. In this study, the CNPDSS is applied to a case study in an agricultural catchment in Central China to develop the most cost-effective ternary N&P control strategies that ensure the catchment water quality within Criterion III of the Chinese Surface Water Quality Standard GB3838-2002 is met (total N concentration≤1.0 mg L⁻¹and total P concentration≤0.2 mg L⁻¹). Our results demonstrate that the CNPDSS is feasible and also possesses an adaptive design and flexible architecture to enable its generalization and extension to support strong hands-on applications in other catchments.

Peanuts (Arachis hypogaea) areimportant sources of vegetable oil, protein, and forage. The genus Arachiscomprises nine intrageneric taxonomic sections encompassing 84 species. Most Arachisspecies are wild plants that serve widely as forage and turfgrass. Furthermore, wild Arachisspecies providevaluable gene resources for broadening the genetic diversity of cultivated peanuts. To date, several key genes have been identified through the use of recombinant inbred lines derived from interspecific crosses within Arachis. Despite this progress, the application of genetic engineering to enhance peanut traits remains limited. This limitation arises primarily from the absence of a robust and reliable genetic transformation protocol for Arachisspecies. Nevertheless, evidence indicates that successful genetic transformation of Arachisplants was first reportedapproximately 30 years ago. Thus, a notable discrepancy exists between early reports of transformationsuccess and the ongoing challenges in stably transferring candidate genes into Arachisgenotypes. This review summarizes existing methods forregeneration and genetic transformation in Arachis, aiming toadvanceunderstanding of transgenictechnologies applicable to this genus.

Aspergillusspecies are ubiquitous fungi that produce mycotoxins (secondary metabolites) known as sterigmatocystin and aflatoxins in many different kinds of foods, which leads to serious contamination in agricultural products, thereby endangering human health. Extensive studies on Aspergillusfungi have been conducted on growth and development, aflatoxin biosynthesis, and their interactions with environment. Here, we summarized a series of functional genes of the main Aspergillusfungi relative to toxins occurrence in foods, which revealed the signal transduction mechanisms of their involvement in growth and development, toxin production, and response to light, anticipating providing theoretical guidance on developing control and prevention technologies for mycotoxin contamination in agricultural products to ensure food safety.

Improved yield potential is the goal of barley domestication and cultivation. During this process, two- and six-rowed barley types emergedand have been utilised in breeding and production. The six-rowed type could produce three times as many grains as its ancestral two-rowed forms, thus dominating barley cultivation for thousands of years. The deficiensform of the two-rowed type, characterised by extremely suppressed lateral spikelets, has gained dominance over the past few decades in barley-growing regions worldwide. We hypothesised that the absence of lateral spikelets in deficiensbarley affects spike architecture and spike-related traits, contributing to its superior yield potential of deficiensbarley cultivation. Currently, a deficiensbarley variety, RGT Planet, is the most popular barley variety in the world. In this study, we used two F₂populations derived from crossing RGT Planet with two canonical two-rowed barley and identified the functional allele Vrs1.t1associated with deficiensmorphology. We observed that the Vrs1.t1allele may contribute to high yield potential by optimising spike architecture through increased spikelet length, grain number, and grain size. Phylogenetic analysis suggests that the deficiensmutation was likely present from the early stages of barley cultivation in the Fertile Crescent and spread to Ethiopia and beyond with agricultural expansion. We conclude that the ancient deficiensallele Vrs1.t1has been a critical driver for the recent success of modern barley improvement by optimising spike architecture.

Recent studies have shown that lipid metabolism is a key factor affecting anther development and male fertility. However, how plants regulating the metabolic balance of multiple lipids to ensure proper anther development and male fertility remains unclear. Analyzing lipid molecules related to anther fertility and genes responsible for their biosynthesis is crucial for understanding the physiological significance of lipid metabolism in crop fertility. In this study, we compared the transcriptome and the composition and content of lipids in anthers of two upland cotton (Gossypiumhirsutum) materials, Shida 98 (WT) and its nearly-isogenic male sterile line Shida 98A (MS). Transcriptomics analysis identified many differentially expressed genes (DEGs) between the two materials, with the genes of the alpha-linolenic acid metabolism pathway being the most significantly associated with the male sterility phenotype. Investigations on lipids revealed that the MS anthers over-accumulated free fatty acids (FFAs), phosphatidic acid (PA), mono- and di-galactosyldiacylglycerol (MGDG and DGDG), and had a decreased content of triacylglycerol (TAG), which was closely related to the abnormal metabolism of alpha-linolenic acid (C18:3); therefore, the major lipids containing C18:3-acyl chains, such as PA, MGDG, DGDG, and TAG, are proposed to play a major role in cotton anther development. We also showed that an excessive level of MGDG and DGDG caused jasmonic acid (JA) overaccumulation in MS anthers, which in turn inhibited the expression of GhFAD3and consequently reduced the C18:3 content, presumably viaa feedback regulation mechanism, ultimately affecting plant fertility. Together, our results revealed the importance of a balanced lipid metabolism in regulating the development of cotton anther and pollen and consequently male fertility.

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 long-term agricultural sustainability. In response, we applied a holistic food–carbon–nitrogen–water–energy–profit (FCNWEP) nexus framework to comprehensively assessthe 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 ricecultivar (Y-liangyou 900). Four crop management treatments were implemented: a control (CK, 0kg N ha⁻¹), conventional crop management (CCM, 210–250kg N ha⁻¹, 7:3 basal:mid-tiller fertilizer ratio), and two integrated crop management (ICM) treatments (ICM1, 180–210kg N ha⁻¹, 5:2:3 basal:mid-tiller:panicle initiation fertilizer ratio; ICM2, 240–270kg 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.

High temperature stress (HT) significantly reduces maize yield by impairing starch accumulation in kernels. However, the mechanism by which HT affects starch synthesis remains controversial-whether through reduced assimilate supply or direct inhibition on kernel metabolism. To clarify these mechanisms, a heat-sensitive maize hybrid, Xianyu 335 (XY), was exposed to 30°C/20°C (maximum/minimum temperature, control) and 40°C/30°C for seven consecutive days during the seed setting stage. Synchronous pollination (SP), apical pollination (AP), and shading treatments were applied to manipulate the inherent source–sink ratio in maize plants. Results showed that apical kernel weight decreased by 11.9% under 40°C in the SP treatment. The ¹³C content, starch accumulation, and cell-wall invertase (CWIN) activity also declined by 15.9, 36.7, and 16.4%, respectively, under HT. Inthe shading treatment, 40°C/30°C caused even greater reductions in ¹³C content, starch accumulation, and CWIN activity due to diminished assimilate supply. Conversely, inthe AP treatment, starch content and CWIN activity increasedby 22.0 and 18.5%, respectively, under 40°C/30°C, resulting in kernel weight and ¹³C content similar to those in SP and shading treatments regardless of temperature. Consistent with apical kernels under AP, HT did not negatively affect middle kernels in either SP or shading treatments, as kernel weight and starch content remained unchanged under HT. Although all kernels were exposed to the same HT or controlenvironment, their responses varied a lot. The impaired starch synthesis in apical kernels under HT was rescued by increasing carbon supply viaAP treatment. The contrasting performance among middle kernels, apical kernels under AP, and apical kernels under SP or shading indicates that reduced carbon supply is a critical factor underlying inhibited starch accumulation. Our findings provide a theoretical basis for further understanding kernel abortion under HT.

Plants encounter dynamic light environments in natural fieldconditions, and species differ in their physiological and biochemical mechanisms for acclimating to fluctuating light (FL). The manner in which soybean (Glycinemax(L.) Merr.) coordinates multiple physiological adjustments to FL remains poorly understood. This study assessed the effects of FL on soybean morphology and photosynthetic traits by examining changes in photosynthetic gas exchange parameters and chlorophyll (Chl) afluorescence under alternating high- and low-light conditions. Results indicated that soybeans exposed to FL exhibited reduced dry matter accumulation, smaller and thinner leaves, and a lower Chl a/Chl blevels-characteristics typically associated with plants grown under continuous low-light. Despite these morphological similarities, their photosynthetic gas exchange rates and photosynthetic capacity were maintained at levels comparable to those under steady high light, unlike plants grown under constant low-light. Thus, acclimation to FL is distinct from adaptation to sustained low-light conditions. Correlation analyses revealed that the decline in carbon assimilation under FL primarily stemmed from two factors: the slow recovery of stomatal conductance upon transition to high light and the delayed relaxation of nonphotochemical quenching when light intensity decreased. Therefore, the reduction in carbon assimilation under FL cannot be attributed to low-light phase adjustments but rather reflects a lag in photosynthetic responsiveness to changing light conditions.

Lodging is a major constraint limiting oil flax production efficiency in northern China. Crop lodging susceptibility is closely related to stem lignin content, and the regulatory mechanisms by which nitrogen and potassium fertilization interactively influence lignin biosynthesis in oil flax stems require further investigation. Therefore, this study aimed to enhance lodging resistance and increase grain yield in oil flax. We examined the interactive effects of different nitrogen (75, 150, and 225 kg N ha^–1) and potassium (60 and 90 kg K₂O ha^–1) fertilizer rates on lignin metabolism, lodging resistance, and grain yield during the 2022 and 2023 growing seasons. Results indicated that nitrogen and potassium fertilizer levels and their interactions promoted lignin accumulation, improved lodging resistance, and increased grain yield. Compared to the control (CK), the 75–150 kg N ha^–1combined with 60 kg K₂O ha^–1treatments significantly enhanced the activities of key lignin-synthesizing enzymes (tyrosine ammonia-lyase (TAL), phenylalanine ammonia-lyase (PAL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD)) and upregulated the expression of 4CL1and F5H3genes, leading to a 29.63–43.30% increase in lignin content, improved stem bending strength and lodging resistance index, and a 23.27–32.34% increase in grain yield. Correlation analysis revealed that nitrogen and potassium fertilizers positively regulated enzyme activities and gene expression related to lignin biosynthesis, thereby facilitating lignin accumulation and enhancing stem mechanical strength and lodging resistance. Positive correlations were observed among lignin-related enzyme activities, gene expression, lodging resistance traits, and grain yield. In summary, the application of 75–150 kg N ha^–1in conjunction with 60 kg K₂O ha^–1promoted lignin biosynthesis and accumulation, enhanced lodging resistance, and increased grain yield in oil flax grown in the dryland farming region of central Gansu, China. Furthermore, this treatment provides a technical basis for cultivating stress-tolerant and high-yield oil flax in arid regions.

Anthocyanins are important flavonoid pigments in the coloration of fruits. To identify candidate genes involved in anthocyanin accumulation, metabolic and transcriptome analyses were conducted in ‘Nanguo’ pear and its red sport cultivar ‘Nanhong’ pear. The results showed that ‘Nanhong’ pear had significantly higher anthocyanin and flavonol contents. Additionally, transcriptomic analysis showed that there were significant differences in the expression of genes involved in phenylpropanoid and flavonoid biosynthesis pathways between the two cultivars, with PuGSTF12being the most upregulated gene in the ‘Nanhong’ cultivar. Further analysis identified a novel MYB transcription factor (PuMYB93), and its silencing repressed PuGSTF12expression and anthocyanin accumulation, suggesting it plays an essential role in the regulation of anthocyanin biosynthesis. Moreover, yeast one-hybrid analysis, electrophoretic mobility shift assay, and β-glucuronidase assay indicated that PuMYB93 can directly bind to the PuGSTF12promoter to positively regulate its expression. Additionally, PuGSTF12silencing suppressed the coloration of PuMYB93-OE peels, suggesting that PuGSTF12act downstream of PuMYB93. Overall, the findings of this study show that PuMYB93 promotes anthocyanin transport in pears by regulating PuGSTF12expression to further enhance anthocyanin accumulation.

Erysiphenecatoris a destructive fungal pathogen that compromises grapevine yield and quality, leading to substantial economic losses. Therefore, elucidating host resistance mechanisms is essential. In this study, we identified an ethylene response factor, VqERF1B, that exhibits sustained high expression during E.necatorinfection in Chinese wild grape Vitisquinquangularisaccession ‘Danfeng-2’. Transient overexpression of VqERF1Bin grape leaves enhanced resistance to E.necatorby elevating transcript levels of pathogenesis-related (PR) genes, including PR1, PR2, PR5, and PR10. Conversely, silencing VqERF1Bresulted in increased susceptibility. Moreover, transgenic Arabidopsislines stably overexpressing VqERF1Bexhibited enhanced resistance to powdery mildew, associated with elevated PRgene expression and increased accumulation of reactive oxygen species (ROS). A series of assays identified VqMAPK3, a phosphorylated mitogen-activated protein kinase, as a direct interactor of VqERF1B. Furthermore, VqERF1B was shown to bind directly to the promoters of VqPRs, thereby activating their transcription. Notably, the VqMAPK3-VqERF1B complex exhibited greater transactivation activity on VqPRpromoters than VqERF1B alone, indicating that VqMAPK3 positively modulates VqERF1B-mediated transcription of PRgenes. This work advances understanding of the molecular basis of grape resistance to E.necatorand provides a foundation for molecular breeding strategies.

Tiller number represents a critical agronomic trait determining sugarcane yield. Strigolactones (SLs) are plant hormones regulating plant architecture. D27, an essential enzyme in the SL biosynthetic pathway, catalyzes a reversible isomerization reaction. ScD27.2, the D27homolog in sugarcane, contains abiotic stress-responsive elements in its promoter, suggesting its potential importance in SL biosynthesis and stress tolerance. ScD27.2potentially optimizes sugarcane agronomic traits, particularly tiller number and yield. Understanding its mechanisms will advance the development of high-yielding, stress-tolerant sugarcane varieties. To investigate the role of D27in sugarcane tillering, the key carotene isomerase gene ScD27.2was silenced (viaRNAi) and overexpressed (OE) in sugarcane cultivar ‘XTT22’ plantlets. ScD27-RNAi-2 sugarcane exhibited decreasedScD27.2 expression and increased tiller numbers compared to the wild type ‘XTT22’. Conversely, overexpression lines (ScD27-OE-1, ScD27-OE-5, and ScD27-OE-9) showed increased ScD27.2expression and decreased tiller numbers. ScD27-OE-9 demonstrated notable lateral bud germination, while ScD27-RNAi-2 exhibited reduced drought tolerance. Under normal light and water management conditions, transgenic sugarcane plants showed significant differences in tiller number and plant height. During extended droughtconditions, ScD27-RNAi-2 height was significantly reduced compared to wild type ‘XTT22’ and ScD27-OE-9, manifesting a dwarf, multi-tiller phenotype. Additionally, ScD27-RNAi-2 showed significantlyreduced SLs content. These findings demonstrate that ScD27.2regulates tillering under drought stress, likely through SL biosynthesis, and that its drought response may be mediated by the transcription factor ScMYB44.

Head-splitting is a prevalent physiological disorder in cabbage that causes substantial economic losses. However, the genetic factors and molecular mechanisms underlying head-splitting resistance remain largely unexplored. This study identified a genomic region (qNLQ3.1) for head-splitting resistance on chromosome C03 through the combination of QTL-seq and GPS analysis in an F₂population derived from hybridizing two cabbage inbred lines, ‘Dazhengfu’ (ZF, susceptible) and ‘103’ (resistant).Traditional genetic linkage analysis narrowed qNLQ3.1to a 74.6 kb region. Furthermore, comparative analysis of the two parental linesusing transcriptomic and metabolic profilingdemonstrated the crucial role of hormones in regulating head-splitting resistance. Bol028000, encoding a homologue of Arabidopsis Cytokinin Response Factor 3 (CRF3), emerged as a promising candidate for head-splitting resistance and was subsequently validated through Sanger sequencing and quantitative RT-PCR (qRT-PCR). Subcellular localisation analysis revealed that Bol028000was mainly expressed in the nucleus. Additionally, one kompetitive allele-specific PCR (KASP) marker from Bol028000was developed and utilized to screen 42 inbred lines. These findings enhance the theoretical understanding of head-splitting resistance and provide valuable insights for the molecular breeding of head-splitting resistant cabbages.

The embryo rescue technique plays an essential role in developing new seedless grape varieties. To enhance the efficiency of seedless grape embryo rescue breeding, this study evaluated 22 hybrid combinations and systematically investigated the effects of parental genotypes and plant hormones on embryo development and germination. Additionally, an in-depth analysis was conducted on the conversion of abnormal plantlets. Results indicate that ‘Ruby Seedless’, ‘Delight’, ‘Huozhouheiyu’, ‘Zitian Seedless’, and ‘Zhengyan Seedless’ are suitable as maternal parents, whereas ‘Zitian Seedless’, ‘Shennongxiangfeng’, ‘Hongqitezao’, and ‘Guibao’ perform optimally as paternal parents. Among these, the crosses ‘Ruby Seedless×Shennongxiangfeng’ and ‘Ruby Seedless×Zitian Seedless’ exhibited the highest embryo rescue efficiency, with embryo development rates of 55.05 and 59.76%, yielding 1,348 and 2,235 viable plantlets, respectively. When 1.0mg L^–1zeatin (ZT) was added to the MM3 medium supplemented with 0.2mg L^–1indole-3-acetic acid (IAA), theembryo development rate of ‘Ruby Seedless×Zitian Seedless’ increased by 64.73%. In the WPM germination medium, supplementation with 0.2mg L^–1ZT and 0.2mg L^–1IAA resulted in the highest germination rate of 85.71% for the hybrid combination ‘Huozhouheiyu×Shine Muscat’. Furthermore, 3,365 abnormal plantlets were rescued viadirect transformation and hypocotyl-induced adventitious bud regeneration, among which 1,234 were transformed into normal plantlets. Following hybridization, a total of 4,287 plants were successfully acclimatized and transplanted. This study provides theoretical insights to improve the efficiency of embryo rescue breeding in seedless grapes and offers valuable genetic resources for future breeding programs.

High-throughput single nucleotide polymorphism (SNP) arrays have emerged as essential genotyping tools, significantly accelerating breeding programs and advancing basic research. In this study, a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing (GBTS), featuring 10,722 SNPs evenly distributed across all 12 chromosomes, including 278 functional loci associated with key economic traits. To demonstrate its utility, genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight. The results revealed that greater genetic distance was associated with higher middle parent heterosis (MPH) for single fruit weight. Furthermore, 56 commercial wax gourd cultivars collected from eight regions were selected and genotyped. Population structure analysis, phylogenetic analysis, and principal component analysis (PCA) collectively indicated that these cultivars fall into two major groups. Group I, comprising black or dark green skinned wax gourds, exhibited lower genetic diversity than Group II, which includes green or light green skinned varieties, reflecting shorter genetic distances within Group I. Finally, 60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars. As the first high-throughput genotyping platform for wax gourd, this SNP array provides an effective and powerful tool for genetic analysis.

In China, Xinjiang is a relatively independent epidemic region of wheat stripe rust, caused by Pucciniastriiformisf. sp. tritici, due to great population genetic divergence of Xinjiang with other inland epidemic regions. In this region, race evolution was usually slower than inland populations. However, many new races have recently been found, and therefore, it is necessary for more understanding of the virulence evolution of the Xinjiang population. So, in this study, a 65 sexual progenies, derived from a Xinjiang single-urediospore isolate BGTB-1 of P.striiformisf. sp. triticiby selfing on alternate host barberry (Berberisaggregata). It was phenotyped on the 25 single Yrlines, and genotyped by 19 kompetitive allele-specific PCR-single nucleotide polymorphism (KASP-SNP) markers. As a result, the 65 progenies were identified as 56 various virulence patterns (VPs), and neither of which was identical to the parental isolate, showed 100% virulence variation. Compared with the parental isolate, of all progenies, 39 (60.0%) had increased virulence, and 18 (27.7%) had decreased virulence. All progenies exhibited avirulence to Yr10, Yr15, Yr32, and YrTr1loci, and avirulence and virulence segregation at the remaining 21 Yrresistance loci. The results showed avirulence to Yr5, Yr7, and Yr76(A:V≈3:1) loci is controlled by a single dominant gene, and that to Yr6, Yr25, and Yr44(A:V≈1:3) loci by a single recessive gene. However, avirulence to the remaining 15 resistant loci including Yr1, Yr2, Yr3, Yr4, Yr8, Yr9, Yr17, Yr26(=Yr24), Yr28, Yr29, Yr43, YrSP, Yr27, YrA, and YrExp2, with various avirulence and virulence segregation ratios, is controlled by two genes with different gene effects, indicating complex genetic traits of the parental isolate. Totally, 65 dissimilar genotypes detected among progenies using overall molecular markers, by which a linkage map was constructed, with a genetic distance of 441.0 cM. Interestingly, although the parental isolate was avirulent to Yr5, but 17 progenies showed virulence, showing the change of pathogenicity from avirulence to virulence at this resistance locus. It was for the first time to report that progenies with virulence to Yr5produced sexually from avirulent parental isolate at this resistance locus. To our knowledge, this study offers an insight into inheritance, sexual reproduction and virulence variation of P.striiformisf. sp. triticiin Xinjiang, facilitating us to understand evolution of the rust pathogen in this region and accounting for Xinjiang population distinguished form other inland populations. Additionally, it is necessary to further confirm the roles of sexual reproduction in the emergence of new races and affecting population genetic diversity of P.striiformisf. sp. triticiunder natural conditions in Xinjiang.

Rice is one of the most important staple crops globally. Rice plant diseases can severely reduce crop yields and, in extreme cases, lead to total production loss. Early diagnosis enables timely intervention, mitigates disease severity, supports effective treatment strategies, and reduces reliance on excessive pesticide use. Traditional machine learning approaches have been applied for automated rice disease diagnosis; however, these methods depend heavily on manual image preprocessing and handcrafted feature extraction, which are labor-intensive and time-consuming and often require domain expertise. Recently, end-to-end deep learning (DL) models have been introduced for this task, but they often lack robustness and generalizability across diverse datasets. To address these limitations, we propose a novel end-to-end training framework for convolutional neural network (CNN) and attention-based model ensembles (E2ETCA). This framework integrates features from two state-of-the-art (SOTA) CNN models, Inception V3 and DenseNet-201, and an attention-based vision transformer (ViT) model. The fused features are passed through an additional fully connected layer with softmax activation for final classification. The entire process is trained end-to-end, enhancing its suitability for real-world deployment. Furthermore, we extract and analyze the learned features using a support vector machine (SVM), a traditional machine learning classifier, to provide comparative insights. We evaluate the proposed E2ETCA framework on three publicly available datasets, the Mendeley Rice Leaf Disease Image Samples dataset, the Kaggle Rice Diseases Image dataset, the Bangladesh Rice Research Institute dataset, and a combined version of all three. Using standard evaluation metrics (accuracy, precision, recall, and F1-score), our framework demonstrates superior performance compared to existing SOTA methods in rice disease diagnosis, with potential applicability to other agricultural disease detection tasks.

The strawberry crimp nematode (Aphelenchoidesfragariae) is a serious pathogen of ornamental crops and a significant quarantine concern in approximately 50 countries and regions, including China. A nematode population belonging to the genus Aphelenchoideswas isolated from symptomatic leaves of fuchsia plants (Fuchsia×hybridaHort. ex Sieb. & Voss.) in Chengdu, Sichuan Province, China. Morphological and morphometric characteristics were determined using light microscopy and scanning electron microscopy. Detailed examination revealed diagnostic features consistent with A.fragariae. Three ribosomal DNA (rDNA) regions, i.e., partial small subunit(SSU) rRNA, D2-D3 expansion segments of the large subunit (LSU) rRNA, andthe internal transcribed spacer (ITS), were amplified and sequenced. Bayesian phylogenetic analyses based on these sequences placed the isolate in a well-supported monophyletic clade withreference A.fragariaespecimens, clearly separated from other Aphelenchoidesspecies. Furthermore, host-suitability assays demonstrated that this nematode population not only infects and reproduces on Fuchsia×hybrida, but also on Fragariaananassaand Pterisvittata, two known hosts of A.fragariae. Collectively, morphological,molecular, and host-range evidence confirm the identification of this nematode as A.fragariae. To our knowledge, this represents the first molecular and morphological confirmation of A.fragariaein China, and the first report ofFuchsia×hybridaas a natural host for this species.

The advantages of genome selection (GS) in animal and plant breeding are self-evident. Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects accurately. Machine learning models have demonstrated remarkable potential in addressing these challenges. In this study, we introduced the concept of mixed kernel functions to explore the performance of support vector machine regression (SVR) in GS. Six single kernel functions (SVR_L, SVR_C, SVR_G, SVR_P, SVR_S, SVR_L) and four mixed kernel functions (SVR_GS, SVR_GP, SVR_LS, SVR_LP) were used to predict genome breeding values. The prediction accuracy, mean squared error (MSE) and mean absolute error (MAE) were used as evaluation indicators to compare with two traditional parametric models (GBLUP, BayesB) and two popular machine learning models (RF, KcRR). The results indicate that in most cases, the performance of the mixed kernel function model significantly outperforms that of GBLUP, BayesB and single kernel function. For instance, for T1 in the pig dataset, the predictive accuracy of SVR_GS is improved by 10% compared to GBLUP, and by approximately 4.4 and 18.6% compared to SVR_G and SVR_S respectively. For E1 in the wheat dataset, SVR_GS achieves 13.3% higher prediction accuracy than GBLUP. Among single kernel functions, the Laplacian and Gaussian kernel functions yield similar results, with the Gaussian kernel function performing better. The mixed kernel function notably reduces the MSE and MAE when compared to all single kernel functions. Furthermore, regarding runtime, SVR_GS and SVR_GP mixed kernel functions run approximately three times faster than GBLUP in the pig dataset, with only a slight increase in runtime compared to the single kernel function model. In summary, the mixed kernel function model of SVR demonstrates speed and accuracy competitiveness, and the model such as SVR_GS has important application potential for GS.

Femoral head necrosis (FHN) is a common leg disorder in the poultry industry often leads to significant cartilage damage. The mechanism behind abnormal apoptosis in FHN broilers, leading to cartilage damage, remains unclear; although endoplasmic reticulum stress (ERS) has been found to play a role in glucocorticoid-induced FHN broilers. In this study, we collected samples from broilers with femoral head separation (FHS) and femoral head separation accompanied with growth plate lacerations (FHSL) in a broiler farm. The aim was to investigate the potential association between the severity of FHN, bone remodeling and cartilage damage. Additionally, primary chondrocytes were treated with methylprednisolone (MP) to construct an invitroFHN model, followed by inhibition or activation of ERS or hypoxiainduciblefactor-1α(HIF-1α) to further investigate the mechanism of apoptosis in cartilage. The results suggested that cartilage appeared to be the appropriate tissue to investigate the potential mechanisms of FHN, as the degree of cartilage damage was found to be closely related to the severity of the disease. Bone quality was only affected in FHSL broilers, although factors related to bone metabolism were significantly altered among FHN-affected broilers. In addition, cartilage in FHN-affected broilers exhibited high levels of apoptosis and upregulated expression of ERS-related and HIF-1α, which was consistent with both invivoand invitrofindings after MP treatment. The results were further supported by treatment with HIF-1αor ERS inhibition or activation. In conclusion, bone remodeling and cartilage homeostasis were affected in FHN broilers, but only cartilage damage was significantly exacerbated with FHN development. Moreover, activation of ERS or HIF-1αresulted in apoptosis in cartilage, thus exhibiting a significant correlation with FHN severity.

Innate immunity is the primary defense against viral infections, with Toll-like receptors (TLRs) playing a crucial role in this process. This study aims to highlight the effectiveness of a pyrrolo[3,2-d]pyrimidine derivative (named TLR713), a potential TLR7 agonist, in inhibiting pseudorabies virus (PRV) replication both invitroand invivo. Tests on PK-15 cells demonstrated that TLR713 had no significant impact on cell viability, cell cycle progression, or apoptosis at concentrations of 0–3 μmol L^–1.TLR713 could promote the phosphorylation of IκBα, p38, and JNK through TLR7, and increase the expression of inflammatory cytokines. Invitro, when cells were treated with TLR713, PRV proliferation was inhibited viaTLR7 pathway. Analysis of the viral life cycle indicated that TLR713 could inhibit the replication of PRV, but not affect viral attachment, entry, assembly, or release. Invivo, TLR713 showed no side effects on mice at a concentration of 25 mg kg^–1. It improved the survival rate of PRV-infected mice, reduced tissue viral load, and alleviated the inflammatory response. In summary, this study highlights the potential of TLR713 as a novel TLR7 agonist capable of inhibiting PRV replication and may offer new opportunities for developing antiviral therapies.

Oral immunization is an alternative or supplementary approach that can significantly improve dog vaccination coverage, especially for free-roaming dogs. Safe and effective oral rabies vaccines for dogs are still being sought. In our previous studies, we generated a genetically modified rabies virus (RABV) ERA strain, rERAG_333E, containing a mutation from arginine (Arg, R) to glutamic acid (Glu, E) at residue 333 of the G protein (G_333E). Our previous results demonstrated that rERAG_333Ewas safe for adult mice and dogs, and oral vaccination with rERAG_333Einduced a strong and long-lasting protective immune response in dogs. Here, we further investigated the safety and immunogenicity of rERAG_333Ein non-target species, including suckling mice, rhesus monkeys, foxes, raccoon dogs, piglets, goats, and sheep. Suckling mice studies demonstrated that the G_333Emutation significantly reduced the virulence of the ERA strain. All of the suckling mice aged 10 days and above survived and showed no apparent signs of disease after intracerebral inoculation with rERAG_333E. Animal studies demonstrated that rERAG_333Ewas safe in rhesus monkeys, foxes, raccoon dogs, piglets, goats, and sheep. None of those animals inoculated orally with 10 times the intended field dose of rERAG_333Eshowed abnormal clinical signs before and after the booster immunization with Rabvac 3, an inactivated rabies vaccine. Meanwhile, oral inoculation with rERAG_333Einduced strong neutralizing antibody (NA) responses to RABV in rhesus monkeys, foxes, raccoon dogs, and piglets. These results demonstrated that rERAG_333Ehas the potential to serve as a safe oral rabies vaccine for dogs.