Rice yellow mottle virus (RYMV) is one of the most destructive viral diseases affecting rice production in sub-Saharan Africa (SSA), where increasing demand and persistent yield gaps continue to compromise food security.  RYMV shows significant genetic and phylogeographic diversity across SSA, driven by mutation, recombination, selection, and restricted regional spread, enabling adaptation to host resistance.  The main resistance genes, RYMV1, RYMV2, and RYMV3, primarily derived from Oryza glaberrima, differ in their molecular mechanisms and the selective pressures they impose on viral populations.  Resistance breakdown linked to RYMV1 primarily stems from mutations in the viral VPg protein, whereas resistance mediated by RYMV2 and RYMV3 is overcome through changes in the P2a polyprotein and coat protein (CP), respectively.  An evolution-informed framework combining viral phylogeography, resistance-breaking pathways, and breeding deployment strategies is proposed to explain regional variation in resistance durability and enhance long-term resistance management.  Currently, using marker-assisted pyramiding of complementary resistance genes is the most promising and scalable strategy for achieving durable resistance, while genomic selection provides opportunities to improve both quantitative and background resistance.  Sustainable management of RYMV will require region-specific deployment of resistant varieties, continuous surveillance of viral populations, integration of quantitative resistance, and better seed system management to reduce selection pressure and virus spread.  Emerging technologies such as genome editing and artificial intelligence-assisted breeding may further expand the resistance toolbox but require careful integration.

Introducing genomic segments from related species into crops is an effective approach to enrich genetic diversity and create novel germplasm.  African cultivated rice (Oryza glaberrima), one of the two cultivated rice species, represents a valuable genetic resource for improving Asian cultivated rice (O. sativa).  Grain size/weight is among the most important components of grain yield in rice.  In this study, we isolated a chromosome segment introgression line harboring a single segment derived from O. glaberrima.  Compared to the recurrent parent, this line displayed a significant increase in grain size, whereas other agronomic traits were not significantly affected.  Using map-based cloning, we identified OgGS3.2 from this fragment as an ortholog of OsSLR1.  A single nucleotide substitution in OgGS3.2 was identified as the causal mutation underlying the increased seed size phenotype.  Haplotype analysis revealed that the vast majority of African rice germplasm carries the G haplotype at the GS3.2 locus.  This study reveals the molecular mechanism by which OgGS3.2 regulates grain size and offers strategic genetic resources for yield improvement in cultivated rice.

Fall armyworm (FAW), Spodoptera frugiperda, is one of the most destructive pests of maize worldwide. Since invading Africa in 2016 and China in 2019, it has caused substantial crop losses, especially across Sub-Saharan Africa. To identify practical, smallholder-friendly pest management tactics, the FAO-China South-South Cooperation FAW Project conducted on-farm trials at two sites in Kenya (Bungoma and Embu) and two in Ghana (Kpong and Pampaso). Baseline surveys revealed infestation rates of 73.3–93.7%, with larval densities of 95–532 larvae per 100 plants. Six treatments were compared against an untreated control: neem oil, Bacillus thuringiensis (Bt), emamectin benzoate and chlorantraniliprole (Kenya) or lambda-cyhalothrin (Ghana), each applied either as a knapsack-spray or as sand granules dropped into the maize whorl. Leaf damage levels (LDL) and number of living larvae (NLL) per plant were recorded weekly. After one season, emamectin benzoate both sprayed and sand-applied consistently provided the lowest leaf damage level ((1.06±0.02)–(1.35±0.07)) compared with the control ((3.21±0.16)–(4.60±0.16)) in Kpone and Pampaso of Ghana. In Kenya, emamectin benzoate also resulted in lower leaf damage levels ((1.21±0.03)–(3.17±0.09)) compared with the control ((4.48±0.05)–(6.30±0.18)) at Embu and Bungoma. Bt sand granules were highly effective in Ghana ((1.20±0.04)–(1.29±0.07)) but performed less well in Kenya ((3.98±0.08)–(6.97±0.16)). Neem oil provided moderate suppression with leaf damage levels ((1.31±0.06)–(2.04±0.12)) in Ghana and ((3.13±0.08)–(3.58±0.16)) in Kenya, whereas lambda-cyhalothrin failed completely. In parallel, we screened five Ghanaian and eleven Kenyan local maize varieties for natural resistance; The Omankwa variety showed significantly lower leaf damage level ((1.91±0.12)–(2.73±0.21)) than the Lake (hybrid) variety ((2.78±0.31)–(3.93±0.17)) in Ghana; In Kenya, Pioneer (2.52±0.12), SC 73 Tumbo (2.58±0.14) and WH508 (2.44±0.11) showed significantly lower leaf damage levels compared with DK777 (5.44±0.08), W301 (5.47±0.07), Tembo (Seedco) (5.71±0.07), and Sungura (Seedco) (3.76±0.07). These trials offer smallholder farmers direct, comparative evidence to support cost-effective and locally adapted FAW management decisions.

Intercropping is a traditional and sustainable agricultural practice that enhances soil fertility, reduces erosion, and promotes plant growth and metabolism.  Despite widespread adoption in tea plantations, intercropping effects on yield, quality, and soil are highly context-dependent, varying with species choice, climate, and site-specific conditions.  Using 157 paired observations from 41 articles, we performed a meta-analysis to quantify how intercropping affects tea yield, quality, and soil, and to determine the primary modulating factors.  Across all included reports, intercropping significantly increased tea yield by 11.9%.  It also elevated the levels of free amino acids (AAs) by 19.08% and reduced the levels of tea polyphenols (TPs) by 7.16%, leading to a notable decrease in the TP/AA ratio, which is associated with tea quality.  Additionally, intercropping increased soil nutrient levels and soil pH.  Initial organic matter and pH had a significant influence on tea yield and quality outcomes, while the type of plants used for intercropping and climatic factors such as mean annual temperature and mean annual precipitation were closely associated with improvements in soil quality.  Overall, intercropping can improve tea yield and quality while enhancing soil conditions in tea plantations, although the magnitude of these benefits depends on companion crop selection, soil status, and climate.

Porcine epidemic diarrhoea virus (PEDV) is a major enteric pathogen of global swine production, yet its true epidemiological burden remains inadequately characterised due to heterogeneity in surveillance systems, diagnostic sensitivity, and reporting frameworks. To clarify the global epidemiological profile of PEDV, we conducted a systematic review and meta-analysis integrating animal- and herd-level data while evaluating the influence of diagnostic methods and population characteristics on detection outcomes. Across 133 studies from 22 countries, PEDV was frequently detected in both clinically affected and apparently healthy pigs, indicating sustained endemic circulation rather than episodic outbreak dynamics. Molecular assays identified ongoing active infection, while serological data demonstrated extensive historical exposure, together revealing substantial silent transmission within swine herds. Detection patterns varied markedly by age group, geographic region, and study period; sows appeared to act as potential viral reservoirs, while neonatal piglets served as principal transmission amplifiers. Among clinically affected pigs, pooled nucleic acid-based detection rate was 46.0% (95% CI: 39.8-52.2), with the highest point estimates observed in sows and boars at 76.5% (95% CI: 28.9-100.0), though these were imprecise with wide confidence intervals, and in suckling piglets at 44.7% (95% CI: 35.6-53.9). Serological analysis revealed a seroprevalence of 14.6% (95% CI: 0.8-40.0) in clinically affected animals, reflecting cumulative population exposure. At the herd level, nucleic acid-based detection yielded a pooled detection rate of 44.6% (95% CI: 33.6-55.9), while serological estimates reached 39.0% (95% CI: 14.6-66.3), collectively supporting widespread herd-level circulation. Substantial between-study heterogeneity was largely attributable to temporal, regional, and herd health factors, underscoring how surveillance design and diagnostic strategy can substantially influence reported prevalence and obscure the true scale of viral spread. Collectively, these findings indicate that PEDV is a globally entrenched, persistently circulating pathogen sustained through subclinical infection and herd-level viral persistence. This work provides the first comprehensive global synthesis of PEDV epidemiology and establishes an evidence-based framework to guide standardised surveillance, contextualise diagnostic outcomes, and inform targeted prevention strategies encompassing vaccination and biosecurity. Strengthening harmonised monitoring systems will be essential to reducing the long-term burden of PEDV in modern swine production.

TCRγδ T cells are a major lymphocyte population in chickens, but their response to avian leukosis virus subgroup J (ALV-J) and recognized antigens remain poorly understood. Here, we report an increase in the proportion and activation state of TCRγδ⁺CD8α⁺ T cells in vivo and in ex vivo cultured T cells from 2 chicken lines (MHC homozygous H-B21 lines and outbred G-WL line) with the earlier and stronger proliferative response observed in the H-B21chickens. Activated TCRγδ⁺CD8α⁺ T cells performed ‘cytolytic' potential via detection of transcription levels of cytotoxic genes with quantitative reverse transcription polymerase chain reaction (qRT-PCR), and IFN-γ protein level with ELISPOT and an intracellular cytokine staining (ICS) assays with more significant response in the H-B21 chickens. Consistently, Furthermore, the viral structural proteins Gag and Pol were identified as major target proteins recognized by chicken TCRγδ⁺CD8α⁺ T cells. Further ELISPOT and ICS analyses mapped the key peptides to Gag_187–215 and Pol_417–445 recognized by Chicken TCRγδ⁺CD8α⁺ T cells against ALV-J infection. Collectively, these findings firstly confirmed that TCRγδ⁺CD8α⁺ T cells could recognize viral antigens and revealed the dominant peptides on ALV-J, enhancing our understanding of anti-ALV-J T cell responses and advancing vaccine design strategies against ALV-J.

Excessive cadmium (GrCdc) and deficiencies of copper (GrCuc) and magnesium (GrMgc) in grains pose serious human health risks.  Common wheat breeding has reduced the genetic diversity within elite germplasm resources, negatively impacting future wheat production.  Thus, identifying loci controlling GrCdc, GrCuc, and GrMgc in tetraploid wheat and introducing them into common wheat is essential for genetic improvement.  In this study, we identified quantitative trait loci (QTLs) for GrCdc, GrCuc, and GrMgc using the Wheat 55K single nucleotide polymorphism (SNP) array-based linkage map and phenotypic data across multiple environments in recombinant inbred lines derived from a cross between a wild emmer accession (LM001) and an endemic tetraploid wheat in Sichuan, China (Ailanmai).  Four major stably expressed QTLs were identified, three of which (QGrCdc.sau-AM-5A for GrCdc, QGrCuc.sau-AM-4A for GrCuc, and QGrMgc.sau-AM-4A for GrMgc) were novel.  These loci were validated using tightly linked kompetitive allele specific PCR (KASP) markers in various genetic backgrounds.  Several candidate genes with sequence variations (TRIDC5AG052690, TRIDC5BG060070, and TRIDC4AG008520) were predicted to influence Cd, Cu, or Mg absorption and transport within these QTL intervals.  Correlation analysis revealed that GrCdc was not correlated with GrCuc or GrMgc, although GrCuc was significantly correlated with GrMgc.  Furthermore, no significant effects of GrCdc, GrCuc, or GrMgc on agronomic traits were detected, as no correlations between them and any of the 11 agronomic traits investigated were observed.  In addition, QGrCuc.sau-AM-4A colocalized with QGrMgc.sau-AM-4A, suggesting potentially shared physiological and/or genetic control.  Altogether, these stably expressed QTLs across environments provide theoretical guidance for further germplasm improvement and fine mapping.

The Huang-Huai-Hai wheat region (HHHR) is characterized by the largest cultivation area and highest yield among all the major wheat-producing regions in China.  Over the past 70 years, significant advances in wheat breeding have been achieved in this region, resulting in high and stable yields as well as improved disease resistance.  However, a notable deficiency remains in the systematic molecular-level analyses of wheat breeding advantages in HHHR.  To bridge this gap, we used a Wheat 55K SNP array to evaluate 384 accessions from a core collection of wheat germplasms across China, and then systematically analyzed the distribution patterns of beneficial haplotypes associated with traits related to yield and powdery mildew resistance specific to HHHR.  The findings indicate that varieties from HHHR demonstrate significantly superior performance in terms of yield-related traits and powdery mildew resistance compared to those from other wheat regions.  A genome-wide association study (GWAS) analysis identified the quantitative trait nucleotides (QTNs) associated with both grain yield and powdery mildew resistance.  Importantly, beneficial haplotypes were found at significantly higher frequencies in the HHHR than in other wheat-growing regions.  Based on these haplotypes, the MFP-a gene was identified as potentially regulating jasmonic acid synthesis while also playing a role in grain development and conferring powdery mildew resistance.  Furthermore, identity by descent (IBD) analysis revealed specific conserved genomic segments that have become fixed through selective breeding practices in HHHR, which may serve as valuable resources for the targeted enhancement of yield and disease resistance traits in other wheat-growing areas.  Finally, the Aimengniu breeding lineage was used as a case study to elucidate the genetic basis underlying the key founder parental formations utilized in breeding programs.  This study not only provides essential references and guidance for future molecular breeding initiatives in China but also has implications for enhancing wheat production worldwide.

Leaf rolling is an important morphological trait in wheat (Triticum aestivum L.) that is strongly correlated with photosynthesis, transpiration, and respiration, especially in abiotic stress conditions.  The identification of quantitative trait loci (QTLs) and genes underlying leaf rolling is essential for wheat breeding.  In this study, the ethyl methanesulfonate (EMS) induced mutant Y536 was isolated in a Nongda 3753 background with extreme abaxial leaf rolling.  The F₂ and F_2:3 populations derived from a cross between Jing411 and mutant Y536 with contrasting leaf rolling morphologies were developed to map the locus controlling leaf rolling.  A public SSR marker was isolated on chromosome 6DL that had a high linkage level with leaf rolling index (LRI).  QTL analysis revealed a stable QTL associated with LRI, named QLRI.cau-6D, which explained 7.69 to 10.86% of the total phenotypic variation and had LOD scores ranging from 10.00 to 13.32.  TraesCS6D02G237000 (TaHDZIV-D1) was identified as the priority candidate gene according to coding sequence differences between the two parents and gene functional annotations.  Consistently, knocking out TaHDZIV-A1/B1/D1 in common wheat line ‘JW1' significantly increased the LRI compared to the wild type, while overexpression of TaHDZIV-D1 in ‘JW1' significantly reduced the LRI until the leaves rolled in the opposite direction.  Moreover, genetic evidence suggested that TaHDZIV-A1/B1/D1 affects leaf rolling in a dose-dependent manner.  Collectively, these findings provide novel insights into the genetic basis of leaf rolling in common wheat.

Soybeans, a crucial grain and oil crop, are valued for their high protein and oil content.  Soil salinization is a significant abiotic stress that negatively impacts soybean growth and development, resulting in reduced yield and quality.  The germination period represents a critical phase in soybean development.  This study evaluated salt tolerance in 165 soybean mutant lines during germination, identifying five elite salt-tolerant germplasm resources.  Multi-environment genome-wide association studies (GWASs) identified 11 significantly associated and 44 suggestive single nucleotide polymorphisms, alongside five novel quantitative trait loci linked to salt tolerance.  Analysis of candidate regions qtl5-1 and qtl5-2 identified Glyma.05G097200 and Glyma.05G240200 as promising candidate genes, exhibiting distinct expression patterns between salt-tolerant and -sensitive genotypes.  Functional characterization in Arabidopsis demonstrated that overexpression of the soybean gene GmMACPF1 induced salt sensitivity, while the macpf1 mutant of Arabidopsis displayed enhanced salt tolerance.  Additionally, GmMACPF1 underwent selection during soybean domestication, with haplotypes Hap1 and Hap3 conferring improved salt tolerance.  These results indicate that GmMACPF1 functions as a negative regulator of salt tolerance during germination, offering novel insights into the molecular mechanisms governing soybean response to salt stress during this crucial developmental stage.

The universal stress proteins (USPs) play important roles not only in abiotic stress tolerance but also in plant growth and development.  However, the role of USPs in regulating starch biosynthesis has not been reported.  In this study, the IbUSP17 gene was isolated from the sweetpotato line H283 with a high starch content.  The IbUSP17 protein was localized in the nucleus.  IbUSP17 was highly expressed in lines with high starch contents and during the rapid thickening and starch accumulation period of storage roots.  Overexpressing IbUSP17 increased the storage root starch content, especially the amylopectin proportion, without a storage root yield penalty in sweetpotato.  Overexpression of IbUSP17 up-regulated the genes involved in starch biosynthesis and increased the activities of enzymes related to amylopectin biosynthesis.  The contents of components related to starch biosynthesis were also increased in IbUSP17-overexpressing plants.  Silencing this gene produced the opposite effects.  These results suggest that overexpression of IbUSP17 increases the starch content by up-regulating the genes involved in starch biosynthesis and increasing the activities of enzymes related to starch biosynthesis, especially amylopectin biosynthesis.  The role of the USP gene in starch biosynthesis is revealed for the first time in this study.  This gene is expected to be used to increase the starch yield and improve starch quality in sweetpotato.

Hybrid rice generally showed higher grain yield than inbred rice, but its overall performance is largely affected by lodging and lower grain quality.  Limited attention has been given to exploring genotypic variation and varietal traits for achieving high yield, superior quality, and strong lodging resistance simultaneously in both inbred and hybrid rice.  To address this gap, field experiments with five representative rice varieties from each rice type were conducted in Central China in 2020 and 2021.  The results showed that the average yield of hybrid rice in 2020 and 2021 was 8.01 and 8.63 t ha^–1, respectively, representing significant increases of 10.3 and 13.4% compared to inbred rice.  Importantly, hybrid rice showed comparable grain quality and lodging resistance to inbred rice.  Substantial genotypic variation was observed among the varieties for yield, grain quality, and lodging-related traits.  Efengsimiao (inbred) and Jinliangyou 534 (hybrid) showed the most balanced and superior agronomic performance within each variety type.  Key traits associated with the integration of high yield, superior quality, and strong lodging resistance included high spikelets per unit area, low grain length–width ratio, and short basal internode.  These findings highlighted the potential to select and breed rice varieties that optimize multiple desirable traits, offering a promising strategy to meet growing food demands in both quantity and quality.

Alternate wetting and drying (WD) irrigation is an effective water-saving practice for rice production but often increases nitrous oxide (N₂O) emissions.  Plant growth-promoting bacteria such as Bacillus subtilis (BS) can enhance crop growth; however, the combined effects of WD and BS on rice yield and N₂O emissions remain unclear.  A 3-year field experiment using two japonica rice cultivars was conducted to evaluate the effects of two irrigation regimes (continuous flooding (CF) and WD) and BS application (without BS, –BS; and with BS, +BS) on rice yield and N₂O emissions.  The results showed that BS application significantly increased the rice yields under both irrigation regimes.  Compared with CF–BS, CF+BS and WD+BS increased the yields by 3.9–9.0% and 5.8–12.6%, respectively, mainly due to a higher total spikelet number.  CF+BS had no significant effect on N₂O emissions, whereas WD–BS markedly increased cumulative N₂O emissions, while WD+BS reduced emissions by 34.8–45.9% compared with WD–BS.  The WD+BS treatment enhanced root oxidation activity and increased root surface area and volume density in the 20–40 cm soil layer.  It also reduced the soil NO₃⁻-N content, raised the NH₄⁺/NO₃⁻ ratio, and enhanced urease and sucrase activities, thereby promoting the accumulation of dissolved organic carbon (DOC) and microbial biomass nitrogen (MBN), along with a higher abundance of the nitrous oxide reductase gene (nosZ) associated with N₂O reduction.  Overall, integrating WD with BS increased rice yield while mitigating N₂O emissions.  The enhanced root function and aboveground agronomic traits, improved soil enzyme activity, and optimized nitrogen transformation and microbial processes were the key mechanisms for achieving a high yield with reduced environmental impacts.

Wheat (Triticum aestivum L.) is a major food crop grown worldwide.  However, field-grown wheat is generally restricted to only one generation per year and has a fluctuating yield, which limits wheat improvement and will fail to meet future food demands.  To minimize the generation time and increase total annual wheat production, five light regimens with varying day lengths and spectral distributions - 12 h light/12 h dark+white light (P12W), 17 h light/7 h dark+white light (P17W), 22 h light/2 h dark+white light (P22W), 22 h light/2 h dark+red:green:blue light at 6:3:2 (P22RGB), and 22 h light/2 h dark+red:blue light at 6:1 (P22RB) - were developed by adjusting the light-emitting diodes (LEDs) in a controlled environment.  The results showed that controlled wheat cultivation under LED lighting with varying day lengths and spectral distributions can potentially provide “faster” and “greater” grain production.  Prolonging the day length (from 12 to 17 h and then to 22 h) accelerated wheat development, particularly shortening the duration before flowering, and the longer the prolonged time, the earlier the flowering.  However, a 22 h day length (e.g., the P22W treatment) affected plant morphological traits, reduced dry matter accumulation, and resulted in a loss of yield-related components due to increased stress and disrupted pollen development.  Surprisingly, regulating the spectral distribution toward the red-light region under long-day conditions (e.g., the P22RB treatment) could partially restore the grain yield of wheat.  The light regime with a rich red-light region contributed to greater dry matter accumulation, carbohydrate flow to reproductive tissues, and sporopollenin biosynthesis, resulting in improved plant morphology and grain yield.  Collectively, the optimized light regimes represented by the P17W and P22RB treatments in controlled environment agriculture can produce 5–6 generations of wheat per year, yielding 3.16–5.87 kg m^–2 yr^–1, which is 3.59–6.68 times higher than field cultivation.  Thus, using appropriate LED light regimens is a favorable way to achieve rapid generation cycling and high productivity in controlled wheat cultivation.

Plastic film mulching (PFM) increases crop yields in semi-arid regions by reducing water losses and increasing soil temperatures, while crop production in these areas also serves as a significant source of ammonia (NH₃) emissions.  The effects of PFM on NH₃ emissions are mostly unknown because of interactions between greater N mineralization at higher temperatures and the film cover preventing NH₃ diffusion.  Therefore, our objectives were to (1) evaluate the effects of PFM on NH₃ emissions under field conditions, and (2) identify the maize yield and NH₃ emissions under climate change and atmospheric N deposition conditions using the DeNitrification-DeComposition (DNDC) model.  The experiment included four treatments: (1) no plastic film mulching without N fertilization (control), (2) plastic film mulching without N fertilization (PFM), (3) N fertilization without plastic film mulching (N), and (4) plastic film mulching with N fertilization (PFM+N).  The PFM increased maize yields by 211% and yield stability across the years when combined with N fertilization.  PFM reduced NH₃ emissions by 35% through three mechanisms: i) the high water content under PFM saturates soil pores, hindering NH₃ gas movement to the atmosphere; ii) the hot and wet conditions under PFM accelerate the nitrification rate, thus increasing pH buffering capacity during urea hydrolysis; and iii) the physical barrier created by PFM reduces NH₃ exchange between soil and air.  Daily NH₃ emissions increased with soil temperature, NH₄⁺ content, and pH, but declined with soil moisture under N fertilization.  The NH₃ emissions under PFM+N increased with NH₄⁺ content.  The parameterized DNDC model simulated the yield and daily NH₃ emissions very well.  PFM+N increased yield and reduced NH₃ emissions under the shared socioeconomic pathway (SSP) scenario and with N deposition.  Yield under PFM+N increased with increasing N deposition, whereas NH₃ emissions under PFM+N increased only under the high N deposition (N4) scenario compared with the no-deposition scenario, with no apparent increase under the N2 and N3 scenarios.  In conclusion, PFM increases yields and mitigates NH₃ emissions, and it can also potentially achieve similar benefits under future conditions.

Research on the yield-enhancing mechanisms of maize through ‘smart' plant morphology under dense planting conditions is a critical focus in modern agriculture.  However, the issue of yield stability in densely planted maize, particularly regarding lodging resistance, remains insufficiently examined in the literature.  A three-year field experiment was conducted using three hybrids (XD20, DH618 and DH605) and three plant density treatments (6.0×10⁴, 7.5×10⁴, and 9.0×10⁴ plants ha^–1) to investigate the effects of planting density on the lodging resistance and yield of summer maize hybrids with different plant morphologies.  According to the results, increasing the planting density significantly boosted the yield of DH605, while the yields of XD20 and DH618 exhibited initial increases followed by stabilization.  Compared to the low-density (L) treatment, the height parameters and center of gravity of summer maize under the high-density (H) treatment were significantly elevated.  This was accompanied by a pronounced reduction in light transmittance within the bottom and ear layers, a reduction in the mechanical strength of basal internodes, and an increased risk of lodging, particularly for the XD20 hybrid.  DH605 improved mechanical strength by enhancing the light distribution within the ear and bottom layers, and by optimizing basal internode characteristics.  Ultimately, the grain yield under the DH605-H treatment increased by 10.68 to 34.11% relative to XD20-H, with a concurrent reduction in lodging rates ranging from 72.66 to 92.29%.  Cellulose content within the basal internodes and the total area of vascular bundles in the outer layer were key factors, explaining 61.70% of mechanical strength variance.  Therefore, a high planting density significantly increased the yield but also lodging susceptibility.  Optimizing plant morphology improved the canopy light distribution, dry matter composition and anatomical structure of basal internodes, thereby enhancing lodging resistance and grain yield in densely planted maize.

Ensuring an adequate and nutritious food supply for the global population is a significant challenge in agricultural production practice.  Water and fertilizer are the main limiting factors in improving crop yield and quality.  However, it remains unclear whether the substitution of a portion of chemical nitrogen fertilizer with organic fertilizer, combined with reduced irrigation, can increase maize yield and quality through improvements in photo-physiological traits and nitrogen transportation.  A split-plot field experiment of maize was established in an arid area of northwestern China from 2021 to 2023.  Two irrigation levels formed the main plot: local conventional irrigation (I2, 4,050 m³ ha⁻¹) and reduced by 20% (I1, 3,240 m³ ha⁻¹).  Five equivalent nitrogen substitution ratios of chemical nitrogen with organic fertilizers formed a split plot, including sole chemical nitrogen fertilizer (F1), organic fertilizer substituting for 25% (F2), 50% (F3), 75% (F4), and 100% (F5) of chemical nitrogen fertilizer.  This study investigated the effects of combining organic and chemical nitrogen fertilizers under reduced irrigation on maize yield, quality, photo-physiological traits, and nitrogen transportation.  The results showed that reduced irrigation decreased maize yield and quality.  However, organic fertilizer substitution for 25% of chemical nitrogen increased maize yield and quality, with this effect greater than that observed with other equivalent nitrogen substitution ratios of chemical fertilizer with organic fertilizer.  A 20% reduction in irrigation combined with organic fertilizer substitution for 25% of chemical nitrogen (I1F2) increased maize grain yield and biomass by 13.0 and 8.9%, respectively, compared to local conventional irrigation and sole chemical nitrogen fertilizer (I2F1).  Meanwhile, I1F2 improved grain protein content by 10.0%, enhanced amino acid and vitamin B contents by 60.4 and 30.6%, and raised straw crude fat and crude protein contents by 23.1 and 5.6% compared to I2F1 in maize, respectively.  The reason for improving maize yield and quality with I1F2 was attributed to (1) improving leaf area index and leaf area duration at the blister (R2)−dough (R4) stage by 6.2 and 4.1%, increasing net photosynthetic rate by 43.8%, and enhancing pyruvate phosphate dikinase, phosphoenolpyruvate carboxykinase, and Rubisco activities by 9.8, 9.7, and 10.5%, respectively; (2) promoting nitrogen uptake and nitrogen accumulation after the R1 stage by 5.6 and 5.4% while maintaining nitrogen transportation quantity before the R1 stage.  Therefore, reducing irrigation by 20% combined with organic fertilizer substitution for 25% of chemical nitrogen can improve maize yield and quality via improving photo-physiological traits and nitrogen transportation in arid irrigation areas.

Echinacea purpurea is a perennial herbaceous horticultural plant belonging to the Asteraceae family.  It is easy to cultivate and well-known for its medicinal ingredients (e.g., chicoric acid) and high ornamental value.  However, studies on the synthesis and regulatory mechanisms of its secondary metabolites are limited.  Therefore, to advance research on E. purpurea, this study aimed to establish gene expression and silencing systems in E. purpurea.  First, a transient gene expression system mediated by Agrobacterium tumefaciens was developed in E. purpurea leaves.  After optimization, we found that injecting the fourth newly emerged leaf with the EHA105 strain and culturing for 4 d yielded the best expression results.  Then, a previously reported cut-dip-budding (CDB) system was adapted and improved to establish a gene expression system based on Agrobacterium rhizogenes.  By infecting the roots with A. rhizogenes, we detected efficient expression of the target gene after 30 d.  Using this system, we achieved expression of EpHTT, a key gene involved in chicoric acid synthesis, and significantly increased the accumulation of chicoric acid.  By expressing double-stranded RNA targeting EpHTT, we successfully silenced EpHTT expression and reduced chicoric acid accumulation.  We further investigated the protoplast-based transient gene expression system, studied key parameters such as enzyme concentration and osmotic pressure, and successfully achieved transient expression of the target gene in protoplasts.  Finally, a gene-silencing system in E. purpurea mediated by the tobacco rattle virus (TRV) was established, and EpCHLH was identified as the optimal silencing reporter gene, with the maximal silencing effect observed in 15-d-old seedlings.  By silencing genes involved in the chicoric acid biosynthesis pathway, such as EpHCT, EpHTT, and EpCAS, we successfully reduced chicoric acid accumulation.  In summary, this study successfully established various gene expression and silencing systems for E. purpurea, providing a valuable toolkit for further functional studies.

Vacuolar composition, particularly the type and abundance of metabolites and tonoplast proteins, critically determines fruit quality and flavor.  However, the specific vacuolar composition of fruits with different flavors at the fully ripe stage, especially regarding sugar accumulation, remains unclear.  In this study, we established an optimized protocol to overcome technical barriers in isolating intact vacuoles from fresh ripe citrus juice sacs of four citrus cultivars: NFMJ, Nanfeng tangerine (Citrus reticulata ‘97-2'); WZMG, Wenzhou satsuma (C. unshiu ‘Miyagawa'); NHER, ‘Newhall' navel orange (C. sinensis ‘Newhall'); MJY, Majiayou pomelo (C. grandis ‘Xipi Majia').  Subsequently, quasi-targeted metabolomics analysis and 4D-label-free proteomics analysis were conducted, identifying 640 metabolites and 1,782 proteins, respectively.  Notably, amino acids, flavonoids, lipids, carbohydrates, and organic acids collectively represented 70% of the total vacuolar metabolites.  Pummelo MJY vacuoles exhibited the highest sucrose accumulation, whereas tangerine NFMJ showed minimal sucrose content.  Proteomic profiling revealed vacuolar proteins participating in protein fate determination, metabolism, vesicle trafficking, solute transport, and energy supply.  Comparative analysis demonstrated significantly greater protein abundance variation between MJY and NFMJ than between other varieties.  In total, 158 transport proteins, including sugar-related transporters, were identified, and most of them were more abundant in MJY vacuoles.  The protein abundance of CsTST2 and CsERDL6 was greater in MJY vacuoles compared to other varieties, and the relative expression patterns of their encoding genes were consistent with sugar accumulation during fruit ripening.  Subcellular localization analysis confirmed their tonoplast localization.  Importantly, transgenic tomato fruits overexpressing these genes demonstrated both enhanced gene expression and increased sugar content.  This study systematically revealed cultivar-specific vacuolar composition and sugar accumulation strategies in ripe citrus fruits and provided key tonoplast proteins responsible for fruit quality improvement.

Cold storage of amber-fleshed black plums triggers anthocyanin biosynthesis and accumulation in fruit flesh, resulting in flesh reddening under low-temperature conditions. bHLH transcription factors have potential functions in response to cold induction and anthocyanin biosynthesis. To investigate the role of bHLH genes, two amber-fleshed and blackskinned cultivars (Prunus salicina Lindl. ‘Friar' and ‘Angeleno') were selected as fruit materials to conduct transcriptomic and bioinformatics analyses. Differentially expressed bHLH genes were identified by RNA-seq and validated using qRTPCR. Ten bHLH genes (five upregulated, five downregulated) showed the most significant expression changes during cold- triggered flesh reddening. We characterized the protein structures of these 10 bHLH members and constructed a phylogenetic tree. Among them, the gene evm.TU.Chr8.2504 (the corresponding protein ID is evm.model.Chr8.2504), named PsbHLH3, was cold-responsive and contains MYB-binding sites. Further experiments involving transient overexpression were performed to validate the function of PsbHLH3 in facilitating anthocyanin biosynthesis. Yeast twohybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays demonstrated that PsbHLH3 interacts with PsMYB10.1. Dual-luciferase assay showed that PsbHLH3 promoted the activation of PsMYB10.1 on the promoter of PsUFGT, and consequently augmented the transcription of structural genes related to anthocyanin biosynthesis. The study reveals that cold storage upregulates PsbHLH3, which acts as a molecular switch governing cold-triggered flesh reddening in plum fruit. These findings clarify the regulatory function of PsbHLH3 in cold-triggered anthocyanin biosynthesis in postharvest plums.

Gibberellin 2-oxidases (GA2ox) play an important role in regulating the balance of bioactive gibberellins in plants, while their role in the drought response mechanism of grapes remains unclear. In this study, the subcellular localization analysis revealed that the VvGA2ox5 protein was predominantly localized to the cytoplasm and nucleus. Transient transformation experiments on ‘Pinot noir' grape leaves showed that overexpression of VvGA2ox5 reduced relative electrical conductivity (REC) and malondialdehyde (MDA) levels and increased proline content, antioxidant enzyme activity, and expression of drought-responsive genes. In contrast, virus-induced gene silencing (VIGS) silenced leaves showed the opposite results. Additionally, the overexpression of VvGA2ox5 in ‘Pinot noir' grape calli and Arabidopsis thaliana (Arabidopsis) further validated its positive function. In CRISPR-Cas9-edited grape calli, the results were opposite to those of overexpression lines. Meanwhile, yeast two-hybrid (Y2H) screening identified a drought-responsive protein, dehydration-induced 19 homolog 3 (VvDEH). RNA-seq analyses showed that overexpression of VvGA2ox5 significantly participates in the hormone signaling pathway. Accordingly, VvGA2ox5 is a crucial regulatory gene in enhancing drought tolerance in grapes and serves as a potential candidate gene for improving drought tolerance in plants. This finding offers significant theoretical support for drought tolerance breeding in grapes.

The tea plant (Camellia sinensis) is an economically important leaf crop in which the flowering process consumes substantial nutrients, thereby negatively impacting tea yield and quality. Therefore, deciphering the molecular basis of floral transition is essential for enhancing tea cultivars and optimizing plantation management. The non-flowering tea plant line ‘Ziyang 1' (ZY1H), which has failed to flower for several consecutive years, and the normal-flowering cultivar ‘Ziyang' (ZYQT) were used to study the molecular mechanisms underlying the non-flowering phenotype in ZY1H. Phenotypically, ZY1H exhibited shortened internodes, prolonged vegetative growth, and failure to develop floral meristems. Chromosomal analysis confirmed that ZY1H maintains a normal diploid chromosome number (2n=30), excluding triploidy as a causal factor for its non-flowering trait. Transcriptome analysis revealed an impaired vegetative-to-reproductive transition in ZY1H, manifesting as low expression of SPL genes and sustained high expression of flower-repressive AP2-like genes. Additionally, elevated expression of the flowering repressor SVP and reduced expression of the floral integrator FT further disrupted the convergence of floral inductive signals. Notably, brassinosteroid (BR) levels and CsBZR2 expression were elevated in ZY1H. Functional assays showed that CsBZR2 directly binds the CsFLC promoter and suppresses its expression, thereby blocking the flowering process. Collectively, these results demonstrate that disrupted BR signaling and sustained vegetative growth jointly trigger the floral transition defect in ZY1H. This work provides novel insights into the molecular mechanisms of flowering regulation in tea plants and valuable theoretical support for cultivar improvement.

Low temperature is involved in regulating plant growth, development, and quality formation.  The mechanism by which low temperature affects sucrose accumulation in oriental melon fruit is currently unclear.  Here, high-sucrose (HS) melons were used as the research materials and subjected to two temperature regimes of 30°C/18°C (day/night) and 22°C/10°C (day/night) at the onset of ethylene production.  Low temperature significantly inhibited ethylene release and sucrose accumulation in melon fruit, while ethephon treatment at low temperature partially restored the ethylene production and sucrose content.  Using yeast one-hybrid (Y1H), GUS activity analysis, and luciferase assay, we found that the transcription factor CmCBF3 could bind to CmACO1 (ACC oxidase 1) promoter and inhibit its activity, thereby suppressing ethylene production.  Overexpression of CmCBF3 under low temperature significantly inhibited the synthesis of ethylene and sucrose.  Further research showed that low temperature promoted CmERFV-2 expression, and CmERFV-2 could bind to CmCBF3 promoter to further inhibit ethylene synthesis.  In addition, CmMYB44, a transcription factor that negatively regulated fruit ethylene production and sucrose accumulation, repressed the expression of CmACO1 and CmSPS1 (sucrose phosphate synthase 1).  CmERFV-2 further affected the expression of CmACO1 and CmSPS1 by binding to CmMYB44 promoter, thereby regulating ethylene and sucrose content at low temperature.  In summary, this study revealed the mechanism by which CmERFV-2 affects ethylene release and sucrose accumulation in oriental melon fruit, laying a foundation for breeding high-quality melon varieties suitable for low-temperature cultivation.

Colletotrichum higginsianum, a plant pathogenic fungus threatening cruciferous crops, necessitates advanced genetic tools to study its pathogenesis and host interactions. However, selection markers available for fungal genome editing are often limited by scarcity and variable efficacy across species. Acetolactate synthase (ALS), a key enzyme in branched- chain amino acid (BCAA) biosynthesis, is the target of the herbicide chlorimuron ethyl (CE). Here, we utilized AlphaFold3- guided structural prediction to engineer ALS in C. higginsianum into a dual-functional endogenous selection marker. AlphaFold3-predicted ChALS structures revealed conserved catalytic regions and identified hydrophobic residues (V191, A200, F201) potentially critical for CE binding. Notably, introducing a single A200D substitution conferred the resistance of C. higginsianum to CE without impairing fungal growth, conidiation, or pathogenicity. Molecular docking simulations confirmed that the introduced aspartate side chain causes steric clashes that destabilize CE binding. Leveraging this mutation, we developed a homology-directed integration system enabling precise genetic tagging at the endogenous ChALS locus using the A200D allele for selection. Colletotrichum higginsianum strains expressing fluorescent proteins targeted to the nucleus, mitochondria, peroxisomes, or cytoplasm exhibited stable expression and unaltered infection dynamics in Chinese flowering cabbage (Brassica parachinensis). This work presents a dual-functional marker that addresses limitations in fungal genome editing tools. Moreover, the facility with which the A200D mutation confers resistance serves as a cautionary note on the potential evolutionary instability of single-target enzyme inhibitors in pathogen management.

Citrus Huanglongbing (HLB) has caused extensive damage to the global citrus industry. ‘Candidatus Liberibacter asiaticus' (CLas), the primary causal agent of HLB, utilizes effectors to modulate host defense responses, though the mechanisms of these effectors remain unclear. This study demonstrates that the citrus armadillo (ARM)-repeated protein CsARM26 interacted with CLIBASIA_00185 (CLas0185) in vivo and in vitro. CLas0185 enhanced the abundance of CsARM26, whereas CsARM26 destabilized the effector. Additionally, the transient co-expression of CLas0185 and CsARM26 facilitated infection by Xanthomonas citri subsp. citri. Moreover, transgenic CsARM26 citrus plants suppressed the accumulation of free salicylic acid (SA) and the expression of SA-associated genes. This study reveals that an ARM-repeated protein plays a role in the immune response to the CLas–citrus interaction, establishing a foundation for further investigation of the molecular mechanisms of CLas infection.

The oriental fruit moth, Grapholita molesta  Busck, is a major pest of fruit trees worldwide, it is necessary to develop green control technology instead of the traditional chemical pesticide. Although the sterile insect technique (SIT) is a safe and effective method for controlling G . molesta , the high cost of mass rearing irradiated pupae hinders its widespread adoption. In this study, we identified the optimal sub-sterilizing X-ray dose for G . molesta  adults and evaluated its effects on the mating competitiveness of males, growth and reproduction of the F 1   generation population, and the sterility rate of field- caught males. The results showed that the sub-sterilizing dose of 1-day-old male was 130 Gy, which rendered most males sterile (76.34%) and females nearly sterile (97.41%). Moreover, the sterile trait of the male parents that had been irradiated with 130 Gy of X-rays was successfully transmitted to the F 1   generation, whose sterility rate (84.13–93.61%) exceeded that of F 0   males. The F 1   generation population exhibited significantly lower values for the net reproductive rate (R 0 ), intrinsic rate of increase (r ), and finite rate of increase (λ ) compared to the non-irradiated group. Furthermore, the competitive mating index and sterility rate of irradiated males were the highest when they were paired with unirradiated males and females at a release ratio of 20:1:1. The irradiating wild males captured by sex pheromones in peach orchards with the sub-sterilizing dose achieved a 75.69% sterility rate, comparable to the laboratory-reared population. This study introduces a novel X-ray irradiation method for adult G . molesta  captured in the orchard field and lays a theoretical foundation for promoting the wide application of the SIT.

The lack of knowledge regarding how the genome is regulated during skeletal myogenesis in pigs hinders the identification of genetic variants for meat traits. Here, we systematically characterized the cis-regulatory elements (CREs, including promoters, enhancers, and others) by using Hi-C coupled chromatin cleavage and tagmentation (HiCuT, H3K27ac), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and RNA-seq to analyze primary myoblasts and in vitro well-differentiated myotubes, and generated an atlas of promoter-enhancer interactions (PEIs) during myogenic differentiation. In total, 179,895 and 159,255 loops were identified in myoblasts and myotubes, respectively, which could be grouped into 3 categories: the interactions between promoter and enhancer (P–E), between promoter and promoter (P–P), and between other genomic regions (O–O). Furthermore, 22,645 cis-expression quantitative trait loci (eQTLs) were pinpointed by integrating public genome-wide association studies (GWAS) and eQTL datasets. Notably, novel promoter-like enhancers were verified, and cis-eQTLs in promoter-like enhancers might influence gene expression over long ranges. In addition, 39,069 structural variants (SVs) within the CREs were identified. A transcription factor (TF)-promoter/enhancer regulatory network for myogenesis was generated, revealing several novel TFs relevant to myogenic differentiation. This work provides a valuable resource for understanding genomic regulation in pig muscles and filtering potential variants to develop breeds with desirable traits.

Understanding the genetic changes behind the phenotypic variation of Chinese donkeys is helpful to the genetic improvement and breeding of donkeys. However, the population structure and novel genes associated with morphological (coat color and body size) and adaptive (high-altitude adaptation) traits of Chinese donkeys remain largely unknown. Here, we analyzed 391 whole-genome sequencing (WGS) data of Chinese donkeys. Population genomic analyses showed that Chinese native donkey breeds mainly consist of three distinct populations (Southwest plateau, North plain, and Guanzhong plain), and a newly discovered population (Guanzhong plain) was identified. Moreover, we characterized a high-confidence list of 127, 117, and 169 selective signal genes for coat color, body size, and high-altitude adaptation, respectively. We discovered ARID3B gene with strong signals of selection, which may account for coat color in Chinese donkeys. Our study identified EPAS1 as a high-altitude adaptive gene. However, the FAM184B gene shows a stronger signal in response to high-altitude environments in Chinese donkeys. The selective sweep and GWAS analysis showed that LCORL and TMEM154 genes are potentially associated with body size in Chinese donkeys. Utilizing PacBio HiFi sequencing data, this study presents 15,954 highly reliable structural variations (SVs) between large-sized and small-sized donkeys. Utilizing SV data and a graph-based method, we identified an 880-bp deletion in the TMEM154 gene in Sichuan donkeys (small-sized) compared to Guanzhong donkeys (large-sized), which was verified by PCR and is a candidate SV related to body size. Transcriptome sequencing data showed that the TMEM154 gene is highly expressed in the muscle of Guanzhong donkeys (large-sized) compared to Sichuan donkeys (small-sized). Multi-species alignment analysis revealed that the region surrounding the 880-bp deletion in the TMEM154 gene region is conserved in horse, zebra, kiang, as well as two large-sized donkey breeds (Dezhou and Guanzhong), except in in the small-sized Sichuan donkey. Furthermore, after the 880 bp deletion was transfected into 3T3-L1 and HEK293T cells, it was demonstrated that the relative luciferase activity of the mutation was markedly decreased in comparison with that of the wild type. These results suggest that this 880-bp deletion in the TMEM154 gene may play an important role in body size trait of donkey. This study provides valuable genome resources for donkey breeding and sheds light on the domestication history of Chinese donkeys.

Grassland resources are the foundation of the sheep industry, and the development of artificial pastures provides a solution for alleviating the livestock-carrying pressure on natural grasslands. Based on the impact of lipid metabolism on muscle fatty acid composition, studying the differences in rumen and liver lipid metabolism between grazing and indoor feeding lambs helps to analyze the causes of high-quality grazing lamb meat and to improve the productivity of artificial pasture-based grazing systems. A total of 22 weaned lambs with similar weights were assigned to two groups: one fed pellets and hay in separate pens (AF) and the other grazing exclusively on artificial pasture (AG) for 90 d. The results showed significantly higher serum glucose and triglyceride concentrations and significantly lower serum lipase activity in the AF vs. AG group (P<0.05). The metabolome revealed that crucial differential metabolites (DFMs) participating in lipid metabolism, oleic acid and palmitic acid, were down-regulated in the rumen of the AG group. In the liver, oleic acid, α-linolenic acid, and stearic acid were down-regulated in the AG group, while linoleic acid was up-regulated. Meanwhile, rumen hydroxypropanoate and liver succinic acid, enriched in propionate metabolism processes, were down-regulated in grazing lambs. Subsequently, liver transcriptome sequencing revealed that grazing inhibited fatty acid oxidation and lipid synthesis by down-regulating Malic enzyme 1 (ME1), fatty acid-binding protein 1 (FABP1), hydroxyacyl-CoA dehydrogenase alpha subunit (HADHA), Perilipin-2 (PLIN2), and acetyl CoA acyltransferase 2 (ACAA2). The significant correlation between CYP4A6 and propionate metabolites suggested a potential regulatory role of propionate metabolism in liver lipid metabolism. Moreover, oleic acid, palmitic acid, and stearic acid in muscle, rumen, and liver were closely correlated, revealing an essential contribution of rumen and liver lipid metabolism to muscle fatty acid deposition. Through the multi-omics assessment of the rumen and liver, this study systematically revealed the lipid metabolism mechanisms in lambs under different feeding patterns, which are influenced by comprehensive factors such as diet and environment. These findings contribute to the goals of high quality grazing lamb production and efficient grassland productivity.

African swine fever (ASF) is an acute, hemorrhagic disease caused by the African swine fever virus (ASFV), with a mortality up to 100%. The disease poses a serious threat to the global swine industry, yet no commercial vaccines or antiviral drugs are available other than in Vietnam. ASFV attenuation through serial passages is a key approach for vaccine development. In this study, a cell-adapted virus, named HLJ18/BK33, was successfully generated by serially passaging the ASFV Pig/HLJ/18 in wild boar kidney cells (BK2258). This adapted virus exhibited clear cytopathic effects (CPE) and replicated stably and efficiently in BK2258 cells and porcine alveolar macrophages. Whole-genome sequence analysis revealed that, compared with the Pig/HLJ/18 virus, HLJ18/BK33 had a large deletion of 6,162 bp from sites 181,027 to 187,188, and four single nucleotide deletions that led to frameshift mutations, resulting in the truncated expression of three open reading frames (ORFs) (ASFV_G_ACD_00120, ASFV_G_ACD_00350, and A179L), and the fusion expression of two ORFs (MGF_110-14L and MGF_110-11L). Additionally, four genes exhibited missense mutations, leading to single amino acid changes. Five pigs intramuscularly inoculated with 10⁶ TCID₅₀ of HLJ18/BK33 remained healthy with normal body temperatures and no clinical signs, indicating a high attenuation of virulence for HLJ18/BK33 in pigs. Upon challenge with the parental Pig/HLJ/18 virus, four of the five inoculated pigs developed persistent high fever and ASF-related clinical signs and died within 13 days post-challenge (dpc); the remaining pig developed transient fever but survived until the end of theobservation period. These results indicate that the HLJ18/BK33 virus is highly attenuated but cannot induce protection against the parental virulent virus. Even though the HLJ18/BK33 virus is not a good vaccine candidate, its stable replication and distinct CPE in BK2258 cells as well as its low biosafety risk make it a valuable resource for studies on virus–host interactions, antiviral drug screening, diagnostic methods, and biological characteristics.

Soil nitrogen activation (N_act) is pivotal for the global N cycle, influencing crop N availability and environmental N losses.  However, it remains unclear how climate and fertilization individually, or jointly, affect soil N_act over multiple decades.  Here, we examined the dynamic shifts in N_act between the first decade and later period in soils treated with non-fertilizer, mineral fertilizer with/without manure, mineral fertilizer with stover return, in 1982 and 1990, in six typical agricultural zones.  Results revealed that soil total N (TN) and available N (AN) increased at rates of 10.1–58.2 and 1.41–4.13 mg kg^–1 yr^–1, respectively, by manure application at five sites, suggesting that manure enhanced both soil N storage and availability.  The GZL site exhibited the highest annual change rate (ACR) in TN (48.3–58.2 mg kg^–1 yr^–1), while the ZY site had the lowest (10.1 mg kg^–1 yr^–1).  Conversely, the YL site showed the highest ACR in AN (3.65–4.13 mg kg^–1 yr^–1), whereas the ZZ site exhibited the lowest (1.41–2.23 mg kg^–1 yr^–1).  Notably, the N_act rates with manure application were higher in the first decade (42–181 mg g^–1) than in the later period (33–92 mg g^–1) at all sites.  Overall, the average N_act of all treatments in the first decade (79–105 mg g^–1) across six study sites was higher than in the later period (30–78 mg g^–1).  Variance portioning analysis indicated that soil properties' contribution to N_act increased from 35% to 45% over time, while climatic conditions' effect decreased from 19% to 8%.  Structural equation modeling confirmed a direct impact of annual temperature on N_act, with path coefficients of 0.86 in the first decade and 0.45 in the later period.  These results show that the impacts of climate on soil N_act were attenuated under long-term fertilizer application, while the interactions between climate and soil had an enhanced impact on N_act in the later period of fertilization.  This context-specific insight can guide soil management strategies to enhance N availability, modulate the effects of climate change on agricultural production, and minimize environmental N losses.

This study explored the complex mechanisms of methane (CH₄) emissions in paddy fields, focusing on the often-overlooked role of soil texture.  Through the analysis of 31 paddy soil samples, the research investigated the complex interactions among soil texture, organic carbon composition, soil nutrients, and microbial abundance in regulating CH₄ emissions during the tillering stage of rice.  The results revealed significant variations in CH₄ emissions among different soils, which were notably associated with soil texture, organic carbon, nutrients levels, and microbial abundance.  Soil texture, particularly clay content, emerged as a key factor influencing the composition of organic carbon, showing a significant positive correlation with mineral-associated organic carbon (MAOC).  While organic carbon components significantly enhanced CH₄ emissions, their effects were not uniform: particulate organic carbon correlated negatively with emissions, whereas MAOC showed a positive association.  Soil texture also influenced nutrients availability, with clay content significantly correlated with soil nitrogen and phosphorus content, which in turn affects the abundance of functional genes.  Specifically, mcrA abundance was positively correlated with available potassium, while pmoA abundance was positively correlated with available phosphorus.  Additionally, dissolved organic carbon promoted pmoA abundance, although this effect was mitigated by higher clay content.  Network analysis further emphasized the central role of soil texture, with clay exhibiting the highest degree and closeness centrality.  In conclusion, soil texture is a fundamental and core factor influencing CH₄ emissions at tillering of rice, exerting its influence through multiple pathways including modulating the composition of organic carbon, nutrient availability, and the abundance of methanogens and methanotrophs.  These findings provide theoretical foundations for developing low-carbon cultivation strategies tailored to different soil textural characteristics.

While excessive nitrogen fertilizer application enhances crop yields, it does so at the expense of ecosystem health, making the enhancement of nitrogen use efficiency (NUE) an imperative for sustainable agriculture. This study investigates the mechanisms underlying the response to low nitrate (LN) stress in two Brassica juncea genotypes: a high-NUE (H158) and a low-NUE (L159), aiming to identify genetic resources for improved NUE. Hydroponic experiments revealed that H158 displayed enhanced antioxidant capacity, nitrogen assimilation, and nitrogen uptake efficiency (NUpE) under LN conditions relative to L159. Field trials corroborated these findings, with H158 demonstrating higher yields and greater agronomic nitrogen use efficiency (ANUE) across a gradient of nitrogen application rates. Genomic analysis identified 1,654 genes associated with NUE, including NIN-LIKE PROTEIN 4 (BjuB04.NLP4), whose G/C variants influenced transcriptional regulation and root-to-shoot ratio responses to nitrogen availability. Notably, BjuB04.NLP4-HAP2 (H158) was predominant in low-nitrogen soils, while BjuB04.NLP4-HAP1 (L159) was more common in high-nitrogen soils. Collectively, our findings uncover and characterize valuable genetic resources for breeding rapeseed varieties with enhanced NUE, providing both elite germplasm and functional molecular markers.

Warming and altered precipitation frequently co-occur and jointly influence key carbon cycling processes in alpine ecosystems. However, the interactive effects of these two global change factors on ecosystem respiration (Re) and methane (CH₄) fluxes remain unclear. To address this gap, a long-term field experiment was conducted in an alpine meadow on the Qinghai-Tibet Plateau, combining warming (+2°C) and increased precipitation (+20%). Warming significantly reduced Re by 14.2%, concurrent with a shift from fungal to bacterial dominance. In contrast, increased precipitation enhanced Re by 34.1%, driven by improved soil moisture and greater plant carbon inputs. CH4 uptake increased under warming (+31.0%) but decreased under increased precipitation (−26.3%), linked to the change in methane-oxidizing bacterial communities. Candidatus Methylumidiphilus, Methylococcus, and Methylomagnum were identified as key predictors. Combined warming and increased precipitation enhanced Re while suppressing CH₄ uptake, indicating that future warming-wetting conditions may intensify carbon losses and weaken the carbon sink capacity of alpine meadows. These findings underscore the necessity of integrating microbial ecological responses into ecosystem models to better predict carbon-climate feedbacks under multifactorial global change.