Table of Content

    16 September 2023, Volume 56 Issue 18
    Genome-Wide Association Analysis of Yield Traits in Xinjiang Winter Wheat Germplasm
    MA YanMing, LOU HongYao, ZHANG ShengJun, WANG Wei, GUO Ying, NI ZhongFu, LIU Jie
    Scientia Agricultura Sinica. 2023, 56(18):  3487-3499.  doi:10.3864/j.issn.0578-1752.2023.18.001
    Abstract ( 18 )   HTML ( 4 )   PDF (2290KB) ( 10 )   Save
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    Objective】To discover new high yield genes in wheat by association analysis, which can provide technical supports for the innovation and genetic improvement of high yield germplasm resources in wheat.【Method】Totally 188 bread wheat cultivars in Xinjiang were genotyped using the wheat 55K genotyping assay. GWAS was carried out to identify the signifcant single nucleotide polymorphisms (SNPs) which were associated with 9 wheat yield traits in 6 environments. The MLM algorithm in TASSEL5.0 was used to analyze the nine traits related to wheat yield traits.【Result】Totally 1309 SNPs explained 7.259%-70.792% of the phenotypic variation. 38 SNP loci were identifed, which were significantly correlated with 5 plant height weight SNP loci, 10 spike length weight SNP loci, 10 spikelet number SNP loci, 6 fertile spikelet number SNP loci, 6 spike grain number SNP loci, and 1 thousand grain weight SNP loci. These loci can explain 9.10%-23.81% of phenotypic variations. Comparing these 38 loci with the published wheat genome loci, only 3 functional genes were found, which annotated with gene function. There genes are: TraesCS2A01G448800 on chromosome 2A, which is close to the plant height associated site AX-108794050 and is related to the metabolic synthesis of transcription factor bHLH71; TraesCS2A01G448800, located on chromosome 1A at a distance similar to the spike length associated site AX-110689765, is related to protein coding; TraesCS4B01G031100, located on the 4B chromosome at a distance similar to the 1000 grain weight associated site AX-110399975, is associated with the encoding serine/threonine protein kinase SD1-8 and is involved in regulating cell proliferation and differentiation. 【Conclusion】38 QTL loci associated with wheat yield traits were detected. After verification, it was found that the associated excellent alleles have the effect of reducing plant height, increasing spike length, spikelet number, fertile spikelet number, grain number per spike, and thousand grain weight.

    Genome-Wide Association Study of Nitrogen Use Efficient Traits in Sweetpotato Seeding Stage and Screening and Validation of Candidate Genes
    YU YongChao, FAN WenJing, LIU Ming, ZHANG QiangQiang, ZHAO Peng, JIN Rong, WANG Jing, ZHU XiaoYa, TANG ZhongHou
    Scientia Agricultura Sinica. 2023, 56(18):  3500-3510.  doi:10.3864/j.issn.0578-1752.2023.18.002
    Abstract ( 13 )   HTML ( 2 )   PDF (1249KB) ( 5 )   Save
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    Objective】The objective of this paper was to analyze the genetic mechanisms of nitrogen use efficiency (NUE), and to explore the loci and candidate genes associated nitrogen (N) efficient traits, to provide support for the N-efficient molecular breeding and genetic improvement of sweetpotato.【Method】A total of 129 sweetpotato cultivars from all over the world were treated with N deficiency (0 mmol·L-1) and normal N (14 mmol·L-1). A hydroponic experiment was conducted to facilitate the genome-wide association study (GWAS) of six phenotypic traits (shoot biomass increment, root biomass increment, shoot N accumulation, root N accumulation, shoot N physiological utilization efficiency, and root N physiological utilization efficiency) of sweetpotato at the seedling stage. The N-efficient candidate genes were identified based on the GWAS and subsequently- verified using RT-qPCR.【Result】There were wide variations among the six traits related to NUE in sweetpotato under the normal N and N deficiency treatment conditions. The coefficient of variation (CV) of the shoot biomass increment under the N deficiency treatment condition was the greatest at 69.5%. The CV of the root N physiological utilization efficiency under N deficiency treatment condition was the smallest at 12.1%. All five traits were significantly correlated except for root N physiological utilization efficiency. The MLM model was used to conduct a GWAS of the six phenotypic trait values. A total of 134 QTL and 888 SNP loci were identified as being significantly associated with four out of the six traits, namely, shoot biomass increment, root biomass increment, root N accumulation, and shoot N physiological utilization efficiency. A total of 93 SNP markers across ten regions were significantly associated with shoot N physiological utilization efficiency with a high reliability. Six N efficiency candidate genes were obtained via gene annotation. RT-qPCR verified that the three candidate genes (itf01g08120.t1, itf01g22030.t1 and itf01g221000.t2) encoded glutamate dehydrogenase, NPH3 protein and TIP41-like protein, respectively, which warrants further research.【Conclusion】A total of 888 SNP loci associated with N utilization traits were detected in 129 sweetpotato cultivars. Among these, 93 SNP loci were significantly associated with shoot N physiological utilization efficiency, and six candidate genes were identified. Preliminary verification indicated that the itf01g08120.t1, itf01G2203.t1 and itf01g22100.t2 genes hold promising value for further research.

    Effects of Different Controlled Nitrogen Ratios on Leaf Senescence and Grain Filling Characteristics of Summer Maize
    YU HaoDong, CHU ZhenYu, WANG ShunYuan, GUO YanQing, REN BaiZhao, ZHANG JiWang
    Scientia Agricultura Sinica. 2023, 56(18):  3511-3529.  doi:10.3864/j.issn.0578-1752.2023.18.003
    Abstract ( 13 )   HTML ( 1 )   PDF (673KB) ( 4 )   Save
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    Objective】Supplying nitrogen timely and effectively could delay leaf senescence and improve grain filling characteristics of maize. The effects of controlled-release fertilizers with different controlled nitrogen ratio on leaf senescence, grain filling and yield of summer maize were studied to explore the appropriate controlled nitrogen ratio for summer maize in Huang-Huai-Hai region. 【Method】This study was conducted in 2019-2021 cropping seasons, using the middle-early maturing hybrid Denghai 518 (DH518) and the middle-late maturing hybrid Denghai 605 (DH605) as experimental materials. The types of nitrogen fertilizer are controlled release urea and ordinary urea mixed, ordinary urea. Five controlled nitrogen ratios: 10% (T1), 20% (T2), 30% (T3), 40% (T4) and 50% (T5) were set for studying the effects of controlled-release fertilizers on leaf senescence, grain filling characteristics, and their inter-relationship of summer maize, using urea fertilizer treatment as control (CK). 【Result】The results showed that using controlled release fertilizers could significantly increase the yield of summer maize. Among these, the yield increased most significantly in T3 treatment. Compared with CK, using controlled release fertilizers significantly increased the leaf area index (LAI), SPAD value, and the antioxidant enzymes activities, thus improving the grain filling characteristics. Among these, T3 treatment increased the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in summer maize leaves at the late growth stage, reducing the accumulation of malondialdehyde (MDA), thus delaying leaf senescence most significantly. In addition, the maximum growth (Wmax), grain filling rate (Gmax), days of active filling period (P), and grain dehydration rate were increased mostly in T3 treatment, accordingly the 1000-kernel weight and grain yield of summer maize were increased mostly. Correlation analysis showed that the yield was positively correlated with Wmax and Gmax; Wmax and Gmax was positively correlated with the activities of SOD and POD, but negatively correlated with MDA content. Grain dehydration rate and grain filling rate were positively correlated with the activities of SOD and CAT, but negatively correlated with MDA content. The water content of kernels was negatively correlated with the activities of SOD and CAT, and positively correlated with MDA content. Therefore, using controlled release fertilizers, especially T3 treatment, effectively optimized the grain filling characteristics by increasing the antioxidant enzyme activities, thus increasing the grain yield of summer maize.【Conclusion】Using controlled-release fertilizer could effectively increase the activities of leaf antioxidant enzymes, thus delaying leaf senescence, improving grain filling characteristics and increasing grain yield of summer maize. Among these, T3 treatment increased the grain yield most significantly.

    Influence of Future Climate Change on the Climate Suitability of Potato Cultivation in China
    ZHANG ZhiLiang, HE ZhiHao, RU XiaoYa, JIANG TengCong, HE YingBin, FENG Hao, YU Qiang, HE JianQiang
    Scientia Agricultura Sinica. 2023, 56(18):  3530-3542.  doi:10.3864/j.issn.0578-1752.2023.18.004
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    Objective】As the fourth staple food crop in China, potato suitability evaluation is of great significance to ensure national food security. Based on climate data, this study constructed an integrated species distribution model to predict the climate suitable area of potato in China in the future, and provided an important scientific reference for optimizing potato planting in China.【Method】In this study, the future climate data derived from six different global climate models (GCMs) were used to drive an ensemble of five different species distribution models (SDMs) to simulate the temporal and spatial distribution characteristics of climate suitable areas of potato cultivation in China in the historical (1970-2000) and four future (2021-2040, 2041-2060, 2061-2080, and 2081-2100) periods under four greenhouse gas emission scenarios (ssp126, ssp245, ssp370, and ssp585). 【Result】 (1) The precipitation in the wettest month, the highest temperature in the warmest month, and the average temperature in the coldest quarter were the main meteorological factors that affected the climate suitability of potato in China, with their contribution rates of 54.7%, 21.4% and 18.1%, respectively. (2) In four scenarios of greenhouse gas emission, the prediction results of various suitable areas were basically the same, showing the similar trends that the areas of suitable and low suitable would become larger, while the area of high suitable would become smaller. Only in Hainan, Tibet, Xinjiang and some other regions, the climate was not suitable for potato planting. The suitable potato planting areas (including both suitable and high suitable) exceed 50% in all cases. (3) In the future, the low suitable and suitable areas for potato planting will increase greatly, while the high suitable areas will decrease. The order of areas of different suitable grades would remain: suitable areas>low suitable areas>high suitable areas. (4) With the increase of greenhouse gas emission level, the high suitable area in China would be greatly reduced. For spatial distribution, the high suitable areas were mainly in Northeast China, Gansu, western Xinjiang, and some parts of southwest China. From the perspective of time, the future climate change would greatly affect the northwest of Shaanxi, the middle and lower reaches of the Yangtze River, the central and western Inner Mongolia and other regions. The climate suitability of potato planting would obviously decrease. 【Conclusion】In this study, the integrated species distribution models were constructed to predict the temporal and spatial distribution characteristics of potato climate suitable areas in the future. Northeast, Gansu, Southwest and other regions of China could be the main potato planting areas, while Xinjiang and other regions could be the main development areas. The rest regions should be given priority to the development of other staple crops and cash crops according to local conditions.

    Effects of Different Tillage Practices on Soil Physical Properties and Crop Yield in the Region of Southern Ningxia
    LI Rong, YAN HuiFang, ZHANG Long, MIAO FangFang, MIAN YouMing, HOU XianQing
    Scientia Agricultura Sinica. 2023, 56(18):  3543-3555.  doi:10.3864/j.issn.0578-1752.2023.18.005
    Abstract ( 11 )   HTML ( 1 )   PDF (569KB) ( 2 )   Save
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    Objective】In order to solve the problems of insufficient precipitation, shallow plough layer and low water use efficiency in the dry land of Southern Ningxia, we investigated the effects of different tillage practices on soil physical properties and crop yield in the region of southern Ningxia, and provided certain theory support for improving the topsoil structure reasonably in dryland, selecting the suitable tillage practice and increasing crop yield and benefit. 【Method】using potato and spring wheat as test crops, two tillage methods and four tillage depths of conventional ploughing 20 cm (C20, as a control), deep ploughing 30 cm (C30), subsoiling 30 cm (S30), subsoiling 40 cm (S40) and subsoiling 50 cm (S50) were set in arid region of southern Ningxia between 2019 and 2020 for the two-year field experiment to study the effects of different tillage methods with depths on soil bulk density during the harvest period, soil compactness water storage, and crop biomass during the growth periods,, yield and water use efficiency. 【Result】The average soil bulk density at 0-60 cm layer in potato season and spring wheat season under the S50 treatment was significantly decreased by 6.49% and 6.94%, compared with the control treatment. In the whole growth period, the average soil compactness with the S50 treatment in potato season and spring wheat season was the lowest, which was significantly increased by 19.32% and 8.11%, respectively, compared with the control treatment. The improvement in the soil water storage with the S50 treatment during the whole growth period in potato season and spring wheat season was the best, which was significantly increased by 13.58% and 25.66%, respectively, compared with the control treatment. The S40 treatment had the highest dry matter accumulation in potato season and spring wheat season. Crop yield, net income and water use efficiency were the highest under the S40 treatment in potato season and spring wheat season, which were significantly increased by 15.20%, 18.90% and 9.10% in potato season, and increased by 59.24%, 88.20% and 28.98% in spring wheat season, when compared with the control treatment. The tillage methods with depths had extremely significant effects on soil water storage, crop biomass and yield, while soil density and compactness were extremely affected by tillage methods. 【Conclusion】The tillage method combined with depth could significantly improve the topsoil structure, and increase soil water storage during the crop growing period, thereby promoting the increase of crop yield and water use efficiency. The subsoiling 40 cm treatment had the best effect of crop yield and income increasing in potato and spring wheat season, and it could be further promoted and applied in the cultivation of potato and spring wheat for high yield and efficiency in the region of southern Ningxia.

    Fluorescent Labeling and Observation of Infection Structure of Fusarium verticillioides
    HA DanDan, ZHENG HongXia, ZHANG ZhenHao, ZHU LiHong, LIU Hao, WANG JiaoYu, ZHOU Lei
    Scientia Agricultura Sinica. 2023, 56(18):  3556-3573.  doi:10.3864/j.issn.0578-1752.2023.18.006
    Abstract ( 14 )   HTML ( 1 )   PDF (9339KB) ( 4 )   Save
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    Objective】Taking the dominant pathogen Fusarium verticillioides causing maize ear rot and producing fumonisin as the research object, the objective of this study is to construct fluorescent strains that constitutively express green fluorescent protein GFP, red fluorescent protein DsRED, peroxisome targeted marker protein DsRED-PTS1 and F-actin cytoskeleton binding protein LifeAct-GFP, observe the penetration structure of F. verticillioides infecting maize silk epidermis, and to clarify the regulatory mechanisms and influencing factors regulating the infection structure formation of F. verticillioides.【Method】Fluorescent expression vectors pCOM-GFP, pCOM-DsRED, pCOM-DsRED-PTS1, and pCOM-LifeAct-GFP were transformed into the wild-type strain D85-2 of F. verticillioides through Agrobacterium-mediated genetic transformation. The transformants containing the target genes were identified by PCR, and the expression and distribution of various fluorescent proteins were observed under laser confocal microscopy. Maize was inoculated to observe the infection structure. The penetration structure and dynamic assembly of F-actin were observed by simulating the plant epidermal penetration experiment with cellophane membrane. The influencing factors of penetration structure formation were detected using F-actin polymerization inhibitor Latruculin A, tricyclazole, and reactive oxygen species (ROS) inhibitor DPI (diphenyleneiodonium chloride).【Result】A genetic transformation method using geneticin G418 as a resistance marker was established. FV-GFP and FV-DsRED strains have clear and bright green fluorescence and red fluorescence, respectively. The red fluorescence in FV-DsRED-PTS1 strain is distributed as round dots in conidia and hypha, which is consistent with the distribution characteristics of peroxisome in fungi. FV-LifeAct-GFP strain has filamentous green fluorescence in conidia and hypha, which is consistent with the distribution characteristics of F-actin protein in fungi. During the infection process of maize silk epidermis, an infection structure resembling a hyphopodium was observed at the top of the hyphae. The ring-forming assembly of F-actin protein in the penetration structure was observed in the mimic penetration experiment on the cellophane membrane. Drug stress experiments have shown that the formation of penetrating structures is regulated by F-actin protein polymerization and ROS. Meanwhile, tricyclazole can inhibit penetration.【Conclusion】Four fluorescent labeled strains were constructed, with clear cell localization and normal growth phenotype and pathogenicity, which can meet the research needs related to pathogenic mechanisms. F. verticillioides can form a hyphopodium like infection structure with swollen hyphae at the top when infecting maize. It is confirmed that F-actin cyclization and polymerization, cytoskeleton assembly and ROS regulation are the key factors affecting the formation of infection structure of F. verticillioides.

    Real-Time Quantitative PCR Detection of Citrus Yellow Mosaic Virus and Its Spatial and Temporal Distribution in Host Plants
    CAO Peng, XU JianJian, LI ChuXin, WANG XinLiang, WANG ChunQing, SONG ChenHu, SONG Zhen
    Scientia Agricultura Sinica. 2023, 56(18):  3574-3584.  doi:10.3864/j.issn.0578-1752.2023.18.007
    Abstract ( 14 )   HTML ( 2 )   PDF (1701KB) ( 6 )   Save
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    Background】Citrus yellow mosaic virus (CYMV) is a member of badnaviruses that was first discovered in India and caused serious damage to its citrus industry. At present, CYMV has been listed as a quarantine pest in the United States, Japan, New Zealand, Europe and the Mediterranean region, which has the potential risk of being introduced into China.【Objective】The objective of this study is to establish a real-time quantitative PCR (qPCR) detection system for CYMV, screen sensitive citrus varieties to CYMV, elucidate the spatial and temporal distribution of CYMV in host plant, and to provide technical support for monitoring of the virus.【Method】According to the conserved sequences of CYMV coat protein (CP) gene in NCBI, eight pairs of qPCR primers were designed using software Primer Premier 5, and were screened by conventional PCR for primer pairs with good amplification effect and high specificity. The concentration and annealing temperature of the primers were optimized to establish the CYMV qPCR detection system. The specificity of the system was evaluated by detecting different citrus pathogens. Conventional PCR and qPCR were performed in parallel with 1.98×109-1.98 copies/μL of plasmid standards diluted in a gradient as template to evaluate the sensitivity of the established system. The field citrus samples were collected randomly and detected using conventional PCR and qPCR in parallel to evaluate the applicability of the method. Fifteen citrus varieties including Yuhuanyou (Citrus grandis), Chandler pomelo (C. grandis), No.22 karatachi (Poncirus trifoliata), etc., were inoculated with CYMV for symptom observation and molecular detection to screen sensitive indicator plants. Samples from different tissues of Madam Vinous orange (C. sinensis) plants were collected at different times post inoculation, and qPCR assays were performed with C. sinensis elongation factor 1 alpha as an internal reference gene to clarify the spatial and temporal distribution patterns of CYMV in the host plants.【Result】The qPCR detection system for CYMV was established with the optimal primer of CYMV-qF7/R7, the optimal concentration 200 nmol·L-1 and the optimal annealing temperature 63 ℃. The results of the evaluation experiments showed that the specificity of the established qPCR system is strong, and the detection sensitivity is 1 000 times that of the conventional PCR. The detection results of 660 field citrus samples from different regions showed that the qPCR assay was consistent with the conventional PCR assay, and no CYMV-positive plants were detected except for the positive control. Among the 15 citrus varieties in the inoculation experiment, Yuhuanyou and Chandler pomelo showed strong and typical yellowing mosaic symptoms of CYMV infection at the earliest, suggesting that both could be used as sensitive indicator plants. The detection results of qPCR showed that the titer of CYMV in old leaves was the highest, the titer of virus in old cortex and root was higher, and the titer in tender cortex was lower. The relative content of CYMV in plants was highest from July to September, then decreased month by month, and reached the lowest value in January of the next year. From February of the next year, the relative content of CYMV began to rise, which was consistent with the change trend of the environmental temperature.【Conclusion】A qPCR assay for CYMV detection with high specificity and sensitivity was established, and the spatial and temporal distribution pattern of CYMV in the host plants was determined. In addition, Yuhuanyou and Chandler pomelo can be used as CYMV-sensitive indicator plants.

    Effects of Returning Chinese Milk Vetch and Rice Straw to Replace Partial Fertilizers on Double Season Rice Yield and Soil Labile Organic Carbon
    XIE Xue, LU YanHong, LIAO YuLin, NIE Jun, ZHANG JiangLin, SUN YuTao, CAO WeiDong, GAO YaJie
    Scientia Agricultura Sinica. 2023, 56(18):  3585-3598.  doi:10.3864/j.issn.0578-1752.2023.18.008
    Abstract ( 13 )   HTML ( 2 )   PDF (2514KB) ( 3 )   Save
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    Objective】 The purpose of this study was to investigate the effects of replacing partial chemical fertilizers with Chinese milk vetch and rice straw on double rice yield and the soil labile organic carbon fractions, carbon pool management index of the paddy soil based on four consecutive years of field experiment. 【Method】 The double-season rice field experiment was conducted, and then yield of rice yield early and late rice, contents of soil organic carbon, soil high labile, medium labile, labile and no labile organic carbon were measured after four years experiment, then soil carbon pool management index were calculated. There were six treatments: (1) Winter fallow + N, P, K (CF); (2) Chinese milk vetch+N, P, K (MV); (3) Winter fallow + low weight of rice straw returning+N, P, K (RSl); (4) Winter fallow+high weight of rice straw returning+N, P, K (RSh); (5) Chinese milk vetch + low weight of rice straw returning+N, P, K (MV+RSl); (6) Chinese milk vetch + high weight of rice straw returning+N, P, K (MV+RSh). After harvest of late rice, 0-15 cm surface soil was collected. Potassium dichromate method was used to determine the content of soil organic carbon, and potassium permanganate oxidation method was used to determine the content of soil organic carbon with high labile (33 mmol·L-1), medium labile (167 mmol·L-1) and labile (333 mmol·L-1). 【Result】 Under the equal nitrogen, phosphorus and potassium nutrient inputs, the double-season rice yield under the MV+RSh treatment differed significantly from the CF and RSl treatments, while there was no significant difference in rice yield between the other treatments, and the total double-season rice yield was the highest under the RSl treatment at 13 347 kg·hm-2 and the lowest in the MV+RSh treatment at 11 687 kg·hm-2. After four years of continuous trials, the MV+RSh, RSh, MV+RSl, RSl, and MV treatments significantly increased soil organic carbon by 42.0%, 32.9%, 29.9%, 28.3%, and 26.3% (P<0.05), respectively; soil labile organic carbon content was increased by 23.9%-56.4% in each treatment, and soil no labile organic carbon content under MV+RSh, RSh, MV+RSl, RSl, and MV treatments significantly was increased by 37.3%, 28.6%, 25.8%, 24.1% and 23.4% (P<0.05). Compared with the CF treatment, soil high labile organic carbon was increased by 12.3%-27.7%, medium labile organic carbon was increased by 5.6%-20.0%, and labile organic carbon was increased by 9.9%-26.3% under MV+RSh, MV+RSl, MV, RSh and RSl treatments. The CF、MV、RSl、MV+RSl、RSh、MV+RSh treatments increased the soil organic carbon pool management index by 25.5%-61.7%.【Conclusion】 Under four consecutive years of equal nitrogen, phosphorus and potassium nutrient inputs, returning Chinese milk vetch and rice straw replacing part of the chemical fertilizer dosage could ensure double-season rice yields and increase soil organic carbon content, and also help to increase the content of high labile, medium labile, labile and no labile soil organic carbon, all of which were most significantly increased by the treatment of MV+RSh. The contribution of rice straw alone to the increase in soil organic carbon content was greater than that of Chinese milk vetch alone. To sum up, in the southern double-season rice area, within a certain range of substitution, the return of Chinese milk vetch and rice straw to the field could reduce the amount of chemical fertilizer and ensure rice yield, which was of great significance for green and sustainable rice production.

    Straw Returning and Post-Silking Irrigating Improve the Grain Yield and Utilization of Water and Nitrogen of Spring Maize
    WANG YongLiang, XU ZiHang, LI Shen, LIANG ZheMing, XUE XiaoRong, BAI Ju, YANG ZhiPing
    Scientia Agricultura Sinica. 2023, 56(18):  3599-3614.  doi:10.3864/j.issn.0578-1752.2023.18.009
    Abstract ( 15 )   HTML ( 2 )   PDF (620KB) ( 7 )   Save
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    Objective】The irrigation system for spring maize production in the eastern Loess Plateau is unclear. In view of this, the effects of straw return and post-silking irrigation on grain yield and use efficiency of water and nitrogen of spring maize were studied in order to explore effective management measures to achieve sustainable and efficient utilization of water and nitrogen in spring maize in the region, so as to provide a theoretical basis for the high yield, high resource efficiency, and environmentally friendly agricultural sustainable development of spring maize in the region.【Method】Based on a 7-year long-term positioning experiment (2014-2020), a field experiment was carried out from 2021 to 2022. A split design was applied for the treatments, the main factors included straw returning (R) and no straw returning (U), and sub-factors included five post-silking irrigation gradients (I0, I50, I100, I150, and I200 mm). The correlation between dry matter accumulation at post-silking and evapotranspiration of spring maize was analyzed, and the effects of different treatments on grain yield, economic benefits and use efficiency of water and nitrogen were studied.【Result】The grain yield, economic benefit and use efficiency of water and nitrogen of spring maize were significantly improved by straw returning and irrigating at post-silking. Compared with conventional tillage, the grain yield, the economic benefit and the water use efficiency of straw returning treatment increased by 15.1%-43.5%, 15.9%-49.1%, and 16.8%-36.9%, respectively. The N recovery use efficiency, N agricultural efficiency, and N partial productivity of spring maize were significantly improved by 15.8%-62.0%, 26.5%-126.0%, and 15.1%-43.6%, respectively. The relationship between dry matter accumulation and evapotranspiration at post-silking was a quadratic function. Compared with conventional tillage, the straw returning treatment showed a stronger water productivity at post-silking. Though the yield response factor, the straw returning treatment had stronger water buffering capacity under water stress. Under the condition of straw returning, the grain yield and water and nitrogen use efficiency of the treatment with irrigation rate at post-silking were the highest under I150 treatment. In addition, the straw returning and irrigating at post-silking significantly promoted root growth of spring maize, but excessive irrigating (I200 treatment) inhibited root growth.【Conclusion】To sum up, in the spring maize production system in the eastern valley plain of the Loess Plateau, straw returning with the irrigating rate of 150 mm at post-silking could be used as a management measure for the efficient and sustainable use of water and nitrogen of spring maize.

    Effects of Long-Term Application of Organic Fertilizer on Rare and Abundant Bacterial Sub-Communities in Greenhouse Tomato Soil
    LIU Lei, SHI JianShuo, ZHANG GuoYin, GAO Jing, LI Pin, REN Yanli, WANG LiYing
    Scientia Agricultura Sinica. 2023, 56(18):  3615-3628.  doi:10.3864/j.issn.0578-1752.2023.18.010
    Abstract ( 9 )   HTML ( 1 )   PDF (1914KB) ( 2 )   Save
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    Objective】The objective of the present study was to distinguish the rare and abundant bacteria from the whole community and to explore their responses to long-term application of organic fertilizer respectively, so as to provide new insights into the relationships between soil biodiversity and ecosystem functioning under major agricultural activities. 【Method】Based on the long-term fertilization experiment of greenhouse tomato, soils were collected under four different treatments, including no fertilizer (M0), low organic fertilizer 5.68 t·hm-2 (M1), medium organic fertilizer 8.52 t·hm-2 (M2), and high organic fertilizer 11.36 t·hm-2 (M3). Illumina MiSeq platform was used to analyze the diversity, community composition, co-occurrence network and potential functions differences of the rare and abundant bacterial sub-communities, and their various responses to long-term fertilization, to illustrate the key factors driving the distinct distribution patterns and responses for rare and abundant bacteria. 【Result】Compared with the abundant bacterial sub-community, the rare bacterial sub-community showed higher α- and β-diversity and distinct community composition, as well as potential functions. A functional prediction detected that abundant bacteria contributed primary functions in the greenhouse ecosystem, such as nutrient and energy metabolism, meanwhile rare bacteria contribute a substantial fraction of auxiliary functions (e.g., metabolism of cofactors), which indicated they played important roles in the functional redundancy of microbial communities. Contrasting responses of rare and abundant bacterial sub-communities to long-term fertilization were revealed in this study, in which the rare bacteria was more sensitive. Compared with no fertilizer, the long-term application of organic and chemical fertilizer significantly increased the OTU richness, Shannon diversity, and total relative abundance by 19.8%-53.8%, 5.8%-8.0%, and 1.1-1.2 times, respectively, and changed the community composition and structure of rare bacterial sub-communities. In addition, with the increased application rates of organic fertilizer, the OTU richness of rare bacteria also increased significantly, accompanied by obvious changing in community composition and structure. However, the abundant bacteria exhibited less sensitivity to long-term fertilization, with only the community composition altered. Besides, the co-occurrence network complexity increased with organic fertilizer rates, especially in rare sub-communities. Both the results of the NMDS and mantel test revealed that the controlling factors affecting rare and abundant bacterial sub-communities were different. A variety of soil factors associated with deterministic processes, i.e., SOC, soil nutrients of total N and P, Olsen-P and available K, and pH, as well as macro- and medium-aggregate, significantly influenced abundant bacteria. Structural equation model (SEM) further showed that soil organic matter and total phosphorus directly drove abundant bacterial diversity. On the other hand, less effects of environmental filtering and more scattered distribution patterns were found in rare bacteria, indicating different assemblies of rare and abundant sub-communities. 【Conclusion】Compared with the abundant bacteria and the whole community, the rare bacteria sub-community showed higher diversity and unique community composition, which improved the functional redundancy of the microbial community. Long-term fertilization altered the whole bacterial community mainly by affecting rare bacteria (i.e., increasing diversity, changing community composition, increasing co-occurrence network complexity) rather than the abundant bacteria. The controlling factors that mediated the assembly of the rare and abundant bacterial sub-communities were also different.

    Identification and Cloning of Ferritin Family Genes in Grape and Response to Compound Amino Acid-Iron Spraying During Different Fruit Developmental Stages
    SONG ZhiZhong, WANG JianPing, SHI ShengPeng, CAO JingWen, LIU WanHao, XU WeiHua, XIAO HuiLin, TANG MeiLing
    Scientia Agricultura Sinica. 2023, 56(18):  3629-3641.  doi:10.3864/j.issn.0578-1752.2023.18.011
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    Objective】Ferritin plays an important role in plant growth and development, and its biological function in fruit trees are essentially unknown. Cloning of grape Ferritin family genes and revealing their expression patterns at different fruit developmental stages and their response differences to foliar spraying of amino acid iron (Fe) compound fertilizers could provide a theoretical basis for studying the molecular mechanisms of Fe nutrition and metabolism in fruit trees. 【Method】The Ferritin family genes were screened and identified in grape genome by homologous cloning. The detailed characteristics of Ferritin genes and their encoded proteins were analyzed by using bioinformatical methods. The tissue-specific expression patterns of Ferritin family genes during distinct fruit developmental stages and differential response to foliar spraying of amino acid-iron compound fertilizer were determined by carrying out real-time fluorescent quantitative PCR. 【Result】In total, 4 Ferritin family genes were retrieved and cloned from grape, entitled with VvFer1-VvFer4, which were distributed on No. 6, 8 and 13 chromosomes, containing 7 introns with different lengths. VvFer proteins were mainly located in chloroplast and nucleus. The amino acid sequence identity of Ferritin homologs from 16 plant species was as high as 61.48%. Phylogenetic tree analysis indicated that Ferritin homologs belonging to the same genus, such as Arabidopsis and turnip of Cruciferae, tobacco and potato of Solanaceae, soybeans, peanuts and chickpeas of Leguminosae, rubber trees, cassava and castor of Euphorbiaceae, and apples, peaches and strawberries of Rosaceae, possessed a closer genetic distance during evolution. Grape VvFer3 was closely clustered with Solanaceae homologs. The expression levels of VvFer genes were different among distinct tissues or organs of 5-year-old Mathelan grape trees during different fruit developmental stages. In particular, the expression level of VvFer3 was the most abundant, and the maximum expression was observed in fruits from hard core stage to mature stage, followed by VvFer2 and VvFer4. The content of Fe Marselan fruits was slightly different among distinct grape developmental stages, which was gradually increased from young fruit stage, and reached the highest value at veraison stage, and then slightly decreased until mature stage, but still higher than that of young fruit stage and hard core stage. Foliar spraying treatment significantly enhanced Fe content of fruits at mature stage, accompanied by ACO (aconitase), NIR (nitrate reductase) and SDH (succinate dehydrogenase). Genes of VvFer2-4 were significantly up-regulated by foliar spraying of amino acid-iron compound fertilizer, which was closely related to distinct grape tissues/organs and different fruit developmental stages. In details, the expression of VvFer2 in fruits was sensitive to foliar spraying treatment during the whole period of grape development. The expressions of VvFer3 in all tested tissues were sensitive to foliar spraying treatment from young fruit stage to veraison stage. The expressions of VvFer4 in phloem and leaves were continuously induced by foliar spraying treatment during the whole period of grape development, whereas in fruits from young fruit stage to veraison stage. The expression of VvFer1 was relatively low, but very uniform, and there was no response to foliar spraying treatment at the transcription level. 【Conclusion】Four Ferritin family genes were cloned and identified in grape, whose expression were significantly different among distinct tissues during different fruit developmental stages and were prone to be up-regulated under foliar spraying treatment of amino acid-iron compound fertilizer. The overall expression level of VvFer3 gene was the highest in all tested tissues (especially in fruits) during the whole fruit development stage, and was up-regulated in fruits under foliar spraying treatment from young fruit stage to the verason stage.

    Genome Wide Association Study for Resistance to Citrus Brown Spot Disease
    YANG ShengNan, CHENG Li, TAN YueXia, ZHU YanSong, JIANG Dong
    Scientia Agricultura Sinica. 2023, 56(18):  3642-3654.  doi:10.3864/j.issn.0578-1752.2023.18.012
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    Objective】The study objective was to explore candidate genes associated with resistance to Alternaria brown spot disease in citrus mandarin, so as to provide the basis for developing suitable molecular markers for further citrus resistance breeding work. 【Method】In summer and autumn of 2022, the young leaves of 136 citrus mandarin accessions were picked and inoculated with the fungus mycelium of Alternaria alternata in the laboratory. The combined results of two experiments were used to obtain the reliable results of 121 citrus mandarins responding to Alternaria brown spot. The phenotypes of 121 citrus mandarins were selected to verify the effectiveness of the CAPS marker developed in a previous study. Then, in order to obtain the candidate SNPs related to Alternaria brown spot resistance, the phenotypes of 121 citrus mandarins and corresponding SNP genotype data from GBS sequencing were analyzed with PCA, GWAS, and Fst methods, respectively. Candidate genes had been selected from the flanking region of 25 kb sequences surrounding the candidate SNPs site, and then they were screened out according to phytozome annotations. The expressions of candidate genes were analyzed after inoculating with the pathogen fungus on leave of Chengtuo hongju and Clementina (Algeria) for 24, 48, and 72 h. 【Result】Among 121 citrus mandarins, 67 varieties such as Clementine and Satsuma were resistant to Alternaria brown spot disease, whereas 54 varieties such as Hong Ju and Ponkan were susceptible. Some varieties resistance to Alternaria brown spot disease could discriminated by CAPS, but its accuracy only accounted for 76.86% in the study. GWAS analysis identified six significant SNPs highly associated with disease resistance, among which SNP1 located in Ciclev10021676 at 24 838 146 bp of chromosome 3 could be used to predicate the resistance of varieties, and their genotype showed a strong correlation with phenotype. Eight significant SNPs highly associated with disease resistance selected by Fst analysis. Finally, five genes of Ciclev10018604, Ciclev10023485, Ciclev10023486, Ciclev10024586 and Ciclev10019874 were screened out. The expression levels of these five genes in Chengtuo Hongju were up-regulated extensively after inoculating leaves with the pathogen fungus, and their expression levels reached the highest 48 hours later. 【Conclusion】Through GWAS, the SNP at 24 838 146 bp on chromosome 3 was found to be the most significant one with high resistance correlation to Alternaria brown spot disease, and the genotype at this location could be effectively used to distinguish the resistant varieties. The candidate genes responding to Alternaria brown spot disease in mandarin were discussed, i.e., Ciclev10019874, Ciclev10018604, Ciclev10023485, Ciclev10024586, and Ciclev10023486.

    Effects of Different Drying Methods on the Quality Characteristics of Dried Zanthoxylum armatum Leaves
    WANG AnNa, WANG Yun, PENG XiaoWei, WU YuFang, KAN Huan, LIU Yun, QUAN Wei, LU Bin
    Scientia Agricultura Sinica. 2023, 56(18):  3655-3669.  doi:10.3864/j.issn.0578-1752.2023.18.013
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    Objective】In order to ensure improved drying quality of Zanthoxylum armatum (Z. armatum) leaves with low processing cost and high nutritional value, the effects of different drying methods on the quality of Z. armatum leaves were studied, so as to provide a reference basis for its development and utilization. 【Method】With Z. armatum leaves as test materials, 5 different drying methods were set, including natural drying (ND), hot air drying (AD), heat pump drying (PD), vacuum drying (VD), and vacuum freezing drying (FD). The effects of 5 different drying methods on their drying characteristics, functional characteristics, microstructure, content of polyphenol, flavonoid, protein, fat, and total sugar, as well as antioxidant capacities and volatile compounds, were investigated. 【Result】The moisture ratios of Z. armatum leaves under 5 different drying methods all exhibited an exponential downward trend, and the time required to reach the end of drying was 32, 7, 6, 16 and 28 h for ND, AD, PD, VD and FD, respectively. During the drying period, the faster the water diffusion, the greater the drying rate and the shorter the elapsed time, and the drying rate was PD>AD>VD>FD>ND. The effects of different drying methods on the color of Z. armatum leaves was VD>ND>PD>AD>FD, where AD and FD could better retain their chlorophyll content at 12.74 and 12.85 mg∙g-1, respectively. The microstructure showed that temperature had a significant effect on the internal structure of Z. armatum leaves, which was more seriously damaged by high temperature, and FD exhibited a porous structure with better water-holding capacity of 5.85 g∙g-1. ND had the highest retention of sugars at 6.53 g/100 g, resulting in a higher water-solubility of 35.93%. PD retained its protein and fat better, with content of 2.43 and 4.86 g/100 g, respectively. The retention of polyphenols and flavonoids in dried Z. armatum leaves was high, with polyphenol content ranging from 72.16 to 109.50 mg∙g-1 and flavonoid content ranging from 45.60 to 82.23 mg∙g-1, where AD and FD were high and relatively close in polyphenol and flavonoid content. The scavenging capacities of DPPH∙, ABTS+∙ and the power of FRAP reduction were FD>AD>PD>ND>VD, with positive correlation between the content of polyphenols, flavonoids and antioxidant capacities. Simultaneously, the volatile compounds were determined by headspace solid-phase microextraction-mass spectrometry coupled with gas chromatography-mass spectrometry, and a total of 49 species were detected, which could be classified into seven categories according to structures, including olefins, ketones, aldehydes, esters, alcohols, benzenes, and phenols. It was found that the types, numbers, and relative content of volatile compounds in Z. armatum leaves varied under 5 different drying methods, among which olefins were dominant, with a total of 26 species and relative content ranging from 58.02% to 75.18%.【Conclusion】Based on the comprehensive quality indexes of materials and actual operation cost, it was found that AD was more suitable for drying Z. armatum leaves, with higher efficiency, lower cost, as well as relatively better quality of color and antioxidant capacities.

    CircCEP85L Regulates the Proliferation and Myogenic Differentiation of Bovine MuSCs
    WEI Yao, ZHANG RuiMen, AN Qiang, WANG LeYi, ZHANG YongWang, ZOU ChaoXia, ZHANG ErKang, MO BiYun, SHI DeShun, YANG SuFang, DENG YanFei, WEI YingMing
    Scientia Agricultura Sinica. 2023, 56(18):  3670-3681.  doi:10.3864/j.issn.0578-1752.2023.18.014
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    Objective】At present, studies have proved that circRNA plays important roles in the development of bovine muscle, but its molecular regulation mechanism remain elusive. Screening circRNAs related to bovine muscle development can lay a foundation for further elucidating the molecular mechanism of bovine muscle development.【Method】In this study, RNA-seq sequencing results of proliferating (GM) and myogenic differentiation (DM) yellow bovine muscle stem cells (MuSCs) analyzed in the previous stage were used to screen for significantly differentially expressed circRNA, circCEP85L. Tissue samples of heart, liver, spleen, lung, kidney, muscle, intestine and stomach were collected aseptically from fresh yellow fetal calves, and yellow muscle stem cells were isolated and cultured and induced into myogenic differentiation. GM and DM cells cultured in vitro from yellow calves were collected, RNA was extracted and reverse transcribed into cDNA, respectively. Quantitative real time PCR (qRT-PCR) was used to detect the expression of circCEP85L in different tissues and different cell states. Meanwhile, specific primers were designed to amplify the full length of circCEP85L, and the overexpression vector p-circCEP85L was constructed. The plasmid was transfected into MuSCs and overexpressed circCEP85L cell samples were collected. Using overexpression plasmid pCD5-ciR cell samples as control, qRT-PCR, flow cytometry, Western Blot and immunofluorescence were used to detect the effects of overexpression of circCEP85L on proliferation, apoptosis and myogenic differentiation of yellow bovine MuSCs.【Result】The electrophoresis of PCR product proved the existence of circCEP85L. CircCEP85L was expressed in various tissues, and the expression level in DM stage was significantly higher than that in GM stage (P<0.001). To further investigate the effect on circCEP85L scallion MuSCs. The overexpression vector p-circCEP85L was transfected with the control vector pCD5-ciR in vitro cultured yellow bovine MuSCs and the EdU results showed that overexpression of circCEP85L significantly reduced the proportion of EdU positive cells (P<0.001) after continuing the culture for 24 h. Flow cycle analysis showed that overexpression of circCEP85L increased the proportion of cells in G0/G1 phase and significantly decreased the proportion of cells in S phase (P<0.001). Flow cytometry showed that overexpression of circCEP85L significantly inhibited the apoptosis rate of MuSCs (P<0.05). qRT-PCR and western blot were used to detect the expression of proliferation and apoptosis-related genes in MuSCs, respectively. The results showed that overexpression of circCEP85L significantly reduced the mRNA expression levels of proliferation and apoptosis-related genes in bovine MuSCs (P<0.001), and the expression of apoptotic protein BAX was also significantly reduced (P<0.01). In addition, in order to detect the effect of circCEP85L overexpression on myogenic differentiation of cattle MuSCs, the differentiation medium was replaced 24 hours after transfection to induce cell differentiation. Western blot and immunofluorescence results showed that overexpression of circCEP85L significantly promoted the expression level of differentiation marker gene MyH6 (P<0.001), and the number and size of myotubes formed by cell fusion were significantly higher than those of the control group.【Conclusion】The results of this study indicate that circCEP85L affects the growth and development process of skeletal muscle in cattle by inhibiting the proliferation and apoptosis of MuSCs and promoting myogenic differentiation of cells, which is expected to be a key circRNA for subsequent mechanistic studies to regulate the growth and development process of skeletal muscle in cattle.

    Research Progress on Machine Learning for Genomic Selection in Animals
    LI MianYan, WANG LiXian, ZHAO FuPing
    Scientia Agricultura Sinica. 2023, 56(18):  3682-3692.  doi:10.3864/j.issn.0578-1752.2023.18.015
    Abstract ( 8 )   HTML ( 1 )   PDF (570KB) ( 1 )   Save
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    Genomic selection is defined as using the molecular marker information that covered the whole genome to estimate individual’s breeding values. Using genome information can avoid many problems caused by pedigree errors so as to improve selection accuracy and shorten breeding generation intervals. According to different statistical models, methods of estimated genomic breeding value (GEBV) can be divided into based on BLUP (best linear unbiased prediction) theory, based on Bayesian theory and others. At present, GBLUP and its improved method ssGBLUP have been widely employed. Accuracy is the most used evaluation metric for genomic selection models, which is to evaluate the similarity between the true value and the estimated value. The factors that affect the accuracy can be reflected from the model, which can be divided into controllable factors and uncontrollable factors. Traditional genomic selection methods have promoted the rapid development of animal breeding, but these methods are currently facing many challenges such as multi-population, multi-omics, and computing. What’s more, they cannot capture the nonlinear relationship between high-dimensional genomic data. As a branch of artificial intelligence, machine learning is very close to biological mastery of natural language processing. Machine learning extracts features from data and automatically summarizes the rules and use to make predictions for new data. For genomic information, machine learning does not require distribution assumptions, and all marker information can be considered in the model. Compared with traditional genomic selection methods, machine learning can more easily capture complex relationships between genotypes, phenotypes, and the environment. Therefore, machine learning has certain advantages in animal genomic selection. According to the amount and type of supervision received during training, machine learning can be classified into supervised learning, unsupervised learning, semi-supervised learning, and reinforcement learning. The main difference is whether the input data is labeled. The machine learning methods currently applied in animal genomic selection are all supervised learning. Supervised learning can handle both classification and regression problems, requiring the algorithm to be provided with labeled data and the desired output. In recent years, the application of machine learning in animal genomic selection has been increasing, especially in dairy and beef cattle. In this review, machine learning algorithms are divided into three categories: single algorithm, ensemble algorithm and deep learning, and their research progress in animal genomic selection were summarized. The most used single algorithms are KRR and SVR, both of which use kernel tricks to learn nonlinear functions and map data to higher-dimensional kernel spaces in the original space. Currently commonly used kernel functions are linear kernel, cosine kernel, Gaussian kernel, and polynomial kernel. Deep learning, also known as a deep neural network, consists of multiple layers of connected neurons. An ensemble learning algorithm refers to fusing different learners together to obtain a stronger supervised model. In the past decade, the related literature on machine learning and deep learning has shown exponential growth. And its application in genomic selection is also gradually increasing. Although machine learning has obvious advantages in some aspects, it still faces many challenges in estimating the genetic breeding value of complex traits in animals. The interpretability of some models is low, which is not conducive to the adjustment of data, parameters, and features. Data heterogeneity, sparsity, and outliers can also cause data noise for machine learning. There are also problems such as overfitting, large marks and small samples, and parameter adjustment. Therefore, each step needs to be handled carefully while training the model. This paper introduced the traditional methods of genomic selection and the problems they face, the concept and classification of machine learning. We discussed the research progress and current challenges of machine learning in animal genomic selection. A Case and some application suggestions were given to provide a certain reference for the application of machine learning in animal genomic selection.

    Response of Functional Traits of Key Species in Meadow Steppe to Long-Term Grazing and Grazing Exclusion
    SI YuFan, LI Hui, LI ZiHao, JIANG CuiXia, GUO HaoNan, YANG PeiZhi, XI JieJun, YAN RuiRui, WURENQIQIGE, SHAN Dan, XIN XiaoPing
    Scientia Agricultura Sinica. 2023, 56(18):  3693-3708.  doi:10.3864/j.issn.0578-1752.2023.18.016
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    Objective】The response of plant functional traits to environmental changes and external disturbances reflects the phenotypic plasticity, survival strategies and adaptability of plants. The study on the changes of functional traits of grassland plants under long-term grazing and the recovery response after stopping grazing can provide a theoretical basis for grassland restoration management. 【Method】In this study, the changes of leaf functional traits (leaf dry mass, leaf total water content, leaf area, specific leaf area, leaf nitrogen content, leaf phosphorus content, leaf C/N raito, leaf N/P ratio) of six key species (Leymus chinensis,Carex pediformis,Cleistogenes squarrosa,Astragalus adsurgens,Artemisia tanacetifolia L.,Pulsatilla turczaninovii) in Hulunbuir meadow steppe under different grazing intensities during growing season were studied. The immediate recovery response of leaf functional traits of key species in meadow steppe after stopping grazing during growing season was discussed. 【Result】(1) The relative biomass and importance values of the six key species decreased with the increase of grazing intensity, and the values of light and heavy grazing intensity after stopping grazing were greater than that after continuing grazing. (2)The leaf dry mass and leaf C/N ratio of six key species decreased with the increase of grazing intensity; the leaf total water content, specific leaf area and leaf nitrogen content increased with the increase of grazing intensity; the leaf area of all species except Artemisia tanacetifolia L. decreased with the increase of grazing intensity; the leaf phosphorus content increased with the increase of grazing intensity except Cleistogenes squarrosa ; with the increase of grazing intensity, the leaf N/P ratio of Leymus chinensis,Carex pediformis,Cleistogenes squarrosa,Pulsatilla turczaninovii showed an increasing trend, while that of Astragalus adsurgens,Artemisia tanacetifolia L. decreased. (3) After stopping grazing, the resilience of heavy grazing was higher than that of light grazing, and the functional traits of 6 key species recovered better as a whole, leaf dry mass, leaf total water content, leaf area, specific leaf area and leaf N/P ratio showed positive response, leaf phosphorus content showed negative response, leaf nitrogen content and leaf C/N ratio showed different positive and negative responses among six key species, the negative response of leaf nitrogen content was less than positive response, and the positive response of leaf C/N was more than negative response. (4) The leaf morphological traits of grasses and the nutrient characteristics of miscellaneous grasses were more sensitive to recovery after stopping grazing, and the responses of leaf dry mass, leaf area and leaf phosphorus content to the interaction between grazing intensity and species were more significant. After stopping grazing, leaf dry mass of leaves increased with the increase of leaf area, leaf nitrogen content and leaf N/P of the six key species.【Conclusion】Long-term grazing led to individual miniaturization of grassland plants. After stopping grazing, the positive response of plant functional traits is more than negative response, and the grassland vegetation function shows an obvious recovery response, which increases the productivity of the grassland. Above-ground biomass of the meadow grassland increases.