Table of Content

16 January 2025, Volume 58 Issue 2

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CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS

Heterosis Groups Research in Maize Inbred Lines Based on Machine Learning

CAO ShiLiang, ZHANG JianGuo, YU Tao, YANG GengBin, LI WenYue, MA XueNa, SUN YanJie, HAN WeiBo, TANG Gui, SHAN DaPeng

Scientia Agricultura Sinica. 2025, 58(2):  203-213.  doi:10.3864/j.issn.0578-1752.2025.02.001

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【Objective】The objective of this study is to optimize the classification and discriminant method of maize heterotic groups, and provide guidance and reference for maize breeding practices.【Method】Solid-phase chips were used to genotype 60 waxy maize inbred lines, and high-quality SNP markers with different density were obtained through quality control. Population structure analysis and genetic distance clustering were used to classify the 60 waxy maize inbred lines into different groups, and the differences between different classification methods were compared. On this basis, random forest and support vector machine methods were used to sample and discriminate the results of different classification methods. Five-fold cross-validation was used for sampling, and the prediction accuracy of maize group classification based on different classification methods was compared.【Result】Using different quality control standards, 11 431 and 4 022 molecular markers were obtained, respectively. Based on these two molecular marker densities, 60 materials were divided into 5 and 4 clusters, respectively. When using 11 431 SNP markers, the population structure analysis and genetic distance clustering results showed that the intra-cluster sample consistency was 63.33%. When using 4 022 SNP markers for clustering, the intra-cluster sample consistency was 90.00%. The prediction accuracy results for discriminating maize inbred line clusters showed that the average prediction accuracy (91.43%) of Random Forest and Support Vector Machine using 4 022 markers were higher than that of 11 431 markers (86.25%). Among them, the highest prediction accuracy was achieved by Random Forest using 4 022 markers, with a prediction accuracy of 94.17%.【Conclusion】Clustering analysis ultimately divided 60 waxy maize inbred lines into 4 clusters. Sampling and cross-validation results using Random Forest and Support Vector Machine for cluster classification showed that Random Forest achieved higher prediction accuracy than Support Vector Machine.

Screening and Identification of Drought-Tolerant Sweet Potato Germplasm Resources

CHEN YongXian, CHEN RuiJiang, DU YiZhi, ZHU JunJie, CHEN WanXia, ZHAO ZiHan, WANG JiChun, DU Kang, ZHANG Kai

Scientia Agricultura Sinica. 2025, 58(2):  214-237.  doi:10.3864/j.issn.0578-1752.2025.02.002

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【Objective】Seeking key indicators and methods for accurately characterize drought tolerance in sweet potato, and screening and identifying drought-tolerant sweet potato germplasm resources, to provide effective methods for the rapid and accurate identification of drought-tolerant sweet potato germplasm resources, and to provide material and theoretical basis for selection and breeding of high quality and drought-tolerant sweet potato varieties. 【Method】Fifty-four sweet potato germplasm resources were used as materials for drought stress experiments. By using two treatments including drought stress and control, and combining with drought pool cultivation experiment and field test, the effects of drought stress on the growth and development, physiological and biochemical characteristics, antioxidant metabolism, photosynthetic characteristics and yield of different sweet potato germplasm resources were investigated, the response characteristics of different sweet potato germplasm resources to drought were analyzed, and the effective indicators for drought tolerance evaluation in sweet potato were selected. The drought tolerance evaluation was preformed using principal component analysis, correlation analysis, direct evaluation of drought resistance coefficient, and calculation of comprehensive drought tolerance measurement value (D value) based on membership function, and the drought-tolerant sweet potato germplasm resources were screened and identified.【Result】The results obtained from the drought pool cultivation experiment showed the influences of drought treatment on the main stem length, aboveground fresh weight, underground dry weight and fresh weight of storage root were extremely significant (P<0.01), and eight drought-tolerant germplasm resources were screened based on cluster analysis of D values. In the field test, the main stem length, stem diameter, number of branches, leaf area index, leaf relative water content, total chlorophyll content, stomatal conductance, net photosynthetic rate, transpiration rate, intercellular carbon dioxide concentration, proline (Pro), malondialdehyde (MAD), peroxidase (POD), superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) showed highly significant differences (P<0.01) under drought stress when compared with control. Through the establishment of regression models, it could be initially determined that eight indicators including the leaf area index, root tip, leaf POD, leaf APX, storage root Pro, storage root SOD, storage root CAT, and yield could be used as indicators for drought tolerance identification in sweet potato. XN18111-1, 20XN18-1, XN1834-11 and XN17104-46 were classified as drought-tolerant germplasm resources according to grading of drought resistance coefficient based on yield. The D values of XN18111-1, 20XN18-1 and XN1862-61 were over 0.6 and showed high drought tolerance based on comprehensive drought tolerance evaluation. 【Conclusion】Based on results of comprehensive drought tolerance evaluation in drought pool cultivation experiment, as well as the comprehensive drought tolerance evaluation and yield evaluation in field test, XN18111-1 and 20XN18-1 were finally identified as drought-tolerant germplasm resources, which can be used as drought-tolerant breeding materials or ideal resource materials for study on drought-tolerance mechanism in sweet potato.

TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY

The Impact of Diversified Crops and Wheat-Maize Rotations on Soil Quality in the North China Plain

ZHANG SiJia, YANG Jie, ZHAO Shuai, LI LiWei, WANG GuiYan

Scientia Agricultura Sinica. 2025, 58(2):  238-251.  doi:10.3864/j.issn.0578-1752.2025.02.003

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【Objective】Based on the long-term experiment in the North China Plain (NCP), the differences in soil nutrient and aggregate nutrient distribution between diversified crops and wheat-maize rotation systems were investigated. Additionally, it provided a comprehensive evaluation of soil quality indices (SQI), offering a scientific basis for enhancing soil quality and productivity in the NCP. 【Method】Four diversified crop rotation systems were evaluated, including spring sweet potato-winter wheat-summer maize (Psw-WM), spring peanut-winter wheat-summer maize (Pns-WM), spring sorghum-winter wheat-summer maize (Ps-WM), with winter wheat-summer maize (WM-WM) serving as the control. The soil samples from the 0-40 cm depth were collected during the second rotation in 2022, at the flowering and harvesting stages of winter wheat. The soil enzymes activities, aggregate stability, organic matter, and concentrations of nitrogen, phosphorus, and potassium in soil and aggregates of different sizes (>2.00 mm, 0.50-2.00 mm, 0.25-0.50 mm, and <0.25 mm) were assessed. The SQI for each crop rotation system was then comprehensively evaluated. 【Result】Compared with WM-WM, the three other crop rotations increased soil inorganic nitrogen content. Psw-WM significantly enhanced organic matter in the 0-20 cm layer, total nitrogen in soil aggregates (>2.00 mm, 0-10 cm), and organic matter in soil aggregates (>2.00 mm and 0.50-2.00 mm, 0-10 cm), which also increased cellulase, catalase, and alkaline protease activities. Pns-WM improved organic matter in the 20-40 cm layer and available potassium in soil aggregates (0.25-0.50 mm and >2.00 mm, 10-20 cm), as well as organic matter in soil aggregates (0-10 cm, >2.00 mm and 10-20 cm, >0.50 mm), which also increased sucrase, urease, and alkaline protease activities. Psw-WM improved the stability of 0-10 cm soil aggregates, while Pns-WM improved the stability of 0-30 cm soil aggregates. Both Pns-WM and Psw-WM significantly improved the SQI, with Pns-WM showing a higher improvement than Psw-WM. The path analysis revealed that the average weight diameter (MWD) of aggregates was a direct and significant affecting SQI. It also had a significant indirect positive effect on SQI by influencing inorganic nitrogen. Additionally, the increased organic matter led to a higher proportion of large aggregates, which significantly affected SQI indirectly. 【Conclusion】Legume (peanut) and root crop (sweet potato) rotations with wheat-maize rotations could significantly improve soil quality and enhance the soil nutrient supply capacity in the NCP.

Inversion of Nitrogen Content in Chili Pepper Leaves Based on Hyperspectral Analysis

LIU Jing, WANG Hong, ZHANG Lei, XIAO JiuJun, WU JianGao, GONG MingChong

Scientia Agricultura Sinica. 2025, 58(2):  252-265.  doi:10.3864/j.issn.0578-1752.2025.02.004

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【Objective】Nitrogen is one of the essential nutrients for plant growth and development, and it plays an important role in strengthening chlorophyll synthesis in crops, enhancing plant resistance, and improving yield and quality. This study harnessed hyperspectral technology to swiftly, precisely, and non-invasively monitor nitrogen levels in pepper foliage throughout its growth cycle, delving into the correlation between leaf nitrogen content (LNC) and spectral reflectance characteristics. 【Method】The study was based on the hyperspectral data of pepper leaves collected from Guanzhuang Demonstration Base in Pepper Research Institute of Guizhou Academy of Agricultural Sciences in 2021. The research encompassed four pepper varieties (Qianjiao No. 8, Hongla No. 18, Layan 101, and Hong Global) and five different nitrogen fertilizer application rates (0, 120, 240, 360, and 480 kg·hm^-2). The pepper leaf spectral data were processed, involving Multiple Scatter Correction (MSC), Savitzky-Golay (SG) and First Derivative (FD), followed by the selection of sensitive bands using Pearson correlation coefficient, Successive Projections Algorithm (SPA) and Competitive Adaptive Reweighted Sampling (CARS). Subsequently, three machine learning algorithms, such as Partial Least Squares Regression (PLSR), Random Forest (RF) and Radial Basis Function Neural Network (RBFNN), were employed to construct models for monitoring nitrogen levels in pepper leaves, to achieve the goals of enhancing agricultural production efficiency and accuracy, and realizing intelligent management and precise fertilization. 【Result】After preprocessing, the original spectra improved correlation coefficients significantly. Among these, the spectral data's inversion performance was notably superior after SG processing, with the effectiveness ranking as SG>FD>MSC>original spectra. Contrasting various band selection methods, the employing Pearson correlation coefficient for band selection resulted in bands being overly concentrated, leading to either redundant information or incomplete information extraction. While CARS algorithm selected bands across a broad range and in large quantities, its effectiveness was inferior to SPA due to containing more redundant information and noise. SPA-selected nitrogen content characteristic bands effectively reduced collinearity and redundant information, yielding the optimal model with the highest R² and the smallest RMSE. The performance of different modeling methods for pepper LNC estimation was as follows: RBFNN performed the best, followed by PLSR, with RF exhibiting the poorest performance. Among these, the SG-SPA-RBFNN combined model demonstrated the best inversion accuracy, with modeling results of R² =0.98 and RMSE =0.62, and validation results of R² =0.98 and RMSE =1.21, with an RPD of 3.08. RBFNN model excelled in handling high-dimensional spectral data, surpassing traditional PLSR and RF models. 【Conclusion】The hyperspectral reflectance characteristics were utilized to establish nitrogen content prediction models, which could effectively monitor nitrogen levels in pepper leaves, thereby enhancing agricultural management efficiency and providing the technical support for precise management and variable fertilization in pepper cultivation.

PLANT PROTECTION

Evaluation of the Effectiveness of Two High-Throughput Sequencing Techniques in Identifying Apple Viruses and Identification of Two Novel Viruses

PAN Yuan, WANG De, LIU Nan, MENG XiangLong, DAI PengBo, LI Bo, HU TongLe, WANG ShuTong, CAO KeQiang, WANG YaNan

Scientia Agricultura Sinica. 2025, 58(2):  266-280.  doi:10.3864/j.issn.0578-1752.2025.02.005

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【Objective】Macro-transcriptome sequencing and small RNA sequencing are commonly used high-throughput sequencing techniques in virus identification. The objective of this study is to explore the application efficiency of macro-transcriptome sequencing and small RNA sequencing in the identification of emerging viruses in apples, analyze the impact of different tissue types on the identification results, and to provide a basis for the accurate diagnosis of apple virus diseases.【Method】The samples of apple peel and branch bark were collected from ‘Luli’ apple trees exhibiting novel viral symptoms in Shenzhou County of Hengshui City in August 2022. Total RNA was extracted, and macro-transcriptome libraries and small RNA libraries were constructed for high-throughput sequencing. Bioinformatic techniques and software were utilized to analyze and evaluate the sequencing data. Initially, the indicators from the high-throughput sequencing technique results were compared. Subsequently, a comprehensive evaluation of the effectiveness of each sequencing method was conducted using the analytic hierarchy process (AHP) and a 5-level grading system to calculate the weighted values of these indicators. Finally, RT-PCR was employed to validate the high-throughput sequencing results, and the genomic characteristics and phylogenetic relationships of the emerging viruses were analyzed.【Result】In terms of splicing effect, using the same tissue material, the macro-transcriptome sequencing outperformed small RNA sequencing. When the same technique was applied, the splicing effect for fruit peel tissue was better than that of branch bark. In terms of the number of virus species detected, macro-transcriptome sequencing identified the highest number of virus species in branch bark, including eight viruses: apple chlorotic leaf spot virus (ACLSV), apple stem pitting virus (ASPV), apple stem grooving virus (ASGV), apple necrotic mosaic virus (ApNMV), apple rubbery wood virus 2 (ARWV-2), apple green crinkle associated virus (AGCaV), citrus concave gum-associated virus (CCGaV), and citrus tatter leaf virus (CTLV). In contrast, small RNA sequencing technique detected the fewest virus types in branch bark. There were differences in virus types between fruit peels and branch barks detected through small RNA sequencing technique. When fruit peels were used as the detection target, both methods identified the same number of virus types. After comprehensively comparing the synthesis score of various indicators, the macro-transcriptome sequencing of bark samples scored the highest. The results of high-throughput sequencing were consistent with those obtained through RT-PCR. ARWV-2 and CCGaV were discovered for the first time in Hebei Province, and were designated as ARWV-2-HB and CCGaV-HB. The GenBank accession numbers for the coat protein (CP) gene of ARWV-2-HB and the movement protein (MP) and CP genes of CCGaV-HB are PQ095583, PQ095581, and PQ095582. The genomic sequences of both viruses showed over 96% identity to their respective representative isolates. Phylogenetic trees constructed based on the CP amino acid sequences of ARWV-2 and CCGaV revealed that ARWV-2-HB was most closely related to LYXS (MZ819711), while CCGaV-HB exhibited relatively close relationships with Mishima (MK940543), Gala (MK940542), Gala-BJ (OP820577), Fuji-BJ (OP556109), and AC1 (MH038043).【Conclusion】Using macro-transcriptome sequencing and small RNA sequencing techniques, the fruit peel and branch bark of the same ‘Luli’ apple tree were sequenced separately. Among two sequencing methods, the macro-transcriptome sequencing of branch bark showed the best sequencing effect, discovered the highest number of viruses and relatively complete viral genome sequences. When using small RNA sequencing, only a portion of virus types could be detected in both fruit peels and branch barks. Due to the differences in virus types detected from different tissue materials, it is recommended to test both tissue materials simultaneously. ARWV-2 and CCGaV were reported in Hebei Province in this study, and partial genomic sequences of ARWV-2-HB and CCGaV-HB were revealed, which enriching the genomic sequence information of ARWV-2 and CCGaV. Furthermore, the phylogenetic relationships of these two viruses with other representative isolates have been clarified.

Preparation and Application of DcMucin-like Antibodies in Diaphorina citri

JIANG LiQin, SU QiaoLing, LI You, WEI TaiYun, BIN Yu

Scientia Agricultura Sinica. 2025, 58(2):  281-290.  doi:10.3864/j.issn.0578-1752.2025.02.006

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【Objective】Mucin-like proteins are integral to the formation of salivary sheaths in Hemiptera insects. This research seeks to prepare a specific antibody targeting the Diaphorina citri mucin-like protein (DcMucin-like) and to employ immunofluorescent labeling to identify the feeding sites of D. citri, so as to provide a basis for the study of the biological functions of DcMucin-like.【Method】The salivary glands, midgut, ovaries, and testes of D. citri were dissected for analysis. Specific primers were designed based on the DcMucin-like sequence of the psyllid, and real-time fluorescent quantitative PCR was employed to assess the transcriptional level differences of DcMucin-like across various tissues. The DcMucin-like sequence, excluding the signal peptide, was amplified and subsequently inserted into the pET-28a vector to construct a recombinant plasmid. Following sequence verification, the plasmid was transformed into Rosetta expression strains. The expression of recombinant protein was induced using 0.5 mmol·L^-1 IPTG at 37 ℃ with agitation for 8 h. The presence of the recombinant protein was confirmed via SDS-PAGE gel electrophoresis. Following large-scale bacterial culture, the cells were lysed, and the supernatant was subjected to purify using Ni-NTA affinity chromatography to obtain the antigen. This antigen was subsequently used to immunize rabbits five times. The resulting purified serum IgG yielded the DcMucin-like polyclonal antibody, whose specificity was assessed through Western blot analysis. Real-time fluorescent quantitative PCR and Western blot analyses were employed to compare the transcriptional and protein expression levels of DcMucin-like between healthy and Candidatus Liberibacter asiaticus (CLas) infected D. citri. The feeding sites of D. citri on citrus leaves post-ingestion were labeled using DcMucin-like polyclonal antibodies conjugated with fluorescein isothiocyanate (FITC). These feeding sites, along with the salivary sheaths of D. citri, were subsequently examined under a confocal microscope.【Result】Real-time fluorescent quantitative PCR analysis revealed that the DcMucin-like exhibited significantly elevated expression level in the salivary gland of D. citri compared to the midgut, ovary, and testis. Rosetta expression strains harboring the pET28a-DcMucin were induced with IPTG, resulting in the production of substantial quantities of recombinant protein in the supernatant of the bacterial lysate. The recombinant protein was utilized to immunize rabbits for the production of antiserum, from which purified IgG was subsequently employed to generate DcMucin-like polyclonal antibodies. Western blot analysis confirmed the successful acquisition of specific DcMucin-like polyclonal antibodies. Furthermore, DcMucin-like expression was found to be upregulated in D. citri response to CLas infection. The DcMucin-like (FITC) fluorescent antibody-labeled tissue sections of citrus leaves, following D. citri feeding, were examined using a confocal microscope. Specific FITC fluorescence signals were detected in proximity to the feeding sites, suggesting that DcMucin-like was released into plant tissues during D. citri feeding to participate in the formation of salivary sheaths.【Conclusion】DcMucin-like is highly expressed in the salivary glands of D. citri and exhibits upregulation in response to CLas infection. Specific polyclonal antibodies targeting the DcMucin-like salivary protein of D. citri were successfully generated, demonstrating high specificity. Additionally, it was confirmed that DcMucin-like was secreted into citrus plant tissues during D. citri feeding. These findings provide a foundational basis for further investigation into the role of DcMucin-like in the interactions among CLas, D. citri, and citrus plants.

SOIL & FERTILIZER·WATER-SAVING IRRIGATION·AGROECOLOGY & ENVIRONMENT

Yield Components and Soil Factors Affecting Zinc Concentration in Wheat Grain and Flour in Major Wheat Production Regions of China

SUN RuiQing, DANG HaiYan, SHE WenTing, WANG XingShu, CHU HongXin, WANG Tao, DING YuLan, LUO YiNuo, XU JunFeng, LI XiaoHan, WANG ZhaoHui

Scientia Agricultura Sinica. 2025, 58(2):  291-306.  doi:10.3864/j.issn.0578-1752.2025.02.007

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【Objective】 This study was to clarify differences of zinc (Zn) concentration in wheat grain and flour and the corresponding affecting factors over major wheat production regions, with the purpose to provide the theoretical basis for improving the Zn nutritional quality of wheat grain in China. 【Method】During 2020-2021 and 2021-2022 wheat growing seasons, 421 wheat and soil samples were collected from major wheat production regions in 17 provinces and autonomous regions of China, to explore the relationship of Zn concentration in wheat grain, flour and bran with wheat yield, yield components and soil properties.【Result】The average Zn concentration of the wheat grain, flour and bran was 28.1, 10.8 and 60.6 mg·kg^-1, respectively, with 94.8% of grain and 89.5% of flour samples could not meet with the recommended Zn concentration of 40 mg·kg^-1 for grain and 15 mg·kg^-1 for flour by nutritionists. The highest grain Zn concentration was observed in rice-wheat region (RW), followed by that in wheat-maize regions (MW) and dryland wheat region (DW), and the lowest was in spring-wheat region (SW). In rice-wheat region, the lower pH promoted the activation of soil Zn, and its availability was significantly higher than that in other regions, the lowered phosphorus fertilizer application rate was also conducive to Zn absorption and its translocation from root to the aboveground, and the average Zn concentration in wheat grains and flour was therefore as high as 31.5 and 12.2 mg·kg^-1, respectively. In wheat-maize region, the soil fertility was higher, so that the yield was significantly greater than that in other wheat regions, resulting in relatively lower Zn concentrations in wheat grains and flour, which were 27.1 and 10.3 mg·kg^-1, respectively. In dryland wheat region, the higher soil pH limited soil Zn availability and wheat Zn absorption, leading to the grain and flour Zn concentration being relatively lower as 26.5 and 10.1 mg·kg^-1, respectively. In spring-wheat region, since the soil available Zn concentration was significantly lower than that in other wheat regions, which was not conducive to Zn absorption by wheat and its accumulation in grain, and therefore the Zn concentrations in grain and flour were the lowest as 24.6 and 9.4 mg·kg^-1, respectively, while Zn concentration decreased significantly with the increase of 1000-grain weight.【Conclusion】 Therefore, in order to improve the Zn concentration of wheat grains and flour, it was not only necessary to improve the soil pH, available Zn level and reasonable nitrogen and phosphorus fertilizer application, but also jointly to optimize the yield components to improve the wheat yield and grain and flour Zn concentration.

Characterization and Correlation Analysis of Soil Dissolved Organic Matter and Microbial Communities Under Long-Term Application of Fresh and Composted Manure

YUAN HuiLin, LI YaYing, GU WenJie, XU PeiZhi, LU YuSheng, SUN LiLi, ZHOU ChangMin, LI WanLing, QIU RongLiang

Scientia Agricultura Sinica. 2025, 58(2):  307-325.  doi:10.3864/j.issn.0578-1752.2025.02.008

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【Objective】This experiment was conducted to investigate the optical properties of dissolved organic matter (DOM) and the intrinsic relationship with soil microbial communities diversity and structure under long-term application of fresh and composted chicken/pig manure, so as to provide a theoretical reference of soil ecology for the implementation of recycling agriculture in the red soil area.【Method】Based on an 11-year (2011-2022) long-term experiment (sweet corn-sweet corn-cabbage rotation) of the National Soil Quality Guangzhou Red Soil Observatory Experiment Station, the fertilization regimes included no manure, chicken manure organic fertilizer, fresh chicken manure, fresh pig manure organic fertilizer, and fresh pig manure. Surface soil samples were collected and subjected to soil chemical properties determination, DOM UV-absorption characterization, parallel factor analysis of DOM fluorescence absorption characteristics, and Illumina MiSeq high-throughput sequencing, respectively. The main influencing factors were analyzed based on multivariate analysis.【Result】The composted manure significantly increased soil organic matter (122.5%-354.8%) and nutrient content, among which the chicken manure source treatments effectively increased soil available phosphorus content (1 697.2%-3 455.3%) and total phosphorus content (587.5%-812.5%), while swine manure source treatments mainly increased soil alkali-hydro nitrogen content (286.6%-311.3%) and total nitrogen content (326.4%-373.6%). Livestock manure applications, especially the composted manure, increased soil DOM content (60.3%-227.8%), among which the swine manure source treatments had a better effect on chromophoric dissolved organic matter content (118.1%-231.7%). In contrast, the chicken manure source treatments focused on increasing soil fluorescent dissolved organic matter (FDOM) content (293.4%-834.9%). For FDOM characteristic indexes, the biological index of manure application treatments was lower than that under CK (33.2%-39.2%), but the humification index was higher than that under CK (40.3%-43.3%). Four fluorescence components were identified with parallel factor analysis. The manure applications treatments mainly enriched the C3 (medium-size humus molecule containing fulvic acid and humic acid) and C4 (large-size humus molecule containing tryptophan) components, which promoted the conversion of protein-like components into humus-like components in FDOM. The maximum fluorescence intensities of the C3 and C4 components were higher in composted manure treatments. The composted chicken manure was more advantageous in increasing microbial community α-diversity, for the soil microbial community richness (Chao 1 index:19 065.6) and diversity (Shannon index: 5.6-6.0) were higher. The microbial community structures vary according to different treatments. The chicken manure source treatments were dominated by the eutrophic taxa Proteobacteria (31.2%-33.0%) and Gemmatimonadetes (4.1%), while the swine manure source treatments were dominated by the oligotrophic and efficient carbon-utilizing taxa Acidobacteria (21.0%-21.6%) and the nitrifying bacterial taxa Nitrospirae (2.6%-3.4%). Positive correlations dominated the co-occurrence networks, and Rhodobacteraceae had the highest number of correlations with other microbes. Redundancy Analysis and optimized random forest model showed that microbial communities were mainly influenced by available potassium and the C3 component of DOM, with a more pronounced response from nitrogen cycle-related microbial groups.【Conclusion】Long-term application of different manure sources mainly led to differences in humic components mediated by nutrients and organic matter input. Composted manure treatments improved the soil organic matter content and the degree of DOM humification. The available nutrients in soil and the humic-like components of DOM were the main factors affecting the structure of the soil microbial community. The response of nitrogen cycle-related microbial groups to these factors was particularly obvious and should be paid attention under long-term application of manure.

HORTICULTURE

Relationship Between the Formation of Non-Red Color in the Fruit Skin of Xinjiang Local Peach Varieties and the Variation of PpMYB10.1 Promoter

GUO TianFa, WU JinLong, QIU QianQian, MA XinChao, WANG LiRong, WU CuiYun

Scientia Agricultura Sinica. 2025, 58(2):  326-338.  doi:10.3864/j.issn.0578-1752.2025.02.009

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【Objective】This study aims to explore the molecular mechanisms underlying the formation of Non-red ground color in Xinjiang local peach (Prunus ferganensis and P. persica), providing a theoretical basis for the breeding of new peach varieties with Non-red skin color. 【Method】A phenotypic survey of the skin color of 85 progenies of Xinjiang peach and three cultivated varieties was conducted. The activity of various lengths of the PpMYB10.1 promoter was assessed using β-glucuronidase (GUS) staining. Predictive analysis of the cis-acting elements of the PpMYB10.1 promoter from different materials was performed using the PlantCARE (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/). Genotypes with a 5 243 base pairs (bp) transposon insertion and a 483 bp deletion in the PpMYB10.1 promoter of 88 materials were identified and cloned using polymerase chain reaction (PCR). The transcriptional activation of PpMYB10.1 by Pp.4G186800 was validated through dual-luciferase assays. 【Result】Based on skin color, 85 Xinjiang peach progenies were classified into Non-red and red types. The majority exhibited Non-red colors (green or light yellow) with minimal or no anthocyanin accumulation. Compared to the fully red variety Zhongtao Jinmi, these exhibited significantly lower levels of anthocyanins and reduced expression of PpMYB10.1. Using GUS staining to assess the effects of promoter mutations on activity, the results showed that a 5 243 bp insertion in the PpMYB10.1 promoter caused the fruit discs to display a lighter blue, indicating decreased activity. Conversely, a 483 bp deletion resulted in a darker blue, suggesting increased promoter activity. No such insertions or deletions were found in the PpMYB10.1 promoter of the Xinjiang peach progenies. The promoter sequences of PpMYB10.1 were cloned, and cis-acting elements were categorized into four groups: light-responsive, plant hormone-responsive, abiotic stress and growth development-responsive, and elements of unknown function. Due to the late maturation of the Xinjiang peach progenies, all were found to have a 0 bp/0 bp genotype for the maturity-regulating gene Pp.4G186800. Dual-luciferase assays showed that Pp.4G186800 could bind to the PpMYB10.1 promoter. Notably, when the promoter had a 483 bp deletion, Pp.4G186800 (+9 bp) formed a strong interaction, potentially enhancing early maturation and anthocyanin accumulation in the peach skin. However, in late-ripening peaches, Pp.4G186800 (-9 bp) had no enhancing effect on the promoter’s activity; If the PpMYB10.1 promoter lacked the 483 bp deletion, its intrinsic activity was weak, even though Pp.4G186800 could still interact with it, the effect was minimal.【Conclusion】The presence of insertions and deletions in the PpMYB10.1 promoter is not directly related to the Non-red skin color of Xinjiang peach. In early and mid-ripening varieties, Pp.4G186800 can activate the transcription of PpMYB10.1, facilitating anthocyanin synthesis; however, its influence is reduced or absent in late-ripening peaches.

Genetic Diversity Analysis of Cymbidium faberi Germplasm Resources Based on Phenotypic Traits

TANG GuiMei, LI WeiDong, ZHOU YuXia, KONG YouHan, XIAO XiaoLing, PENG YingShu, ZHANG Li, FU HongYan, LIU Yang, HUANG GuoLin

Scientia Agricultura Sinica. 2025, 58(2):  339-354.  doi:10.3864/j.issn.0578-1752.2025.02.010

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【Objective】To investigate the variation patterns of phenotypic traits and their relationship to genetic diversity in Cymbidium faberi germplasm, to explore reliable comprehensive evaluation methods for germplasm resources, to screen for superior germplasm, and to provide a critical basis for germplasm innovation and new cultivar breeding in Cymbidium faberi Germplasm. 【Method】Using 102 C. faberi germplasm samples, 38 phenotypic traits were measured. Multiple statistical methods were employed, including the genetic diversity index, principal component analysis (PCA) combined with membership function method, cluster analysis, and correlation analysis, to perform phenotypic genetic diversity analysis and a comprehensive evaluation of the germplasm. Superior C. faberi germplasm was screened based on the comprehensive evaluation F-value and target traits.【Result】The coefficient of variation for quantitative traits in the 102 C. faberi germplasm samples ranged from 13.18% to 28.28%, and the genetic diversity index ranged from 1.52 to 1.97, with higher indices observed for traits such as the number of flowers and sepal shape. Significant or highly significant correlations were found among 46 pairs of traits, with most vegetative organ traits showing a highly significant positive correlation with reproductive organ traits. PCA results indicated that 12 principal components were extracted when the cumulative contribution rate of phenotypic traits reached 74.52%. The comprehensive evaluation F values calculated using the membership function method ranged from -0.45 to 1.26, identifying the top 10 superior C. faberi germplasm resources. Systematic clustering grouped the phenotypic traits and germplasm resources into three categories. R-type clustering visually displayed the associations between different quantitative and qualitative traits, consistent with the correlation analysis results. Q-type clustering revealed the phylogenetic relationships and genetic backgrounds among different C. faberi germplasm; 9 of the top 10 germplasm resources based on the comprehensive evaluation F-value were in the third major category. 【Conclusion】C. faberi germplasm exhibits rich diversity in both quantitative and qualitative traits. Utilization of multivariate statistical analysis methods for comprehensively evaluating C. faberi is feasible. The combination of the membership function method and PCA to calculate phenotypic comprehensive values effectively quantifies the comprehensive traits of C. faberi germplasm. Superior germplasm resources identified include C. faberi Dayipin, C. faberi Jinaosu, C. faberi Chengmei, C. faberi Baohuisu, C. faberi Jiangnanxinjipin, C. faberi Zhengxiaohe, C. faberi Dachenzi, C. faberi Xiuhuimudan, C. faberi Huilanhuban, and C. faberi Duanhuimei, among others. Key traits such as plant type, flower color, sepal, and petal posture can serve as critical indicators for the evaluation of C. faberi germplasm, aiding in the selection of breeding parental materials and innovative utilization of germplasm resources.

FOOD SCIENCE AND ENGINEERING

Functional Modification of Genetically Engineered Antibodies and Their Application Strategies in Agriculture and Food Safety

XU ChongXin, SHEN JianXing, JIN JiaFeng, HE Xin, XIE YaJing, ZHANG Xiao, ZHU Qing, LIU Yuan, LIU XianJin

Scientia Agricultura Sinica. 2025, 58(2):  355-386.  doi:10.3864/j.issn.0578-1752.2025.02.011

Abstract ( 117 )   HTML ( 7 )   PDF (2565KB) ( 74 )   Save

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Genetically engineered antibodies (GEAbs) represent a giant leap forward in the artificial directed design of antibodies. They exist in forms such as recombinant antigen binding fragment, single chain variable fragment and nanobodies, etc., and have been widely used in various fields of agricultural and food safety. Relevant innovation exploration and research are still ongoing, and their development is extremely rapid. This paper summarized the main derivative forms of GEAbs, the carrying platforms of phage, yeast, ribosomal and mammalian cells on which they rely, and the corresponding antigen-specific antibody targeting screening system. The key technical characteristics of their characteristic functional modifications, such as affinity maturation and enhancement of environmental stress stability, were analyzed through strategies, such as site-directed mutagenesis, chain-shuffling, error-prone PCR, DNA shuffling, homologous or heterologous antibody functional fragments and functional protein fusion. The preparation of corresponding antibody proteins using the expression systems of insect and animal cells, plant tissues, yeast, Escherichia coli (E. coli) and other microorganisms and the potential optimization strategies were summarized too. The application and research status of GEAbs in the immunoassay of agricultural and food safety hazards, such as environmental hazards of origin growing area, pesticides and veterinary drugs inputs, mycotoxins, foodborne pathogenic microorganisms and their toxic metabolites, foodborne allergens were reviewed. Combined with the latest achievements and research experience in the innovative research and development of the simulants for simulating Bt Cry toxin structure and even anti-insect function of Ab2β anti-idiotypic GEAbs and for simulating vancomycin anti-Staphylococcus aureus (S. aureus) function of Ab2β anti-idiotypic GEAbs from author’s team, which is based on the theoretical basis that Ab2β anti-idiotypic antibody, could simulate the structure of antigen and even the function of biological activity. The future development trend and feasible shortcut of GEAbs in green detection and green prevention and control of agricultural and food safety hazards were further discussed. This paper was expected to provide the latest and comprehensive literature with reference value and potential inspiration for the application of GEAbs in the fields of agricultural, food safety and nutrition quality assessment.

ANIMAL SCIENCE·VETERINARY SCIENCE

Post-Freezing Quality and Targeted Lipidomics Analysis of Rongchang Pig Spermatozoa with Different Freezing Tolerance

GAO XiaoPing, PAN HongMei, GUO ZongYi, ZHANG JunJie, LIN Yan, ZHANG Liang

Scientia Agricultura Sinica. 2025, 58(2):  387-400.  doi:10.3864/j.issn.0578-1752.2025.02.012

Abstract ( 117 )   HTML ( 7 )   PDF (3794KB) ( 91 )   Save

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【Background】Rongchang pig is one of the excellent local pig breeds in China, but the number of purebred Rongchang pigs is decreasing with the introduction of foreign-bred pigs as well as the shift of the market demand, and this trend seriously threatens the diversity of the genetic resources of pigs in China and the sustainable development of the pig breeding industry. In the process of frozen semen production in local pigs, the differences in post-freezing quality of spermatozoa from different boars are all related to their freezing tolerances, while the sperm lipid composition is one of the key factors affecting their freezing tolerance. 【Objective】The aim of this study was deeply analyze the quality characteristics of spermatozoa of Rongchang pigs with different freezing tolerances and their lipid compositions, and to screen out the candidate markers of sperm freezing tolerance. 【Method】Fourteen Rongchang pig semen were collected for freezing and preservation, and their post-freezing motilities were detected. Relative Motility (post-freezing motility / pre-freezing motility) was used as the criterion for freezing tolerance, and Rongchang pig spermatozoa were screened and grouped into groups for high and low freezing tolerance. Plasma membrane integrity, mitochondrial membrane potential, reactive oxygen species level, apoptosis level and in vitro oocyte penetration ability of spermatozoa from different freezing tolerance groups were detected after freezing, and the extent of freezing damages on the surface and internal microstructure of spermatozoa were observed by scanning electron microscopy and transmission electron microscopy. The medium- and long-chain fatty acid composition of fresh spermatozoa from different freeze-resistant groups was detected by targeted lipidomics technology, and differential fatty acids were screened out. 【Result】5 Rongchang pigs with high freezing tolerance spermatozoa and 5 Rongchang pigs with low freezing tolerance spermatozoa were screened by relative motility; the plasma membrane integrity, mitochondrial activity and in vitro oocyte penetration rate of spermatozoa in the high freezing tolerance group were significantly higher than that of spermatozoa in the low freezing tolerance group after freezing (P<0.05); the apoptosis rate of spermatozoa in the high freezing tolerance group after freezing was significantly lower than that of spermatozoa in the low freezing tolerance group (P<0.05). The surface and internal structural integrity of spermatozoa in the high tolerance group was higher than that of spermatozoa in the low tolerance group after freezing. Targeted lipidomics showed that at least 36 fatty acids were present in Rongchang pig spermatozoa. The content of 11 fatty acids, including palmitic acid and pentadecanoic acid, were significantly different between the sperm of the high and low freezing tolerance groups (P<0.05), and all of them were more abundant in the high freezing tolerance group. 【Conclusion】The spermatozoa of Rongchang pigs with high freezing tolerance were significantly better than those of low freezing tolerance in terms of physiological status, morphology and structure, and in vitro oocyte penetration function, and there were significant differences in fatty acid composition. The differential fatty acids screened in this study, such as palmitic acid, pentadecanoic acid, and arachidonic acid, could be used as candidate markers of freezing tolerance in Rongchang pig spermatozoa. These findings not only provided a new perspective for an in-depth understanding of the biological mechanism of sperm cryoinjury, but also laid a theoretical foundation for the development of efficient and safe cryoprotectants.