Chloroplast gene expression relies on nucleus-encoded factors for RNA metabolism processing, but the mechanisms under cold stress remain poorly understood.  In this study, we isolated and characterized a foxtail millet (Setaria italica) mutant, temperature-sensitive chlorophyll-deficient (sitcd1), which exhibited reduced chlorophyll content and abnormal chloroplasts, resulting in an albino phenotype during early leaf development at low temperatures (20°C during the day and 18°C at night).  Map-based cloning revealed that SiTCD1 encoded a P-type PPR protein localized in chloroplasts.  In sitcd1 background, transgenic lines of SiTCD1 overexpression appeared nearly normal green leaves under L20/D18 condition.  SiTCD1 was especially expressed in earlier development of leaves under low temperature.  Additionally, SiTCD1 directly bound to the plastid gene atpF in vitro, which might participate in the splicing of plastid gene atpF under low temperature.  RNA-seq indicated that the expression of genes related to metabolism (such as porphyrin, chlorophyll and glutathione metabolism), which required ATP for energy, was down-regulated in sitcd1, resulting in decreased chlorophyll content, GSH, and its redox couple (GSH/GSSG) at low temperature.  As sitcd1 exhibited more sensitive at the bud bursting stage than germination and seedling stage under cold stress, we identified two haplotypes of SiTCD1 (SiTCD1^Hap1 and SiTCD1^Hap2) in 195 accessions, and found that accessions carrying the SiTCD1^Hap2 allele were more tolerant to cold stress than those with the SiTCD1^Hap1 allele at the bud bursting stage.  In summary, our results suggest that SiTCD1 is essential for early chloroplast development under low temperature in foxtail millet.

Fusarium head blight (FHB) is one of the most important and destructive wheat diseases worldwide, threatening both food security and safety.  In this study, a recombinant inbred line (RIL) population with 269 F₆ lines developed from a cross between ‘Nanjing 8611’ and ‘Ocoroni’ was used to map quantitative trait loci (QTLs) for FHB resistance.  Field FHB trials were conducted for three years in Nanjing, China, using point inoculation, and two years in Mexico with spray inoculation.  A high-density genetic map was constructed for the RIL population using the wheat 55 K single nucleotide polymorphism (SNP) array.  A total of 13 QTLs were detected on chromosomes 1B, 2D, 3B, 5D, 6D, and 7A, among which two major QTL, QFhb.CIM-2D.1 and QDon.CIM-3B.1, were stably expressed in this study.  Conditional QTL analysis suggested that QFhb.CIM-2D.1 contributes to reduced deoxynivalenol (DON) content via decreasing FHB severity, whereas QDon.CIM-3B.1 contributed to FHB resistance by directly controlling the accumulation of DON.  Stacking of QFhb.CIM-2D.1 and QDon.CIM-3B.1 exhibited markedly increase in resistance against both FHB and DON.  Furthermore, two Kompetitive Allele-Specific PCR (KASP) markers, KASP-1369 and KASP-8394, tightly linked to QFhb.CIM-2D.1 and QDon.CIM-3B.1, respectively, were developed and successfully validated in their respective genetic populations.  Altogether, our results broaden our understanding of the genetic basis of resistance to FHB and the developed markers will be useful for marker-assisted breeding of wheat. 

Due to their sessile nature, plants require strong adaptability to complex environments, with stress tolerance often associated with trade-offs in growth and development (Major et al. 2020).  This antagonistic relationship between defense and growth has been interpreted as a competition for limited resources that are allocated to defense at the expense of growth, or vice versa. Recent studies have demonstrated that hormone-based signaling networks trigger transcriptional changes in key genes, leading to trade-offs between growth rates and stress defense (Huot et al. 2014).  Several genes involved in biotic and abiotic stress response have been identified.  These genes contain nonsynonymous variants that show convergent changes in allele frequency across different breeding eras in both China and the United States (Wang et al. 2020), which may reflect the selection of biotic and abiotic stress response genes during modern maize breeding.

Transcription factors (TFs) play vital roles in regulation of gene expression in plant cells, with specific key TFs exhibiting multifunctionality by coordinating various regulatory pathways to promote plant growth (Hufford et al. 2021).  Jasmonates (JAs) are identified among phytohormones for their significant roles in regulating various plant processes, particularly in defense mechanisms against pests. MYC2 is a central transcription factor that orchestrates the JA signaling pathway and defense responses in plants by regulating the expression of numerous genes (Du et al. 2022).  Although MYC2 has been extensively characterized in Arabidopsis, studies in crops have revealed the complexity of MYC2’s function, with reports addressing different aspects, such as growth in wheat (Li et al. 2023) or stress defense in maize (Ma et al. 2023).  However, lack of systematic understanding of the complex regulatory network of MYC2 in crops, particularly in maize constrain the further utilization of MYC2 and its downstream genes in maize genetic modification for breeding elite varieties.  Here, we reported that ZmMYC2 had undergone selection during domestication and modern breeding; it acts as a key regulator of the trade-off between development and defense gene expression in maize, elucidating its regulatory network, which holds significant importance in balancing yield and resistance.

Given that some resistance genes have been selected during modern breeding, we analyzed the history of ZmMYC2 over the processes of maize evolution and artificial selection.  According to maize Haplotype Map v3 (HapMap3) database consisting of 1164 modern maize accessions, 25 landraces, and 21 teosintes (Zea mays. parviglumis) (Bukowski et al. 2018), nucleotide diversity strongly decreased sharply at the promoter region (2000 bp upstream of transcription start site) of ZmMYC2 during breeding, while the coding region and 3’-downstream region of ZmMYC2 showed less dramatic changes in nucleotide diversity changes (Fig. 1-A).  Thus, we hypothesize that the genetic diversity within the promoter region of ZmMYC2 has decreased during the breeding process, with favorable variations being selected.  Moreover, the frequency of three polymorphisms underwent convergent changes during modern breeding in both the United States and China (Fig. 1-B–D).  These three polymorphisms constituted three principal haplotypes: pZmMYC2^Hap1, pZmMYC2^Hap2, and pZmMYC2^Hap3, of which the frequency of pZmMYC2^Hap1 showed an increasing trend during modern maize breeding (Fig. 1-E).  The rare haplotype pZmMYC2^Hap3 (n=4) emerged only during the breeding era of China in 2000.  LUC signal activity for pZmMYC2^Hap3 was significantly lower than that of the other two haplotypes in the promoter region (pZmMYC2^Hap1, pZmMYC2^Hap2) (Fig. 1-F–H), suggesting a differential regulatory potential among the haplotypes.  These data indicate that ZmMYC2 was under-selected during maize evolution and breeding processes of maize.  Next, we investigated the expression level of genome-wide association studies of ZmMYC2 based on 368 maize inbred lines using RNA-seq and genome resequencing data (Fu et al. 2013; Li et al. 2013).  The results showed a strong peak signal containing the genomic region of ZmMYC2 on chromosome 1 (Fig. 1-I).

To mine the genes downstream of ZmMYC2, we performed protoplast transient expression-based RNA-sequencing (PER-seq) analysis to facilitate the discovery of new downstream genes utilizing a consistent protoplast system (Zhu et al. 2023).  In total， 281.6 million clean reads were generated, among which an average of approximately 87% of reads were mapped uniquely to the reference genome (Appendices A and B).  The results demonstrated a significant increase in the expression level of ZmMYC2 in each of three replicates of the pRTL2-ZmMYC2-GFP (MYC2-GFP) construct, exceeding a 500-fold increase compared to the pRTL2-GFP-empty (GFP-empty) construct (Fig. 1-J).  Furthermore, upon analyzing differentially expressed genes (DEGs) with a false discovery rate (FDR) <0.05 as the threshold, it was found that 4480 unique DEGs of MYC2-GFP, among which 2,677 were up-regulated compared to GFP-empty (Appendix C).  These up-regulated genes are enriched in circadian rhythm, cell cycles, plant growth, and in response to stress, indicating that these genes are regulated directly or indirectly by ZmMYC2 (Appendix D-A–B).

Several potential candidate genes were selected in an unbiased manner based on their log₂(fold-change) ≥2.5 (Fig. 1-J).  Gene expression profiling analysis of ZmMYC2 and its potential targets revealed essential coincidence (Appendix E).  The interaction between MYC2 and targets observed in the PER-seq system, were further confirmed through expression quantitative trait loci (eQTL) analysis, dual-luciferase reporter assay (DLR), and electrophoretic mobility shift assay (EMSA).  Among the target genes, the members of cytochrome P450 (CYP) gene family are widely distributed in plants involving in various biological processes, such as detoxification of xenobiotics, secondary metabolites production, and terpenoid synthesis (Chakraborty et al. 2023; Sun et al. 2024).  Our results identified an unreported gene of cytochrome P450 family ZmCYP709H1 as a target of ZmMYC2.  Additionally, eQTL analysis of ZmCYP709H1 revealed a strong trans-eQTL signal in the region of chromosome 1, which contains the genomic region of ZmMYC2 (Fig. 1-K).  Subsequent validation through DLR and EMSA confirmed that ZmMYC2 interacts with the promoter region of ZmCYP709H1 and stimulates its expression (Fig. 1-L; Appendices F-A and G-A).  Moreover, the transcriptional activation effect of ZmMYC2 on the promoter of ZmCYP709H1 was suppressed by ZmJAZ8 (Fig. 1-L).  A recent report showed reduced expression of ZmCYP709H1 in three maize dwarf mutants compared to the wild-type, reflecting its potential role in regulating growth, particularly plant height.  This result supports our proposed function of the ZmMYC2-ZmCYP709H1 model (Gao et al. 2024).  Additionally, two other CYP genes, ZmBX5 and ZmBX6, were identified as potential downstream genes of ZmMYC2 that participate in benzoxazinoid synthesis, which is consistent with the findings of a previous study (Ma et al. 2023).  We further confirmed that ZmMYC2 can physically bind to the promoter region of these two genes and activate their expression (Appendix H-A–F).  Besides, the result showed that ZmMYC2 can activate ZmBRD1 expression, which is a member of the CYP gene family and responsible for the final step of brassinosteroid synthesis (Tian et al. 2019) (Fig. 4-A and B; Appendix I-A–D).

The AUXIN RESPONSE FACTOR (ARF) family consists of plant-specific TFs that are key regulators of gene expression in response to the plant hormone auxin (AUX), and participated in various developmental processes such as vascular tissue differentiation, root and shoot development, and environmental stimuli responses (Hagen and Guilfoyle 2002; Salmon et al. 2008).  However, little evidence has been found to support the regulation of ARF gene expression by the core factor ZmMYC2 in the JA signal transduction pathway in maize.  Our data showed that the expression of ZmARF3 was regulated by a trans-eQTL signal involving the gene region of ZmMYC2 (Appendix F-B).  In addition, ZmMYC2 can bind to the promoter region of the ZmARF3 gene and activate its transcription (Fig. 1-M; Appendix G-B).  Besides, MYC2 can activate expressions of senescence-associated genes in rice and wheat, which could be repressed by physical interactions with TaARF15-A1 (Li et al. 2023).  These data demonstrate the key role of MYC2 in regulating the stress resistance and growth of maize through the synergistic regulation of JA and AUX hormone signaling pathways.

Tonoplast intrinsic proteins (TIPs), a subgroup of the aquaporin family, are integral membrane proteins that are crucial for transporting water and small solutes across cellular membrane to maintain water balance (Chaumont et al. 2001).  We found that ZmTIP3c was activated by ZmMYC2 (Fig. 1-N; Appendices F-C and G-C), which supports the potential role of ZmMYC2 in jointly regulating drought stress and JA signal transduction.  The CER2 gene, which is a member of the ECERIFERUM family, is critical for the synthesis of epicuticular wax (Bourdenx et al. 2011; Zhao et al. 2024).  A recent study demonstrated that wounding-induced wax accumulation was primarily regulated by the JA signaling pathway in Arabidopsis, suggesting the potential of JA signaling in wax synthesis (Huang et al. 2024).  We identified ZmCER2 as a ZmMYC2 target (Fig. 1-O; Appendices F-D and G-D).  Additionally, we confirmed the upregulation of ZmCER2 in response to drought stress in five elite inbred lines representing distinct heterotic groups of maize (Fig. 1-P), as observed by previous studies (Zhang et al. 2018, 2020; Jiang et al. 2023).  The result indicates that the drought-induced trait of ZmCER2 can be observed across different genetic backgrounds, thus supporting the potential role of ZmMYC2 in modulating JA signaling and response to drought stress in maize mediated by ZmCER2.

In summary, our findings support the selection of ZmMYC2 during domestication and breeding, highlighting its critical role in regulating genes involving plant growth and development.  Collectively, our eQTL, DLR, and EMSA data successfully validated several targets (ZmCER2, ZmARF3, ZmBRD1 ZmTIP3c, ZmCYP709H1, ZmBX5, and ZmBX6) of ZmMYC2, that encode diverse proteins and participate in various metabolic pathways (Fig. 1-Q).  Of these, ZmCER2 was confirmed to be induced by drought stress and activated by ZmMYC2, suggesting that ZmMYC2 may play a role in the drought response by regulating synthesizing epicuticular wax.  These findings underscore the diverse functions of ZmMYC2 in maintaining the balance between plant development and defense-response, primarily via the JA signaling pathway.  Our data represent a foundation for the further function and mechanism elucidation of of ZmMYC2 and its “Yin-Yang” roles in regulating plant defense and growth (Fig. 1-Q).  Given the crucial role of ZmMYC2 in balancing development and resistance, further work is needed to confirm to unlock the full potentials of ZmMYC2 in mediating yield and resistance through JA signaling pathway by exploring the function of those downstream targets, which is a significant step toward crop precision breeding. 

Excessive cadmium (GrCdc) and deficiencies of copper (GrCuc) and magnesium (GrMgc) in grains pose serious human health risks.  Common wheat breeding has reduced genetic diversity within elite germplasm resources, negatively impacting future wheat production.  Thus, identifying loci controlling GrCdc, GrCuc, and GrMgc from tetraploid wheat and introducing them into common wheat is essential for genetic improvement.  In this study, we identified quantitative trait loci (QTL) 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 (Ailanmai).  Four major, stably expressed QTL were identified.  Three of these, including 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 (TRIDC5AG052690, TRIDC5BG060070, and TRIDC4AG008520) with sequence variations 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 correlation between them and any of the eleven agronomic traits investigated was observed.  Additionally, QGrCuc.sau-AM-4A colocalized with QGrMgc.sau-AM-4A, suggesting potential shared physiological and/or genetic control.  Altogether, these stably expressed QTL across environments provide theoretical guidance for further germplasm improvement and fine mapping.

Maize/soybean intercropping systems are commonly used in developing countries, but few studies have been performed to elucidate the differences in nutrient efficiency and rhizosphere microbiome, especially when maize is intercropped with different soybean varieties. In this study, field experiments were conducted to compare the growth and yield of two soybean (Glycine max) varieties, BD2 and YC03-3, and one maize (Zea mays) variety, Huazhen, in mono-cropped and intercropped cultures. The plant biomass and N content of both crops in BD2/maize intercropping were significantly improved compared to their monoculture, but no such effects were observed in the plants of YC03-3/maize intercropping. The yield of BD2 intercropped with maize exhibited a 37.5% increment above that of BD2 in monoculture. Moreover, 19.2-29.1% longer root length of maize and 19.0-39.4% larger root volume of BD2 were observed in BD2/maize intercropping than in monoculture, but no growth advantage was observed in YC03-3/maize intercropping. Maize showed root avoidance when intercropped with BD2, but space competition when intercropped with YC03-3. 16S rRNA amplicon sequencing showed that compared with the monoculture system, rhizobacteria community composition in BD2/maize intercropping changed more significantly than that of the YC03-3/maize intercropping system. In BD2/maize intercropping, most of the rhizobacteria community biomarker bacteria of BD2 were positively correlated with plant biomass, as well as plant P and N content. Maize tended to recruit Rhizobiales and Proteobacteria, which showed positive correlation with plant biomass and N content, respectively, as well as soil available N. In conclusion, soybean varieties determined the advantages of maize/soybean intercropping through root-root interactions and modification of rhizobacteria communities. Our insight emphasizes a linkage between root traits and the rhizobacteria community, which shows the importance of optimizing intercropping systems by selection of appropriate crop varieties.

Deep learning-based intelligent recognition algorithms are increasingly recognized for their potential to address the labor-intensive challenge of manual pest detection. However, their deployment on mobile devices has been constrained by high computational demands. Here, we developed GBiDC-PEST, a mobile application that incorporates an improved, lightweight detection algorithm based on the you only look once (YOLO) series single-stage architecture, for real-time detection of four tiny pests (wheat mites, sugarcane aphids, wheat aphids, and rice planthoppers). GBiDC-PEST incorporates several innovative modules, including GhostNet for lightweight feature extraction and architecture optimization by reconstructing the backbone, the Bi-directional Feature Pyramid Network (BiFPN) for enhanced multiscale feature fusion, Depthwise convolution (DWConv) layers to reduce computational load, and the Convolutional Block Attention Module (CBAM) to enable precise feature focus. The newly developed GBiDC-PEST was trained and validated using a multitarget agricultural tiny pest dataset (Tpest-3960) that covered various field environments. GBiDC-PEST (2.8 MB) significantly reduced the model size to only 20% of the original model size, offering a smaller size than the YOLO series (v5 ~ v10), higher detection accuracy than YOLOv10n and v10s, and faster detection speed than v8s, v9c, v10m and v10b. In Android deployment experiments, GBiDC-PEST demonstrated enhanced performance in detecting pests against complex backgrounds, and the accuracy for wheat mites and rice planthoppers was improved by 4.5-7.5% compared with the original model. The GBiDC-PEST optimization algorithm and its mobile deployment proposed in this study offer a robust technical framework for the rapid, onsite identification and localization of tiny pests. This advancement provides valuable insights for effective pest monitoring, counting, and control in various agricultural settings.

Rapeseed is globally important as an oil crop to provide essential edible plant oils for various agricultural products. Currently, manipulating plant height with branching effectively balances biomass and yields. However, the genetic mechanisms to control plant height largely remains unknown in rapeseed. To address this gap, we isolated an extremely dwarf mutant (dm1) from ethyl-methanesulfonate (EMS) mutagenesis, and revealed the dwarfism is result from a significant reduction of cell length. Bulk segregant analysis (BSA) identified BnaA10.CYP90A1 and BnaC09.CYP90A1 as the causative genes of dm1. Both genes encoded the proteins homologous to the Arabidopsis cytochrome P450 AtCPD/AtCYP90A1, which is cruicial for brassinosteroid (BR) biosynthesis. In concern with that, we demonstrated the reduced levels of bioactive BRs, castasterone (CS), and its precursor 6-deoxoCS in dm1, resulting in the down-regulation of various genes for cell expansion. The reduced BR levels also caused negative feedback to promote the expression of BR biosynthetic genes in dm1. Furthermore, we proved that the single mutation of BnaA10.CYP90A1 gene conferred semi-dwarfism, potentially beneficial for producing ideal type of plant to improve cultivars with a balance on yield and machinery harvest through genetic modifications. Collectively, these findings highlighted the critical role of BnaCYP90A1s in BR biosynthesis and validated their influence on the regulation of plant height in rapeseed.

To ensure the reliability of learned information, most insects require multiple intervals of experience before storing the information as Long-term memory (LTM), and this requirement has been validated in insects from the behavioral to the molecular level. Recent studies have shown that some insects can form LTM after a single experience, although the mechanisms underlying one-trial LTM formation are not well understood. Therefore, understanding the mechanisms underlying rapid learning and subsequent preference formation in insects is crucial. Here we show that the agricultural pest Bactrocera dorsalis can rapidly form LTM, which is dependent on protein synthesis, and that the formation of LTM requires high energy support at the cost of reduced survival. Furthermore, based on a liquid chromatography-mass spectrometry (LC-MS) metabolomics approach, we found that LTM-related processes are sequentially coupled to two processes for energy generation, the TCA cycle and oxidative phosphorylation. This was further confirmed by blocking these energy generation processes. Our results provide a theoretical basis for the development of behavioral modulators in oriental fruit flies that target energy generation intermediate metabolites, as well as a new perspective on the rapid formation of LTM in insects.

Exploring the suitability of biochar for improving soil quality under different water and salt conditions is important for maintaining soil health and productivity in the arid regions of Northwestern China. We compared the effects of biochar application practices on soil physical, chemical and biological properties under different irrigation and water salinity levels in a two-year field experiment in a mulched and drip-irrigated maize field in Gansu province, China. Eight treatments in total included the combination of two biochar addition rates of 0 t ha^-1 (B0) and 60 t ha^-1 (B1), two irrigation levels of full (W1) and deficit irrigation (W2; W2=1/2 W1) and two water salinity levels of fresh water (S0, 0.71 g L^-1) and brackish water (S1, 4.00 g L^-1). The minimum dataset method was used to calculate the soil quality index (SQI) under different treatments. Deficit and brackish water irrigation significantly reduced SQI by 3.80-9.80% through reducing some soil physical, chemical and biological properties. Biochar application significantly increased the SQI by 6.13 and 10.40% under full irrigation with fresh and brackish water, respectively. Biochar addition enhanced the relative abundance of beneficial bacteria (e.g., Proteobacteria, Patescibacteria) in the soil in all water-salt treatments. The partial least squares path model showed that biochar application significantly enhanced the SQI mainly by improving soil aggregation and pore structure under particular water-salt conditions. This research provides an important basis for utilizing biochar to improve soil quality in arid regions of Northwest China under various water-salt conditions.

The combined application of organic manure and chemical fertilizers is an effective way to enhance soil organic carbon (SOC) sequestration through its influences on organic carbon (OC) input and the stability of SOC fractions. However, there is limited information on the carbon sequestration efficiency (CSE) of chemically separated SOC fractions and its response to OC input under long-term fertilization regimes, especially at different sites. This study used three long-term fertilization experiments in Gongzhuling, Zhengzhou and Qiyang spanning 20 years to compare the stocks and CSE in four different OC fractions (very labile OC, labile OC, less labile OC, and non-labile OC) and their relationships with annual OC input. Three treatments of no fertilization (CK), chemical nitrogen, phosphorous, and potassium fertilizers (NPK), and chemical NPK combined with manure (NPKM) were employed. The results showed that compared with CK, NPKM resulted in enhanced SOC stocks and sequestration rates as well as CSE levels of all fractions irrespective of experimental site. Specifically for the very labile and non-labile OC fractions, NPKM significantly increased the SOC stocks by 43 and 83%, 77 and 86%, and 73 and 82% in Gongzhuling, Qiyang, and Zhengzhou relative to CK, respectively. However, the greatest changes in SOC stock relative to the initial value were associated with non-labile OC fractions in Gongzhuling, Zhengzhou, and Qiyang, which reached 6.65, 7.16, and 7.35 Mg ha^-1 under NPKM. Similarly, the highest CSE was noted for non-labile OC fractions under NPKM followed sequentially by the very labile OC, labile OC, and less-labile OC fractions, however a CSE of 8.56% in the non-labile OC fraction for Gongzhuling was higher than the values of 6.10 and 4.61% in Zhengzhou and Qiyang, respectively. In addition, the CSE for the passive pool (very labile+labile OC fractions) was higher than the active pool (less-labile+non-labile OC fractions), with the highest value in Gongzhuling. The redundancy analysis revealed that the CSEs of fractions and pools were negatively influenced by annual OC input, mean annual precipitation and temperature, but positively influenced by the initial SOC and total nitrogen contents. This suggests that differential stability of sequestered OC is further governed by indigenous site characteristics and variable amounts of annual OC input.

Global climate warming is characterized by diurnal and seasonal asymmetry, with greater increases at nighttime and in winter and spring, and growing evidence has recognized that night-warming in winter and spring significantly impacts winter wheat production.  Pre-crop straw returning is the principal method for straw utilization currently and in the future, but the interactions between straw returning and night-warming on wheat yield and NUE (N use efficiency) still remain elusive.  Here, a consecutive three-year field experiment with two straw treatments (S0, straw removal; S1, straw returning) and two warming treatments (W0, no warming control; W1, night-warming) found that both S1 and W1 improved wheat grain yield and NUE, with W1 exhibiting more pronounced improvements.  Notably, the interaction between S1 and W1 (S1W1) further enhanced yield and NUE by 13.0 and 16.5% compared to S0W0 through increasing grain number and 1,000-grain weight, respectively (three-year average).  Additionally, root growth and topsoil inorganic N content exhibited reductions in S1 before jointing, thus reducing plant dry matter and N accumulation.  However, W1 exhibited an opposite trend, thereby mitigating these negative effects.  Simultaneously, under S1W1, increased N translocation to grain and post-anthesis dry matter accumulation, driven by greater N distribution to leaves and higher N metabolism enzyme activity, enhanced both yield and NUE.  This improvement was supported by better root morphology and biomass, particularly in the 0−40 cm soil layer, boosting plant N absorption.  Additionally, elevated soil N-acquiring enzyme activity after jointing increased the net N mineralization rate and microbial biomass N, enhancing soil N-supply capacity.  As a result, post-jointing inorganic N content rose in the 0−20 cm layer while decreasing at 20−60 cm, thus reducing the apparent N surplus.  Collectively, straw returning, night-warming, and their interactions enhanced more root distribution and N-supply capacity after jointing in the topsoil layer to increase plant N uptake and its translocation to grains, along with post-anthesis dry matter accumulation, ultimately improving grain yield and NUE.

Re-domestication of diploid potato (Solanum tuberosum) into a seed crop is an innovative breeding method to accelerate genetic improvement. Seed propagation would allow hybrid production and mix superior alleles. However, almost all diploid potatoes in nature are self-incompatible (SI). Gametophytic self-incompatible (GSI) is a widespread SI in Solanaceae and is controlled by the S locus that contains a ribonuclease (S-RNase) and multiple F-box (SLFs); however, the genetic diversity of the S locus in potato is unclear. In this study, we identified 21 S-RNase alleles involved in SI from 194 diploid potato accessions by large-scale transcriptome sequencing. The levels of amino acid similarity among different S-RNase proteins varied from 31.3 to 95.8%. S2 alleles is the most widespread in 194 diploid potato and is mainly distributed in the S. tuberosum Group Phureja. Based on genomic annotation and expression analysis, we identified 12 potential functional SI male-determinant genes, S-locus F-box (SLFs), encoding F-box proteins in the S2 locus on a genomic region of approximately 13 Mb. Comparative genomics analysis showed that eight SLF genes are relatively conserved among four homozygous S locus. The Ka and Ks analysis suggested that S-RNase and intra-haplotypic SLF genes have undergone co-evolved. These findings can not only help to select suitable pollinators but also to combine more hybrid combinations and make full use of heterosis to accelerate diploid potato breeding.

Phytopathogenic fungi can weaken the effectiveness of anti-fungal chemicals from plants and artificial synthesis through xenobiotic detoxification system. Nevertheless, the transcription factors responsible for transcriptional activation of xenobiotic detoxification genes in phytopathogenic fungi are rarely reported. Here, we show that a GATA transcription factor SsGATA1 is regulating the transcription of drug efflux pump genes, thus contributing to the tolerance of various types of chemical fungicides, including propiconazole, caspofungin and azoxystrobin in Sclerotinia sclerotiorum. Similarly, SsGATA1 also plays the role of tolerance to isothiocyanate and flavonols, two reported as broad-spectrum anti-fungal chemicals, by mediating the transcription of isothiocyanates hydrolase SsSaxA. Importantly, SsGATA1 positively regulates pathogenicity, which is attributed to the up-regulation of hydrolases and SsSaxA during infection. Furthermore, SsGATA1 is responsible for tolerance to several stresses. Our findings demonstrated that SsGATA1 plays roles in multidrug resistance and pathogenicity by activating the transcription of hydrolases and xenobiotic detoxification genes.

Genotype imputation is essential for increasing marker density and maximizing the utility of existing SNP array data in animal breeding. Although a wide range of software is available for genotype imputation, a comprehensive benchmark in pigs is still lacking. In this study, we benchmarked 24 combinations of genotype imputation software for SNP arrays in pigs, comprising six independent pre-phasing software (fastPHASE, MaCH, BIMBAM, Eagle, SHAPEIT, Beagle) and four distinct imputation software (pbwt, Minimac, IMPUTE, Beagle), using 1,602 whole-genome sequencing (WGS) pigs from a multibreed pig genomics reference panel (PGRP) in PigGTEx. Our results indicated that the combination of Beagle for pre-phasing and Minimac for imputation achieves the highest imputation accuracy with a concordance of 0.983, especially for low-frequency SNPs (MAF<0.05). Finally, we proposed three recommended strategies: i) the combination of Beagle and Minimac is optimal for achieving the highest accuracy; ii) the combination of Beagle and Beagle is recognized for its convenience and relatively high accuracy despite it being memory-intensive; iii) the combination of Eagle and pbwt is feasible for its minimal computational cost with relatively high accuracy. This study provides valuable insights for implementing genotype imputation for pig SNP arrays toward sequence data and offers a basis for applications in livestock and poultry breeding.

Root-knot nematodes (RKNs) are the most economically damaging plant-parasitic nematodes globally. Xinjiang, encompassing one-sixth of China's landmass, currently lacks comprehensive data regarding the occurrence, distribution, and genetic variation of RKNs infecting vegetables within its borders. Hence, identifying RKNs species and genetic diversity is crucial for devising comprehensive management strategies. Between 2021 and 2023, We present a survey of 130 samples, collected from 86 counties across 14 cities in Xinjiang, aiming to comprehensively understand the occurrence, distribution, damage, and species of vegetable RKNs. The results indicated that 57 out of 130 samples collected from the cities of Hami, Tulufan, Ili, Bayingol, Hotan, Aksu, Kashgar, and Kizilsu in Xinjiang were infected by RKNs, suggesting an expansion of RKN disease in the vegetable-producing regions of Xinjiang. The infected vegetable roots were found to harbor Meloidogyne incognita and M. hapla, with M. incognita being the most prevalent species. A phylogenetic analysis targeting the COI regions of M. incognita revealed significant evolutionary and genetic disparities between Xinjiang and Southeastern China RKN populations. Haplotype analysis of the COI gene revealed that M. incognita populations are categorized into three major lineages: Asia, Europe, and a combined lineage encompassing both America and Africa. Notable gene flow patterns were observed among M. incognita populations, with significant migrations from Europe and America to Asia, specifically from Southeastern China towards Xinjiang. This study's findings indicate a consistent increase in the detrimental effects of vegetables production caused by RKNs in Xinjiang. Implementing effective prevention and control measures is crucial to mitigate the spread of RKNs.

Infectious Bursal Disease (IBD) is an acute, highly contagious disease that affects chicks (MüLler et al. 2003). IBD mainly damages the immune organs of chicks, especially the central immune organ, causing immune suppression in diseased chicks (MULLER et al, 2012). The pathogenic Infectious Bursal Disease virus (IBDV) is a member of the Avira virus genus in the Birnaviridae family. (Dobos et al, 1979; Müller et al, 1979; Harkness et al, 1975). IBDV is prevalent worldwide, causing serious economic losses to the global poultry industry. Currently, vaccination remains the most cost-effective way to prevent IBDV.

Subunit vaccines are based on specific components of pathogens and are typically located on their surface. Therefore, subunit vaccines are considered safer than completely pathogen based inactivated or attenuated live vaccines. VP2 protein is the main host protective antigen that contains most neutralizing sites and is the target protein for developing subunit vaccines using various expression systems. Nowadays, IBDV is widely prevalent, but commercial vaccines are no longer effective in preventing it. It is suspected that it is related to genetic changes in the VP2 gene, causing immune escape. Therefore, in this experiment, IBDV variant strain isolated in the laboratory was used to prepare IBDV subunit vaccine to protect sensitive chicks from IBDV infection.

Adjuvants can enhance the immunogenicity of antigens and enhance their immune efficacy. With the development of biotechnology and the upgrading of vaccines, adjuvants have become an important part of improving vaccine quality. Montanide™ ISA 78 VG is an oil in water adjuvant enhanced by immunostimulatory compounds. Its ingredients are based on fortified oil, which can induce antigen-specific cell-mediated immune responses, thereby enhancing protection against viral diseases. MONTANIDE™ GEL is a semi transparent flowable gel with good and stable fluidity. It is easy to mix the antigen phase and adjuvant, and easy to prepare with low viscosity. Aluminum hydroxide adjuvant is the oldest used vaccine adjuvant and remains the primary adjuvant in animal vaccines to this day. This study selected IBDV VP2 protein as the immunogen and combined it with three adjuvants, while comparing it with the widely used white oil adjuvant. By immunizing chicks and comparing the effects of different adjuvants on immune protection, this provides a reference for the development of universal IBDV vaccines.

The IBDV VP2 protein was successfully expressed in E. coli through a prokaryotic expression system, and the protein exists in the form of inclusion bodies. The BCA method was used to detect the protein concentration, which was determined to be 1.5 mg mL^-1 by the BCA assay kit. The IBDV VP2 subunit was emulsified with Montanide^TM ISA 78 VG, Montanide^TM Gel P, Aluminium hydroxide (Seppic Shanghai Chemical Specialities Co., China), and white oil (ExxonMobil, China) adjuvantat a ratio of 3:7, 9:1, 9:1 and 1:1 (w/v) , while ensuring the same antigen content to produce the IBDV VP2 subunit vaccines. IBDV VP2 subunit vaccines without adjuvant also were compared and PBS was served as control. The preparation methods of each vaccine group were shown in Appendix C.

The chicks without specific-pathogens-free (SPF) provided by Zhejiang Lihua Agricultural Technology Co., Ltd were subdivided into six immunized groups. The grouping of chicks and the proportion of adjuvants were shown in Table 1. All of the chicks were subcutaneously vaccinated into their necks. Primary vaccination was given on day 7, and revaccination was given on day 14. At 28 days of age, half of the chicks in each group were separated and infected with 0.2 mL of IBDV-LY21/2 (1×10⁶ EID₅₀ 0.1mL^-1) (Huang et al, 2023). The positive control group was not vaccinated but was infected, and six infection groups were established thereafter.

During the immunization process, it was observed that the Gel P, Adjuvant-free and PBS control groups' vaccines were fully absorbed 1 minute after injection, partially absorbed at intermediate dosage in ISA 78 VG, Aluminium hydroxide, not absorbed in White oil. Within 48 h after injection, there was redness, warmth and swelling at the injection site in White oil. Within 5 days after injection into GroupIII-white oil, the reaction at the injection site got better and disappeared on its own. In addition, the weight gain trend of chicks in different injection groups was similar, indicating that vaccination had no significant effect on weight gain of chicks.

The clinical reactions of experimental animals after infection induced by IBDV, including virus shedding, morphometric identification, and gross lesions, were shown in Figure 1-A. There is no gross clinical symptoms or mortality of vaccinated chicks after challenged by IBDV. All the unvaccinated animals succumbed to the disease within 10 days post-challenge (dpc) and caused atrophy of the cloacal bursa. After calculating the group's bursa index for virus attack after immunization (Sharma et al., 1989; Lucio & Hitchner, 1979) , the results showed that the BBIX of the ISA 78 VG, Gel P, and Aluminum hydroxide groups were greater than 0.7. Although the BBIX of the white oil and Adjuvant-free groups were greater than 0.7, the BBIX was significantly smaller than the above three groups, and the BBIX of the positive control group was less than 0.7. After 10 days of post-immunization challenge, there were no significant pathological changes in the bursa in the ISA 78 VG, Gel P, and Aluminum hydroxide groups compared to the Negative control group. In the positive control group, there were significant lesions in the bursa with atrophy of the bursa (Figure 1-B). This proved that the vaccine prepared in this experiment can inhibit the atrophy of the chicken's bursa and had a preventive effect on chickens infected with IBDV.

The immune efficacy of IBDV VP2 subunit vaccines prepared with different adjuvants was evaluated. Serum collected on day 7 after the prime-boost manner and on days 7, 14, and 21 after the second dose were detected using indirect ELISA method. The percentage of antibodies in the serum of the ISA 78, GLP, and Aluminum hydroxide groups can detect high antibody levels on the 7th day after the first immunization, and positive antibodies can still be detected on the 28th day after secondary immune enhancement. The white oil group achieved an antibody-positive rate of 80% on the 14th day after secondary immune enhancement. The adjuvant-free group only detected antibodies with a 50% positive rate at the end of the experiment and continued to decrease antibody levels (Figure 1-C).

According to the statistical results of the cell neutralization experiment of each immune group at 96 h p.i., it can be observed that on the 7th day after the first immunization, only the adjuvant-free group did not achieve a neutralization titer of 1:16. The results showed that the neutralizing antibody production time in this experiment was earlier than the antibody production time previously studied, which was 14 days after immunization (Li et al, 2020). On the 7th day after the second immunization, the neutralizing titers of all groups significantly increased. On the 21st day after immunization, the antibody level reached its highest, with the Aluminum hydroxide group having the highest neutralizing antibody level. On the 28th day after immunization, the neutralizing titer of the adjuvant-free group decreased to 1:16, while the antibody level of the ISA 78 VG, Gel P, and Aluminum hydroxide groups remained at a high level. The level of neutralizing antibodies was shown in Figure 1-C.

The IL-2 ELISA detection kit was used to detect IL-2 levels, and the results showed that ISA 78 VG, Gel P, and Aluminum hydroxide groups could produce higher levels of IL-2 (Figure 1-D).

IBDV replication following challenge exposure of the experimental animals was summarized in Figure 7. The total viral RNA of IBDV from bursa tissues of chicks at day 10 post infected with the LY21/2 strain of IBDV, and viral loads were determined by qRT-PCR technique. The vaccine's efficacy in preventing virus isolation from swabs was consistent with tissue samples. Compared to the control group, the number of viral RNA copies is the lowest in the ISA 78 VG group among the immunization groups. The collected pharyngeal and anal swabs of chicks were used to detect detoxification, and the results showed that ISA 78 VG group had the lowest detoxification level, with the GLP group being the second lowest. ISA 78 VG, Gel P, white oil, and Aluminum hydroxide could reduce virus infection in chicks (XIONG et al, 2013) (Fig. 1-E).

In order to evaluate the pathological changes caused by IBDV infection, paraffin sections were prepared for H&E staining and tunel detection of all bursa tissues. The  VP2 subunit vaccine prepared with three adjuvants had normal bursa structure, while some follicles in the white oil and Adjuvant-free groups showed atrophy and vacuolization. The positive control group showed a decrease in lymphocytes, infiltration of macrophages, atrophy of follicles, and proliferation of connective tissue. Tunel detection showed that the ISA 78 VG, Aluminium hydroxide, and Gel P groups showed less apoptosis in the bursa, while the white oil and Adjuvant-free groups showed significant apoptosis with green fluorescence . Indicating that the prepared vaccine had a protective effect on the bursa and had not caused any damage to the bursa (Figure 1-F).

This experiment provides preliminary information on the duration of protection that vaccination can provide for chicks. The safety and efficacy of subunit vaccines prepared with different adjuvants and without adjuvant were evaluated on chicks. Under the same dose of antigen (IBDV), the protective effects of ISA 78 VG, Gel P, and Aluminum hydroxide adjuvants evaluated were enhanced to prevent infection with this pathogen. To confirm whether ISA 78 VG and Aluminum hydroxide can effectively reduce antigen load, long-term evaluation is necessary. A previous study showed that classical strain vaccines can completely prevent classical strain infections, but can only provide partial protection against nVarIBDV (Eterradossi et al, 2020). nVarIBDV strain vaccines can not only provide complete immune protection against homologous nVarIBDV, but also against heterologous vvIBDV variant strains (Wang et al, 2021). The immune protection level of the VP2 protein subunit vaccine prepared in this experiment against other strains have not been studied and further research is needed.

In this study, we report the discovery of a novel bocaparvovirus, identified through viral metagenomic analysis of fecal samples from goats presenting with diarrhea. The complete genomic sequence of this virus shows the highest identity with the ECBOV-tdf70 strain, which was found in the wild animal Elaphodus cephalophus. Its NS1 protein shares 91.2% amino acid identity with the ECBOV-tdf70 strain. According to ICTV criteria, this strain should be classified as same species along with the ECBOV-tdf70 strain. The positive rate of diarrheal fecal samples versus non-diarrheal samples indicates the potential role of viruses in goat diarrhea. The complete VP1 genes of the five strains obtained in this study shared 74.4 - 99.2% nucleotide identity, and 63.7 - 99.1% amino acid identity. This study represents the first report of Bocaparvovirus infection in goats, providing valuable insights into the epidemiology and genetic diversity of the virus.

Streptococcus suis has garnered increasing attention due to its implication in severe infections in both swine and humans, as well as its development of multidrug resistance. The phenomenon of collateral sensitivity, whereby resistance to one antibiotic leads to increased sensitivity to another, provides new opportunities for mitigating the evolution of resistance. In this study, we evolved resistance in S. suis to 11 clinically used antibiotics and characterized the resulting collateral sensitivity profiles, revealing a complex network of interactions. Based on our findings, we identified dozens of such drug pairs and demonstrated collateral sensitivity to gamithromycin in ciprofloxacin-resistant S. suis both in vitro and in vivo. Gamithromycin effectively limits the evolution of resistance and reduces the mutant selection window for ciprofloxacin-resistant S. suis strains. Mechanistic studies indicated that the heightened sensitivity of ciprofloxacin-resistant S. suis to gamithromycin was associated with increased intracellular gamithromycin accumulation due to membrane potential alterations and reduced functions of proton motive force (PMF)-dependent efflux pumps. Furthermore, collateral sensitivity-based treatments significantly resensitized ciprofloxacin-resistant S. suis strains to gamithromycin, resulting in superior efficacy, lower pharmacodynamic targets, and higher treatment success rates in a murine thigh infection model. Our results indicate that gamithromycin sensitivity in S. suis is a collateral consequence of resistance to ciprofloxacin, providing valuable insight for the strategic design of collateral sensitivity-based antibiotic therapies for S. suis infections.

Ketosis, a common metabolic disease during early lactation, is associated with high circulating levels of β-hydroxybutyrate (BHB). A portion of BHB that reaches the mammary gland is utilized as precursor for synthesis of fatty acids. Recent findings from nonruminant studies revealed that long chain fatty acyl-CoA ligase 4 (ACSL4) could play a role in the regulation of cellular fatty acid metabolism, but the mechanisms by which ACSL4 mediates cellular lipid metabolism in response to BHB remains unclear. To achieve the aims, we conducted in vivo or in vitro analyses using bovine mammary gland biopsies and the immortalized mammary epithelial cell line (MAC-T). The in vivo study (n = 6 cows group^-1) involved healthy cows (plasma BHB < 0.60 mmol L^-1) or ketotic cows (plasma BHB > 2.0 mmol L^-1) from which mammary gland tissue was biopsied. In vitro, MAC-T cells were challenged with 0, 0.3, 0.6, 1.2, or 2.4 mmol L^-1 BHB for 24 h to determine an optimal dose. Subsequently, MAC-T were incubated with 1.2 mmol L^-1 BHB for 0, 3, 6, 12, 24, or 48 h. Furthermore, MAC-T cells were treated with small interfering ACSL4 (siACSL4) for 24 h or ACSL4 overexpression plasmid (pcACSL4) for 36 h followed by a challenge with 1.2 mmol L^-1 BHB for 24 h. Results showed that increased mRNA and protein abundance of lipogenic genes were linked to both mammary gland and in vitro challenge with BHB. BHB increased fatty acid content by activating ACSL4 expression, whereas inhibition of ACSL4 reduced BHB-induced reactive oxygen species (ROS) overproduction, enhancement of mitochondrial membrane potential, increase in fatty acid content, and lipid droplet accumulation. Furthermore, we also elevated ACSL4 expression with an overexpression plasmid to clarify its molecular role in response to BHB challenge. ACSL4 overexpression enhances BHB-induced lipid droplet accumulation by increased fatty acid content. Overall, the information showed that ACSL4 is crucial for the process of producing fatty acids from exogenous BHB. Reduced ACSL4 decreased fatty acid content and lipid droplet accumulation, improved mitochondrial function, directed more fatty acids towards oxidation. Thus, ACSL4 plays an important role in determining the fate of intracellular fatty acids and BHB in BMECs.

The Huang-Huai-Hai wheat region (HHHR) is characterized by the largest cultivation area and 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, there is a notable deficiency 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 to systematically analyze the distribution patterns of beneficial haplotypes associated with traits related to yield and powdery mildew resistance specific to HHHR.  Our 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.  Using genome-wide association studies (GWAS) analysis, we identified the 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 invaluable resources for the targeted enhancement of yield and disease resistance traits in other wheat-growing areas.  Finally, using the Aimengniu breeding lineage as a case study, we elucidated 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.

赤霉素在植物生长发育中起着重要作用。作物矮化主要与赤霉素合成或信号转导途径的突变有关。然而，对作物中与赤霉素合成和调控有关的基因知之甚少。本研究分离到一株极端矮化的自然矮杆突变体dwarf4。基于BSA-seq，证实了由SiDWARF4编码的古巴焦磷酸合成酶（CPS）在谷子GA生物合成过程中催化了牻牛儿基牻牛儿基焦磷酸（GGPP）向古巴焦磷酸（CPP）的转化。在dwarf4中，CPS酶底物GGPP水平升高，导致GAs含量降低。外源GA₃处理可以恢复dwarf4的异常表型。SiDWARF4敲除系表型与dwarf4一致。与对照Ci846相比，GGPP含量升高，GAs含量降低，与dwarf4的结果一致。研究结果对改良谷子株型和提高谷子种植密度具有一定的指导意义。

叶锈病是危害小麦生产的主要病害之一，栽培小麦广谱高抗叶锈病基因匮乏。小麦-冰草易位系2PT-5具有来自冰草2P长臂对小麦叶锈病广谱免疫的区段。为了准确定位该抗叶锈病基因区段，本研究利用辐照诱导获得的小麦-冰草2P易位系TT-5、TT-3和TT-26分离群体进行叶锈菌接种鉴定，结合基因组原位杂交（GISH）、分子标记检测和基因组重测序对抗叶锈病基因进行物理定位。将抗叶锈病定位区间由原来的82 Mb缩小至9.2 Mb，定位于2P长臂物理位置926.4~935.6 Mb区间。目标区间内注释了64个冰草特异基因，包含6个典型抗病基因，其中有2个编码NLR蛋白的基因和2个编码受体激酶的基因响应叶锈菌的侵染。抗叶锈病基因目标区段的定位，为进一步克隆和解析转移到小麦中的这一广谱抗叶锈病基因奠定了重要的基础。

Melon (Cucumis melo) is an important economic horticulture crop cultivated worldwide. NAC (NAM, ATAC, and CUC) transcription factors play crucial roles in the transcriptional regulation of various developmental stages in plant growth and fruit development, but little about their gene function is known in melon. Here, we identified 78 CmNAC family genes containing integrated and conserved NAM (no apical meristem) domain in the melon genome by performing genome-wide identification and bioinformatics analysis. Transcriptome data analysis and qRT-PCR results showed that most CmNACs are specifically enriched in the vegetative organ or the reproductive organ in melon. Through genetic transformation, we found that overexpression of CmNAC34 in melons led to the early ripening fruits, suggesting its positive role in promoting fruit maturation. Through performing yeast two-hybrid and bimolecular fluorescence complementation assays, we verified the direct protein interaction between CmNAC34 and CmNAC-NOR. The expression pattern of CmNAC34 and CmNAC-NOR were similar in melon tissues, and subcellular localization also revealed their nuclear protein characteristic. We transformed CmNAC-NOR in melon and found that its overexpression resulted in the early ripening fruits. Then, the yeast one-hybrid and dual luciferase reporter gene assay explored that CmNAC34 protein can bind to the promoters of two Glyoxalase (GLY) genes, which were involved in the abscisic acid signal pathway and associated with the fruit regulation. These findings revealed the molecular characteristics, expression profile, and functional pattern of the NAC family transcription factors genes and provided an insight into the molecular mechanism of CmNAC34 in regulating climacteric fruit ripening.

Abscisic acid (ABA) plays a key role in promoting the growth and development of plants, as well as mediating the response of plants to adverse environmental stimuli. Here, we measured the photosynthetic capacity of wild-type RR, mutant sitiens (sit), and ABA-pretreated sit tomato seedlings following exposure to low-temperature (LT) stress. We found that the net photosynthetic rate, intercellular carbon dioxide concentration, transpiration rate, and stomatal conductance of sit seedlings were lower than those of RR seedlings under LT stress. The chloroplast width, area, and number of osmiophilic granules of sit seedlings were significantly larger than those of RR seedlings, and the chloroplast length/width ratio of sit seedlings was significantly lower than that of RR seedlings. The photochemical activity of sit seedlings was decreased, and the expression of photosynthesis-related genes in sit seedlings was altered following exposure to LT stress. ABA pretreatment significantly alleviates the above phenomenon. We also conducted RNA sequencing analysis and characterized the expression patterns of genes in tomato seedlings following exposure to LT stress. We constructed a total of 15 cDNA libraries and identified several differentially expressed genes involved in photosynthesis, plant hormone signaling transduction, and primary and secondary metabolism. We conducted additional analyses of genes encoding transcription factors and proteins involved in photosynthesis-related processes that showed pronounced changes in expression under LT stress. Luciferase reporter assays and electrophoretic mobility shift assays revealed that the WRKY22 regulates the expression of PsbA. The PSII of WRKY22 and PsbA silenced plants is inhibited. Our findings indicate that ABA plays a role in regulating the process of photosynthesis in tomato and protecting PSII through the WRKY22–PsbA complex under LT stress.

The Regional Comprehensive Economic Partnership (RCEP) has created favorable conditions for building deeply integrated agricultural value chains (AVC) in Asia-Pacific. Based on the RCEP agreement, this study utilized the global trade analysis project (GTAP) model to assess the impact of RCEP on AVC of member countries regarding time, tariff reduction, and reduction of non-tariff barriers (NTB). The results indicate that (1) the implementation of RCEP boosts the value-added to agricultural exports for most member countries, particularly in competitive industries; (2) the increase in domestic production and processing capacity, reflected in domestic value-added (DVA), is the primary driver behind the rise in the value-added of agricultural exports in various industries of member countries; (3) RCEP enhances participation in AVC participation for most regional countries, with varying impacts on AVC positioning, thereby promoting regional AVC development; and (4) RCEP has a positive effect on AVC indicators both in the short and long term, with a more pronounced effect observed over time. Additionally, reducing non-tariff barriers (NTB) enhances the positive effects of tariff reductions on AVC indicators. Based on the analyses, the following recommendations are proposed: (1) Leverage the development opportunities arising from RCEP implementation to enhance the agricultural DVA; (2) Capitalize on cooperative opportunities created by RCEP to build cohesive regional AVC; and (3) Prioritize the effective implementation of RCEP's high-quality rules.

Payment for Ecosystem Services (PES) has been widely acknowledged as an effective tool for mitigating grassland degradation and enhancing ecosystem services provision.  However, critical factors such as herders’ willingness to accept (WTA) preferences and their compensation expectations, are often overlooked, leading to insufficient effectiveness of PES initiatives. This study focused on grassland ecological compensation policy (GECP), quantifying herders’ WTA compensation for grassland grazing bans. Through face-to-face surveys and employing the contingent valuation method, we estimated households’ WTA for participating in a grassland conservation program aimed at bolstering ecosystem service provision. Our findings indicate that herders required an average compensation of 237 CNY mu^-1 yr^-1 to engage in the grazing ban program. Notably, our study revealed that herders’ environmental awareness positively influenced their willingness to participation, whereas larger family sizes were negatively correlated with WTA. Additionally, herders in better health, with higher livestock incomes or categorized as semi-herders, tended to accept lower compensation levels. These insights are crucial for improving the effectiveness of GECP and provide valuable reference points for similar analyses in economically disadvantaged and ecologically fragile regions. 

Peanut varieties are diverse globally, with their characters and nutrition determining the product quality. However, the comparative analysis and statistical analysis of key quality indicators of peanut kernels globally is relatively weak, which hinders the peanut quality evaluation and industry development worldwide. This study aimed to compare and analyze the apparent morphology, microstructure, single-cell structure, engineering, mechanical properties, and major nutrient contents of peanut kernels from 10 different cultivars representing major peanut-producing countries. The surface and cross-section microstructure of the peanut kernels exhibited a dense "blocky" appearance with a distinct cellular structure. The lipid cells displayed a mostly spherical shape with a regular distribution within the cells. The single-cell structure of the kernels from these 10 peanut cultivars demonstrated varying morphologies and dimensions, which were found to correlate with the mechanical and engineering properties. Furthermore, the mass loss versus temperature of the peanut kernels revealed five distinct stages corresponding to moisture loss, volatile loss, protein denaturation, and the degradation process of various biomacromolecules. Variations were also observed in the lipid, protein, and sucrose contents, texture, bulk density, true density, porosity, geometric mean diameter, roundness, and sphericity among the different peanut varieties. This study establishes relationships and correlations among microstructure, engineering properties, and nutritional composition of commonly grown peanut varieties in major peanut processing countries. The findings provide valuable insights into peanut quality evaluation for the peanut industry to enhance their processing and product development efforts. 

A critical challenge for global food security and sustainable agriculture is enhancing crop yields while reducing chemical N inputs. Improving N use efficiency in crops is essential for increasing agricultural productivity. The aim of this study was to evaluate the impacts of intercropping maize with leguminous green manure on grain yield and N utilization under reduced N-fertilization conditions. A field experiment with a split-plot design was conducted in northwestern China from 2018 to 2021. The main plots consisted of two cropping systems: monocropped maize (SM) and intercropped maize/common vetch (IM). The subplots had three N levels: zero N application (N0, 0 kg ha^-1), a 25% reduction from the traditional chemical N supply (N1, 270 kg ha^-1), and the traditional chemical N supply (N2, 360 kg ha^-1). The results showed that the negative effects of N reduction on maize grain yield and N uptake were compensated by intercropping leguminous green manure, and the improvements increased with cultivation years. The integrated system involving maize/leguminous green manure intercropping and a reduced N supply enhanced N translocation from maize vegetative organs to grains and increased the nitrate reductase and glutamine synthetase activities in maize leaves. The supercompensatory effect in maize leaves increased year by year, reaching values of 16.1, 21.3, and 25.5% in 2019, 2020, and 2021, respectively. These findings suggest that maize intercropping with leguminous green manure under reduced chemical N input can enhance N assimilation and uptake in the intercropped maize. By using this strategy, chemical fertilizer is effectively replaced by leguminous green manure, thereby improving N use efficiency and maintaining stable yields in the maize-based intercropping system. 

Chestnuts are important economic forest tree species with enormous application value in the wood, medicine, and chemical industries. Currently, the limited genome-wide SSR molecular marker information on chestnut resources significantly limits research on genetic diversity and identification of chestnut resources. To address this issue, we used GMATA to screen simple sequence repeat (SSR) markers throughout the Chinese chestnut genome. A total of 312,302 molecular markers were obtained with a density of 434.38/Mb. Subsequently, all SSR markers were examined for polymorphism using the HipSTR program and 138,208 polymorphic loci were finally obtained. To verify the identification ability of the developed SSR, we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient chestnut resources from the Yanshan Mountains. The results showed that only 6 pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees, showing that the developed markers have high identification potential. We then evaluated the inter-specific universality and polymorphism of these markers using three species, including 91 chestnut plants. The molecular markers amplified 94% of the interspecies with a PIC value of 0.859. Cluster analysis revealed that testing resources using these developed markers can be well differentiated and these markers have been widely used to identify interspecific boundaries. These results proved that the developed molecular markers have the potential for genotypic diversity, which can provide references for genetic diversity research, variety identification, kinship analysis, selection of good products, and construction of core germplasm resources of chestnut and even chestnut plants. They lay a solid foundation for the molecular design of hybrids to improve breeding and develop germplasm resources.

Asian citrus psyllid (ACP) is a significant pest of citrus crops that can transmit citrus Huanglongbing (HLB) by feeding on the phloem sap of citrus plants, which poses a significant threat to citrus production. Volatile signal chemicals with plant communication functions can effectively enhance the resistance of recipient plants to herbivorous insects with minimal impacts on plant growth. While (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT), (E,E)-4,8,12-trimethyl-1,3,7,11-tridecene (TMTT), (E)-β-caryophyllene, and dimethyl disulfide (DMDS), are known as signaling molecules in guava-sweet orange communication, whether these four chemical signals can enhance the resistance of Citrus sinensis to feeding by ACP adults with no apparent costs in terms of plant growth remains unclear. Therefore, this study measured the effect of non-damaging induction by DMNT, TMTT, (E)-β-caryophyllene, and DMDS on the ability of C. sinensis to resist feeding by ACP, as well as their impacts on the defensive phytochemicals, defensive enzymes, functional nutrients, Photosystem II's utilization and allocation of light energy, photosynthetic pigments, growth conditions, and leaf stomatal aperture in C. sinensis. The results indicate that non-damaging induction by these four chemicals can enhance the activity of the defensive enzyme polyphenol oxidase (PPO) and increase the contents of total phenols, tannins, and terpenoid defensive phytochemicals within C. sinensis, thereby enhancing the resistance of C. sinensis to ACP feeding. Specifically, DMNT and DMDS exhibit more significant effects in inducing resistance compared to TMTT and (E)-β-caryophyllene. The characteristics of chlorophyll fluorescence parameters and changes in photosynthetic pigments in C. sinensis during different post-exposure induction periods revealed these chemicals can maintain the stability of the photosynthetic system in C. sinensis and regulate its capacity to capture, transmit, and distribute light energy, which significantly enhances the non-photochemical quenching ability (Y(NPQ)) of C. sinensis. In addition, detailed measurements of the water content, specific leaf mass (LMA), functional nutrients (soluble protein, soluble sugar, and amino acids), and stomatal parameters in C. sinensis leaves further indicated that the non-destructive induction by these chemicals can optimize the levels of functional nutrients in C. sinensis, primarily manifesting as the upregulation of soluble sugars, proline, or soluble proteins, and reduction of stomatal area and aperture, which maintains a stable leaf water content and LMA, thereby enhancing resistance to ACP while sustaining the healthy growth of C. sinensis. These results fully substantiate that the non-damaging induction by the signal chemicals DMNT, TMTT, (E)-β-caryophyllene, and DMDS can enhance the resistance of C. sinensis to ACP feeding while maintaining the balance between pest resistance and growth. This balance prevents any catastrophic effects on the growth of C. sinensis, so these agents can potentially be integrated with other pest management strategies for the collective protection of crops. This study provides theoretical support and assistance for the development of signal chemical inducers for the prevention and management of ACP in agricultural systems.

Ethylene response factors 2 (ERF2) are essential for plant growth, fruit ripening, metabolism, and resistance to stress. In this study, the levels of expression of the genes for MdERF2 implicated in the biosynthesis of fruit cuticular wax, composition of wax, and ultrastructure in apple (Malus domestica) were studied by the transfection of apple fruit and/or calli with an MdERF2-overexpression (ERF2-OE) and MdERF2-interference (ERF2-AN) vector. In addition, the direct target genes of MdERF2 related to the biosynthesis of wax were identified using electrophoretic mobility shift assays (EMSAs) and dual-luciferase reporter assays (DLRs). The findings indicated that the levels of expression of the wax biosynthetic genes, including long-chain acyl-CoA synthetase 2 (MdLACS2), Eceriferum 1 (MdCER1), Eceriferum 4 (MdCER4), and Eceriferum 6 (MdCER6) were upregulated by ERF2-OE. In contrast, the levels of expression of these genes were inhibited when MdERF2 was silenced. Furthermore, the overall structure and accumulation of the fruit cuticular wax were influenced by the levels of expression of MdERF2. Treatment with ERF2-OE significantly increased the proportion of alkanes and ketones and reduced the proportion of fatty acids and esters. Additionally, the EMSAs and DLRs demonstrated that MdERF2 could bind directly to GCC-box elements in the promoters of MdLACS2, MdCER1, and MdCER6 to activate their transcription. These results confirm that MdERF2 targets the up-regulation of the levels of expression of MdLACS2, MdCER1, and MdCER6 genes, thereby altering the composition, content, and microstructure of apple epidermal wax.

Improving cotton fiber quality can increase the economic income of cotton farmers, however achieving high fiber quality without decreasing cotton fiber yield remains a major challenge in saline-alkaline cotton fields. A field experiment was conducted in 2020 and 2021 on saline-alkaline soil with cotton under drip irrigation to examine how amount and timing of leaching affected soils salinity, cotton fiber yield and quality. There were five leaching amounts (CK: 0 mm, W1: 75 mm, W2: 150 mm, W3: 225 mm and W4: 300 mm) and three leaching timings (T1: once at the seedling stage, T2: twice at the seedling and budding stages, and T3: thrice at the seedling, budding and pollen-setting stages). Soil salinity, soil nitrate nitrogen (NO₃-N), cotton nitrogen (N) uptake, irrigation water productivity (IWP), cotton fiber yield, fiber length, fiber uniformity, fiber strength, fiber elongation, micronaire and fiber quality index (FQI) were investigated. The results indicated that soil salinity and NO₃-N reduced with increasing leaching amount. The N uptake of cotton bolls was greater than in cotton leaves, stems and roots, and total N accumulation increased with increasing leaching amount. The optimal cotton fiber yield and IWP occurred in treatment W3T2, and were 3,199 and 2,771 kg ha⁻¹, and 0.5482 and 0.4912 kg m⁻³ in 2020 and 2021, respectively. Fiber length, strength, elongation, and uniformity increased with increasing leaching amount, while there was a negative relationship between fiber micronaire and leaching amount. Soil salinity,  NO₃-N and fiber micronaire were negatively correlated with fiber quality (i.e., length, strength, elongation and uniformity) and yield, nitrogen uptake of various organs (i.e., root, stems and leaves) and whole plant nitrogen uptake. Pearson correlation analysis revealed that fiber elongation was most sensitive to soil salinity. The method of Entropy–Order Preference by Similarity to Ideal Solution (EM–TOPSIS) indicated that leaching of 300 mm of water applied equally at the seedling and budding periods was the optimal treatment to maintain soil salinity and nutrient levels and achieve high cotton fiber yield and quality. In conclusion, the optimal level of leaching treatment decreased soil salinity and improved nitrogen uptake and was beneficial to achieve high fiber yield and quality. Our results will be significant for guiding drip irrigation practice of leaching on saline-alkaline soils for sustainable cotton fiber production.

The inflorescence and spikelet structural units of rice significantly impact grain development.  Among the grasses, the sterile lemma represents a unique spikelet organ exclusive to rice.  As most studies on sterile lemma genes primarily focus on Asian cultivated rice (Oryza sativa L.), genes influencing the sterile lemma phenotype in African rice remain unreported.  This study identified a gene, lsl3, located on the short arm of chromosome 7, which controlled the sterile lemma length in African rice.  The key mutation of lsl3 leading to long sterile lemmas in African rice was discovered and differed from that in Asian rice.  The investigation of lsl3 not only provides a reference for the molecular evolution of cultivated rice in Africa but also offers new evidence supporting the parallel domestication of rice and the independent origin of O. glaberrima.

Wheat grain morphology is an important breeding target considering its impact on yield and end-use properties.  However, the genetic basis of grain roundness, a major determinant of grain morphology, remains largely unexplored.  In this study, an F₂ and a recombinant inbred line (RIL) populations from Zhongkemai 138 (ZKM138)×Chinese Spring (CS) cross were employed to analyze the genetic basis of grain shape variation.  Kompetitive Allele Specific PCR (KASP) markers were developed according to single nucleotide polymorphism (SNP) from bulked segregant exome sequencing (BSE-Seq) of F₂ and Wheat 55K SNP array data online, and then were used to construct two genetic maps of F₂ and RIL populations, spanning 148.89 cM (30 KASP markers) and 129.82 cM (25 KASP markers), respectively.  By the traditional QTL mapping method based on these two maps, a stable quantitative trait locus (QTL) for grain roundness (GR), QGr.cib-5A, could be repeatedly highlighted in the interval of 444.8-455.5 Mb on chromosome 5A.  Further conditional QTL mapping analysis revealed that grain width was the major contributor to GR at this locus.  Besides, the utilization of two tightly linked markers 5A4-15 and 55k-31 showed a 96.27% transmissibility of ZKM138-derived alleles in 134 ZKM138 derivatives alongside a 7.38% increase in GR, and a 65.19% distribution of worldwide varieties.  Finally, TraesCS5A02G236400, possibly encoding a hydroxyproline-rich glycoprotein family protein, was deduced to be the candidate gene.  Collectively, these results provided the possibility of facilitating wheat grain shape improvement and enhancing wheat market value.

Cadmium (Cd) contamination in wheat farmland is increasing at an alarming rate, posing threats to food security and public health.  Breeding and utilizing wheat varieties characterized by low Cd accumulation levels constitute an effective strategy in the battle against wheat Cd contamination.  The adoption of molecular marker-assisted approaches can greatly expedite the selection and enhancement of wheat varieties with low Cd accumulation.  Nonetheless, research concerning genes associated with wheat cadmium accumulation remains scarce.  In this study, a high-density 660K SNP array was employed for conducting genome-wide association studies (GWASs) on the grain Cd concentration (GCdC), bioconcentration factor (BCF) and translocation factor (TF) in 175 wheat germplasms.  The findings revealed 401 significant SNPs identified across three diverse environments. Linkage disequilibrium analysis revealed 30 core quantitative trait locus (QTLs)capable of reliably modulating wheat Cd accumulation phenotypes.  Through gene annotation, transcriptomics, and gene molecular features, four candidate genes (TraesCS7B02G000200, TraesCS4A02G035900, TraesCS4A02G040900, TraesCS5D02G564000) were identified as potential constituents of the biological process of wheat Cd accumulation.  Furthermore, in this study 6 wheat germplasms exhibiting low grain Cd accumulation were isolated, and two Kompetitive Allele Specific PCR (KASP) markers conducive to breeding selection were developed.  These findings provide valuable genetic resources for cultivating wheat with low Cd accumulation and establish a foundation for understanding the molecular mechanisms underlying low Cd accumulation in wheat.  The candidate genes and KASP markers elucidated in this research have potential for effective employmentuse in genetic enhancement and marker-assisted selection in the breeding of wheat with low Cd accumulation.

Rapeseed mustard (Brassica juncea L.) is the third most important oilseed crop in the world but the genetic mechanism underlying its massive phenotypic variation remains largely unexplored. In this study, specific length amplified fragment sequencing (SLAF-Seq) was used to resequence a population comprising 197 F₈ recombinant inbred lines (RILs), derived from a cross between vegetable-type Qichi881 and oilseed-type YufengZC in B. juncea. In total, 438,895 high-quality SLAFs were discovered, of which 47,644 were polymorphic, and 3,887 of the polymorphic markers met the requirements for genetic map construction. The final map included 3,887 markers on 18 linkage groups and was 1,830.23 cM in length, with an average distance of 0.47 cM between adjacent markers. Using the newly constructed high-density genetic map, a total of 53 QTLs for erucic acid (EA), oleic acid (OA), and linolenic acid (LNA) were detected and integrated into 8 consensus QTLs with two for each of these traits. For each of these three traits, two candidate genes were cloned and sequence analyzed, indicating colocalization with their respective consensus QTLs. The co-dominant allele-specific markers for Bju.FAD3.A03 and Bju.FAD3.B07 were developed and showed co-localization with their consensus QTL and co-segregation with LNA content, further supporting the results of QTL mapping and bioinformatic analysis. The expression level for the cloned homologous genes was also identified, which was tightly correlated with the EA, OA and LNA contents of different lines. The results would facilitate the improvement of fatty acid traits and molecular breeding of B. juncea. More use of the high-density genetic map created in this study is also discussed. 

Soluble solids content (SSC) plays an important role in determining the flavor of tomato fruits. Tomato fruit SSC has been shown to be transcriptionally regulated via sugar metabolism. Previous studies have been predominantly focused on the role of C2H2-type zinc finger proteins in tomato growth and development. However, the specific regulatory mechanism of C2H2 in the accumulation of soluble solids in tomato fruits are yet to be fully understood. This study involved the selection of eight tomato accessions with varying levels of SSC to study the expression of SlC2H2 family genes in red ripe fruits. The study found that the levels of SlC2H2-71 expressions were significantly reduced in high-SSC accessions compared to low-SSC accessions. The Slc2h2-71 mutant lines were developed using the CRISPR-Cas9 system, leading to elevated levels of soluble solids, fructose, glucose, malic, and citric acids in mature red ripe fruits. However, sucrose content in the edited Slc2h2-71 mutant lines generally decreased. RNA-seq analysis revealed that fruits from the mutant lines had altered expression of genes related to sugar and acid metabolic pathways, which was further confirmed by quantitative real time PCR. Specifically, there was an observed increase in the expression of SlLIN5 encoding the cell wall invertase (CWIN). The yeast one-hybrid (Y1H) assay, 35S::UAS-GUS, dual-luciferase reporter systems and electrophoretic mobility shift assay (EMSA) demonstrated that SlC2H2-71 regulates tomato sugar metabolism by directly binding to the promoter region of SlLIN5, culminating in the repression of its transcriptional activity. The activity of acid invertase in the SlC2H2-71 knock-out lines exhibited a significantly higher level compared to that observed in the control lines. In summary, the regulation of tomato fruit SSC by SlC2H2-71 involves the inhibition of SlLIN5 expression.

Pyrus pyrifolia, commonly known as sand pear, is a key economic fruit tree in temperate regions and possesses highly diverse germplasm resources for pear quality improvement. However, research on the relationship between resistance and fruit quality traits during the breeding of fruit species like pear is limited. Pan-transcriptomes effectively capture genetic information from coding regions and reflect variations in gene expression between individuals. Here, we constructed a pan-transcriptome composed of 506 samples from different tissues of sand pear, and explored the intrinsic relationships among phenotypes and the selection for disease resistance during improvement based on expression presence/absence variation (ePAVs). The pan-transcriptome contains 156,744 transcripts, among which the novel transcripts show significant enrichment in the defense response. Interestingly, disease resistance genes are highly expressed in landraces of pear but have been selected against during the improvement of this perennial tree species. We found that genetically diverse landraces can be divided into two subgroups and inferred that they have undergone different dispersal processes. Through co-expression network analysis, we confirmed that the formation of stone cells in pears, the deposition of fruit anthocyanins, and the ability to resist stress are interrelated. They are jointly regulated by several modules, and the expression of regulatory genes has a significant correlation. Moreover, we identified candidate genes such as HKL1 that may affect sugar content and are missing from the reference genome. Our study provides insights into the associations between complex fruit traits, while providing a database resource for pear disease resistance and fruit quality breeding.

Watermelon (Citrullus lanatus) is an economically important horticultural crop. However, it is susceptible to low-temperature stress, which poses a significant challenge to its production and supply. Despite the great economic importance of watermelon, little is known about its response to low-temperature stress at the transcriptional level. In this study, we performed a time-course transcriptome analysis to systematically investigate the regulatory network of watermelon under low-temperature stress. Six low-temperature-responsive gene clusters representing six expression patterns were identified, revealing diverse regulation of metabolic pathways in watermelon under low-temperature stress. Analysis of temporally specific differentially expressed genes revealed the time-dependent nature of the watermelon response to low temperature. Moreover, ClMYB14 was found to be a negative regulator of low-temperature tolerance as ClMYB14-OE lines were more susceptible to low-temperature stress. Co-expression network analysis demonstrated that ClMYB14 participates in the low-temperature response by regulating the unsaturated fatty acid pathway and heat shock transcription factor. This study provides substantial information for understanding the regulatory network of watermelon in response to low-temperature stress, as well as identifies candidate genes for the genetic improvement of watermelon with higher low-temperature tolerance.

Fruit spine density is an important commercial trait for cucumber (Cucumis sativus L.). However, most North China-type cucumbers, which are grown over large areas, have a dense-spine phenotype, which directly affects the appearance quality, storage, and transportation of fruits. Here, we isolated a novel few spines mutant (fs2) from the wild-type (WT) inbred line WD1, a North China-type cucumber with high density fruit spines, by ethyl methanesulfonate (EMS) mutagenic treatment. Genetic analysis revealed that the phenotype of fs2 was controlled by a single recessive nuclear gene. We fine-mapped the fs2 locus using F₂ and BC₁ populations (1802 and 420 individuals, respectively) and showed that the candidate gene of FS2 (Csa4G652850) encoded an ARID-HMG transcription factor containing an A/T-rich interaction domain (ARID) and a high mobility group box domain (HMG). One SNP (C to T) and one InDel (a 40-bp deletion) in the coding region of FS2 resulted in amino acid variation and premature translation termination in the fs2 mutant, respectively. FS2 was highly expressed in the apical buds and young ovaries. In addition, the experiments suggest that FS2 participates in the regulation of fruit spine initiation by activating the expression of the Tril gene in cucumber. This work not only provides an important reference for understanding the molecular mechanisms of fruit spine development but also provides an important resource for fruit appearance quality breeding in cucumber.