Scientia Agricultura Sinica

Research Progress and Prospects on Crop Pan-Genomics

WANG Hui, DING BaoPeng, LI YuXian, REN QuanRu, ZHOU Hai, ZHAO JunLiang, HU HaiFei

Scientia Agricultura Sinica. 2025, 58(11): 2045-2061. doi:10.3864/j.issn.0578-1752.2025.11.001

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The global population continues to rise and climate change imposes severe challenges on food supply, the issue of food security has become increasingly prominent. To meet the growing demand for food, enhancing crop yield and improving environmental adaptability have become critical goals in agriculture. Under this situation, genomics is regarded as an essential method for accelerating crop breeding, as it enables the in-depth exploration and utilization of superior functional genes to not only boost crop productivity but also strengthen stress tolerance and adaptability, thereby providing robust support for ensuring global food security and achieving sustainable agricultural development. Nonetheless, the traditional single-reference genome often fails to capture the entire spectrum of genomic variations accumulated during crop domestication and improvement, which constrains our understanding of functional genes and their regulatory networks. With the continual advancement of high-throughput sequencing technologies, genomics research has now entered the pangenomics era. By integrating multiple high-quality genomes into a comprehensive catalog of genomic content, researchers can precisely identify a variety of genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations (SVs), thereby capturing the extensive genetic diversity present across different cultivars, subspecies, and wild relatives. Pangenomics framework greatly facilitates the exploration of superior functional genes. Moreover, by combining pangenomic data with other multi-omics datasets (e.g., transcriptomics, proteomics, and epigenomics), researchers can accurately identify superior functional genes, enabling the provision of more targeted and accurate genetic loci for molecular breeding. With emerging gene-editing tools such as CRISPR-Cas9, researchers can further modify essential genetic loci in a directed manner to remove undesirable traits or reinforce resistance to environmental stressors. This will lay a foundation for cultivating the next generation of crops that exhibit higher yield, improved quality, and enhanced resilience. This review summarizes recent developments in major pangenome construction methods and formats, and systematically reviews the progress made in crop pangenomes as well as their applications in crop breeding improvement. It also discusses the challenges pangenomics faces in future crop breeding, offering insights into leveraging pangenome resources for crop genetic improvement, and ultimately provides new perspectives and strategies for future molecular breeding.

Map-Based Cloning and Functional Verification of A Novel Split Glume Gene OsSG2 in Rice (Oryza sativa L.)

ZENG YueHui, ZOU WenGuang, ZHAO FuMing, XIAO ChangChun, HUANG JianHong, MA BinLin, YANG WangXing, WEI XinYu, XU XuMing

Scientia Agricultura Sinica. 2025, 58(11): 2062-2080. doi:10.3864/j.issn.0578-1752.2025.11.002

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【Objective】 The sg2 (split glume 2) is a naturally occurring rice mutant derived from an advanced-generation breeding population of the restorer line GK1327 originating from the Sanming Academy of Agricultural Sciences (SAAS). In this work, the OsSG2 (Oryza sativa Split Glume 2) gene in the mutant was performed to conduct genetic analysis, map-based cloning and functional verification, which will provide a theoretical basis and an important germplasm resource for further study on the function of OsSG2 in the development of rice floral organs.【Method】 The morphological characteristics of the sg2 mutant florets were anatomically observed to analyze the features of floral organ development. By investigating the phenotypic and agronomic characteristics of wild-type GK1327 and sg2 mutant, and observing the pollen staining in I₂-KI, the effects of the mutant phenotype on yield-related traits and pollen fertility were analyzed. The F₂ populations developed by crossing sg2 mutant with wild-type GK1327 and 9311, respectively, were used to perform genetic analysis and physical mapping of the OsSG2. Bulked segregant analysis (BSA) combined with next-generation sequencing (NGS) technology (BSA-seq) was used to screen the candidate genes of OsSG2, and a combination of RT-PCR (reverse-transcription PCR) and qRT-PCR (quantitative real-time PCR) was performed to analyze their expression patterns. The OsSG2 candidate genes were cloned and sequenced by PCR amplification and sequencing approaches, and the functional verification was conducted by knockout using CRISPR-cas9 and a complementation test.【Result】 The sg2 mutant exhibited an abnormal spikelet phenotype at the reproductive stage, the palea and lemma of florets were weak, distorted, and dehiscent, and with the proportion of abnormal florets in the panicles were 100%. Compared with the wild-type GK1327, the seed setting rate, the 1000-grain weight, and the seed germination rate of sg2 mutant were markedly lower, whereas the pollen fertility was normal. Genetic analysis demonstrated that a recessive nuclear gene was responsible for the mutant phenotype of sg2. A map-based cloning strategy delimited OsSG2 to a 919.85 kb physical interval on the short arm of chromosome 3, flanked by two InDel (insertion/deletion) markers, InDel-12083 and InDel-17610, that included 75 putative ORFs (open read frames). Moreover, a BSA-seq technology identified a potential candidate gene LOC_Os03g11614 as the OsSG2 gene, which encodes an OsMADS1 transcription factor localized to the nucleus. Expression and sequence analyses revealed that the transcript levels of LOC_Os03g11614 were markedly lower in young panicles of the sg2 mutant compared with those in the wild-type GK1327 during the flowering stage, and a SNP (single nucleotide polymorphism) mutation (G-A) was identified at the third nucleotide position of exon 1 in the LOC_Os03g11614, resulting in the change of the start codon from ATG to ATA, which caused a transcriptional suppression of LOC_Os03g11614 and a functional loss of the OsMADS1 protein. These results further supported the tentative identification of LOC_Os03g11614 as the candidate OsSG2 gene, which was confirmed by knockout using CRISPR-cas9 and a functional complementation test.【Conclusion】 The split glume gene OsSG2, which was successfully isolated from sg2 mutant in this work, was identified as a new allele of OsMADS1 in rice.

Genetic Gain Analysis of Agronomic Traits of Brassica rapa L. in Northern China from 2006 to 2022

ZHANG TianYu, LIU LiJun, YANG Gang, WU JunYan, PU YuanYuan, MA Li, WANG WangTian, LU XiaoMing, MA YuanQiang, SUN WanCang

Scientia Agricultura Sinica. 2025, 58(11): 2081-2095. doi:10.3864/j.issn.0578-1752.2025.11.003

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【Objective】 Based on the experimental results from 2006 to 2022 of 81 winter turnip rape varieties across eight representative ecological zones (extremely arid, arid, and semi-arid regions) including Jiuquan, Zhangye, Wuwei, Lanzhou, Qingyang, Pingliang, Tianshui, and Longxi. The objective was to investigate the evolution of agronomic traits, to offer insights for breeding research and the cultivation of winter rapeseed in northern China. 【Method】 The tested varieties were classified into strong cold tolerant and moderately cold tolerant. The major agronomic traits were subjected to genetic gain analysis, correlation analysis, path analysis, and principal component analysis. The results illustrate, significant enhancements in the agronomic characteristics of northern winter rapeseed over the 17-year period.【Result】 For the strong cold tolerant varieties, plant height, branching position, number of branches, number of siliques per plant, and yield per plant showed a gradual increase, with an average annual increase of 0.87%, 1.07%, 0.0837%, 6.09%, and 0.0281%, respectively. The number of siliques and 1000-grain weight showed a downward trend, with average annual decrease of 0.0289% and 0.012%, respectively. For moderately cold tolerant variety, plant height, branching position, number of branches, number of siliques per plant, and yield per plant also increased, with average annual increase of 2.18%, 2.19%, 1.27%, 0.117%, and 0.0776%, respectively. The number of branches and 1000-grain weight decreased, with average annual decrease of 0.109% and 0.00702%, respectively. Correlation analysis showed a highly significant positive correlation between yield per plant and the number of siliques per plant. Path analysis of agronomic traits and yield per plant revealed that for the strong cold tolerant varieties, the number of siliques per plant (0.961) contributed most to seed yield per plant, followed by the seeds per silique (0.365). The largest contribution of cold tolerant varieties to the yield per plant was the branch position (1.173), followed by the number of siliques per plant (0.544). Path analysis of yield per plant and climatic factors showed that strong cold tolerant varieties were greatly affected by accumulated temperature of 10 °C, while cold-resistant varieties were greatly affected by negative accumulated temperature of 0 °C. Principal component analysis (PCA) screened out three principal components with a cumulative contribution rate of 78.617% of the overall variance, among which the number of siliques per plant, branch position, and 1000-grain weight were the main factors causing the differences among these varieties.【Conclusion】 Substantial advancements have been achieved in the genetic enhancement breeding of agronomic characteristics of winter rapeseed in northern China. The yield per plant has been steadily increasing. The plant type has also been greatly improved. The number of siliques per plant was the main factor to increase the yield of Brassica rapa L.. The adaptability of strong cold tolerant varieties to the external environment surpasses that of moderately cold tolerant varieties.

Effects of Nitrogen Fertilization Levels on Matter Accumulation and Nitrogen Uptake in Different Source and Library Types of Japonica Rice

ZHOU Yu, SUN Tong, ZHANG YanHong, RU Yan, SU Tan, WANG Shuai, ZHU JinYan, HU JinLong, XIONG QiangQiang, ZHANG HongCheng, ZHOU NianBing

Scientia Agricultura Sinica. 2025, 58(11): 2096-2117. doi:10.3864/j.issn.0578-1752.2025.11.004

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【Objective】 This study aimed to investigate the overground part material accumulation and nitrogen transport of japonica rice with different sources and library types under different nitrogen application conditions, in order to select the japonica rice strain with high yield and high nitrogen efficiency, and explore the optimal nitrogen application rate for the growth of this japonica rice variety, ultimately achieve an increase in yield.【Method】 The trial was conducted in 2022-2023, with the source library interaction type Yangchan35003, source restriction type Yangchan35002, and library restriction type Yangchan35004 as test materials, and the split zone design was adopted. Four nitrogen application treatments of 180 kg·hm^-2, 225 kg·hm^-2, 270 kg·hm^-2 and 315 kg·hm^-2 were set. The yield, dry matter accumulation and nitrogen related indexes (mainly taking nitrogen transport efficiency, nitrogen transport contribution rate, harvest index, nitrogen harvest index, grain production efficiency, dry matter production efficiency and nitrogen fertilizer productivity as the evaluation indexes of nitrogen utilization efficiency) of different types of japonica rice under each treatment were measured at the key stage, the changes of different types of japonica rice under different nitrogen treatment were analyzed in the bar chart, and the influence of nitrogen application on material accumulation and transport was delved; the index mean value and variation coefficient of japonica rice were compared, the differences in indicators caused by different nitrogen application amounts were eliminated, and the differences between different types of japonica rice were highlighted; by using the correlation coefficient, the relationship between yield types of japonica rice and nitrogen utilization efficiency were explored, and the influence of nitrogen application on the accumulation of dry matter, nitrogen utilization and yield of japonica rice in heading and maturity period were analyzed.【Result】 (1) Applying additional nitrogen fertilizer within the range of 180-315 kg·hm^-2 could significantly increased the yield of each type of japonica rice (9.68%-29.19%), dry matter and nitrogen accumulation at heading stage (3.26%-28.57% and 8.57%-47.91%), and dry matter and nitrogen accumulation at maturity stage (1.01%-24.84% and 3.83%-57.98%) during the two-year period. Meanwhile, it was also beneficial to improve nitrogen transport capacity of leaves and stem at maturity stage. (2) Under the same nitrogen application conditions, the accumulation of dry matter, the accumulation of nitrogen, 1000-grain weight and setting percentage in Yangchan35003 were higher than that in Yangchan35002 and Yangchan35004 (29.08%-44.12%, 9.32%-29.21%, 11.40%-15.42%, 17.67%-40.70% and 25.93%-44.13%, 18.25%-26.17%, 6.16%-8.30%,-1.50%-13.96%, respectively) during the two-year period, the final yield exceeded the two types of japonica rice (24.26%-32.33% and 21.14%-30.05% higher than the yield Yangchan35002 and 35004, respectively) during the two-year period.(3) The high nitrogen transport capacity was not a unique feature of the source library interaction type strain. In this experiment, under the same nitrogen level condition, the nitrogen transport efficiency of Yangchan35004 was similar to the source library interaction type strain in the experiment, but the nitrogen intake was lower than Yangchan35003 (15.43%-20.74%), and the yield was lower than Yangchan35003 (17.45%-23.11%) during the two-year period, so it was a low yield and high nitrogen efficiency rice strain.【Conclusion】 Under the condition of applying 270 kg·hm^-2 of nitrogen fertilizer, Yangchan35002 could significantly optimize the synergy utilization efficiency of nutrients and temperature-light resources, enhance the nitrogen absorption and transportation capacity of plants, and improve the yield performance of the population. It was determined as the optimal combination in this experiment.

The Possible Effects of Global Warming on Cropping Systems in China XV. Adjustment of China’s Oil Crop Patterns to Adapt to Future Climate Change

GUO ShiBo, ZHANG ZhenTao, GUO ErJing, ZHAO Jin, LIU ZhiJuan, ZHAO Chuang, YANG XiaoGuang

Scientia Agricultura Sinica. 2025, 58(11): 2118-2144. doi:10.3864/j.issn.0578-1752.2025.11.005

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【Objective】 Oil crops are important sources of edible vegetable oil and feed protein. Soybean, canola, and peanut are the three major oil crops of China. This study aimed to clarify the climate suitability, and high-stable yield of oil crops under future climate change, and to propose adjustment of crop patterns framework, provided a theoretical basis for improving the total oil production and ensuring the safety of grain and oil in China under the background of climate change. 【Method】 Based on the yield, climate factors and agricultural technological factors of three oil crops from 1981 to 2019, a random forest model was constructed to predict yield under SSP1-2.6 and SSP5-8.5 scenarios from 2021 to 2060. Based on the crops’ climate suitability and high-stable yield, a comprehensive suitable area was divided. Combined with the impact of climate change, a framework of crops’ patterns adjustment to adapt to future climate change was proposed. Finally, the crops production, environment benefits and economic benefits before and after adjustment were clarified. 【Result】 (1) From 1981 to 2019, the proportion of soybean, canola, and peanut planting areas in the region with suitable climate and high-stable yield was 11.6%, 38.3%, and 46.0%, respectively. Future, the proportion of soybean planting area in this region will decrease, the proportion of canola will increase, and the proportion of peanuts will not change significantly. (2) After future adjustment, the planting area of soybean, canola and peanut will increase by 1.8×10⁶-2.6×10⁶ hm², 3.2×10⁶-3.9×10⁶ hm² and 0.8×10⁶-1.8×10⁶ hm², respectively. (3) The production of soybean, canola and peanut will increase by 140%, 150% and 150%, respectively, while the self-sufficiency rate of oil crop will increase by 7.9%-13.0%. The negative impact of climate change on production will decrease by 1.0×10⁶-1.8 ×10⁶ t. The total amount of nitrogen fertilizer application and greenhouse gas emissions will decrease by 1.1×10⁶-1.5×10⁶ t and 9.7×10⁶-12.7×10⁶ t CO₂-eq, respectively. The total economic benefits will increase by 0.3×10⁵-0.4×10⁵ million yuan. 【Conclusion】 Under future climate change, the framework of adjustment of crop patterns for oil crops based on the climate suitability, high-stable yield and climate change impacts could expand the planting area of oil crops, increase crops production, reduce the negative impact of climate change, reduce total nitrogen fertilizer use and greenhouse gas emissions, and increase economic benefits.

Calcium Regulates Reactive Oxygen Species and Endophytic Bacteria to Enhance Rice Resistance to Sheath Blight

ZHAO ShouShuai, DU MengXiang, GUO SiYu, ZHANG Shuo, ZHAO HongWei, ZHAO ChangJiang

Scientia Agricultura Sinica. 2025, 58(11): 2145-2161. doi:10.3864/j.issn.0578-1752.2025.11.006

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【Background】 Rice sheath blight, caused by Rhizoctonia solani, is a prevalent disease in rice-growing regions worldwide, posing significant challenges to the green ecological cultivation of rice due to the severe lack of resistant varieties.【Objective】 To elucidate the regulatory effect of exogenous calcium treatment on rice disease resistance and its regulatory mechanism.【Method】 Four-leaf stage indica and japonica rice seedlings were sprayed with a 5 mmol·L^-1 calcium regulator at 150 mL and sprayed twice at a 24 h interval. The toothpick insertion method was used to inoculate R. solani in the second- and third-leaf sheaths of rice 48 h after the first spray. Leaves from the same part were taken for determination of reactive oxygen species (ROS)-related indicators, photosynthetic pigment content, and endophytic bacterial analysis.【Result】 Calcium addition treatment (CaCl₂ and Ca(NO₃)₂) enhanced the resistance of the tested rice against R. solani while the chelating agent EGTA treatment weakened their resistance. Compared with the blank control, the calcium content of plants was increased with calcium addition treatment and decreased with calcium reduction treatment; pathogen inoculation resulted in lower calcium content in the plants compared to the corresponding control treatments. All calcium addition treatments caused an increase in the content of and H₂O₂ in rice seedlings, the change of ROS content caused by the calcium reduction treatment was more obvious than that of calcium addition treatment. Calcium addition treatment caused changes in rice ROS content consistent with the trend of lesion area changes, with a positive correlation between the two. Calcium addition treatment also maintained the enzyme activities of SOD, POD, CAT, APX, GPX and content of GSH at relatively high levels. The increase in CAT activity was particularly significant. In most cases, calcium reduction treatment significantly reduced the activity of related enzymes. Calcium addition treatment could reconstruct rice’s ROS homeostasis and enhance disease resistance and immune responses, including ROS production, antioxidant systems, and membrane damage indicators. Compared with the blank control, the positive correlation between the lesion area and H₂O₂ content in rice treated with calcium addition was enhanced, the negative correlation with CAT was enhanced, the negative correlation with ASA was enhanced, the negative correlation with APX was weakened, the correlation with GSH turned from the negative to positive, the positive correlation with MDA was weakened, and the correlation with conductivity turned from negative to positive. Calcium addition treatment reduced the microbial richness of endophytic bacterial community in inoculated rice leaves and limitedly increased the diversity of endophytic bacterial community. Although calcium addition treatment had a limited impact on the endophytic bacterial co-occurrence network in rice, the inoculation of R. solani significantly affected the endophytic bacterial network in rice. Furthermore, the network robustness after calcium addition treatment was significantly higher than that of the control group and the calcium reduction treatment group, both before and after inoculation; the network vulnerability after inoculation was significantly lower than that of the control group and the calcium reduction treatment group.【Conclusion】 Calcium addition treatment can significantly reduce the relative lesion area of tested rice, enhance the activities of SOD, POD, CAT and content of GSH, decrease the accumulation of ROS, reduce membrane damage, maintain the homeostasis of ROS and enhance the disease resistance of rice; simultaneously, calcium addition treatment reduces the richness of endophytic bacterial community, increases its diversity, enhances the proportion of beneficial bacterial genera, restructures the endophytic bacterial community with enhanced stability.

Streptomyces TOR3209 and Its Volatile Organic Compounds Enhance Tobacco Resistance to Fusarium equiseti

ZHAO LinLin, HE YuXi, PENG JieLi, WANG Xu, MA Jia, ZHANG XiuMin, HU Dong

Scientia Agricultura Sinica. 2025, 58(11): 2162-2175. doi:10.3864/j.issn.0578-1752.2025.11.007

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【Objective】The objective of this study is to explore the effect of Streptomyces TOR3209 and its volatile organic compounds (VOCs) on tobacco disease resistance, clarify the direct and indirect mechanism of the strain and its VOCs to improve tobacco disease resistance, and to provide a theoretical basis for the biocontrol application of TOR3209 and its VOCs.【Method】Streptomyces TOR3209 and Fusarium equiseti were selected as research materials, and the inhibition ability of TOR3209 and its VOCs against F. equiseti was evaluated by using plate confrontation method and growth rate method. Tobacco was inoculated with different concentrations of TOR3209 suspension (1.0×10¹, 1.0×10³, 1.0×10⁵, 1.0×10⁷ CFU/mL) and co-cultured with VOCs produced by TOR3209. The effects of the strain and its VOCs on tobacco resistance to F. equiseti were tested. The transcriptome sequencing of tobacco was performed to analyze the differential gene expression. Solid phase microextraction (SPME) method was used to identify the VOCs produced by TOR3209, and a compound with strong specificity (heptadecane) was selected to verify the resistance of tobacco to F. equisetaria. Different concentrations of heptadecane (1 mol·kg^-1, 1 mmol·kg^-1, 1 μmol·kg^-1, 0.001 μmol·kg^-1) were added as treatment groups to verify the effect of heptadecane on tobacco.【Result】Streptomyces TOR3209 and its VOCs had antagonistic effects on F. equiseti, with inhibition rates of 56.9% and 60.0%, respectively. Compared with the control, the severity of tobacco disease was significantly reduced under different concentrations of TOR3209 suspension (P<0.01), and the treatment with the concentration of 1.0×10¹ CFU/mL had the best disease resistance effect. Both the retained strain treatment group and the removed strain treatment group could improve the disease resistance of tobacco, the control effect was 85.7% and 72.5%, respectively. The main way was to induce tobacco systemic resistance during the action of TOR3209 VOCs. Transcriptome analysis of tobacco showed that the VOCs of TOR3209 induced up-regulation of several genes in tobacco, and many of the genes were related to the improvement of plant disease resistance. Among the VOCs produced by TOR3209, several compounds were identified, among which heptadecane could improve the resistance of tobacco to F. equiseti infection after co-culture with tobacco, and the treatment group with a mass concentration of 1 mmol·kg^-1 had a significant effect.【Conclusion】Streptomyces TOR3209 and its VOCs mainly improve the resistance of tobacco by inducing systemic resistance, and the VOCs of TOR3209 can regulate the gene expression of tobacco.

Effects of Intercropping Soybean on Cassava Growth and Soil Characteristics

CHEN HuiXian, HE Wen, RUAN LiXia, HUANG XiaoJuan, LAN Xiu, CAI ZhaoQin, LI HengRui, HUANG ZhenLing, WEI WanLing, LIANG ZhenHua, LI TianYuan, CAO Sheng, LI XiDi, WEI JunCan

Scientia Agricultura Sinica. 2025, 58(11): 2176-2189. doi:10.3864/j.issn.0578-1752.2025.11.008

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【Objective】 This study aimed to explore the impacts of cassava/soybean intercropping patterns on the growth of cassava and its continuous cropping soil, to analyze the potential of cassava/soybean intercropping patterns to alleviate the obstacles of cassava continuous cropping, so as to provide theoretical references for alleviating the obstacles of cassava continuous cropping. 【Method】 On the continuous cropping soil of cassava, the differences in physical and chemical properties of rhizosphere soil, microbial species diversity, community structure between cassava monoculture and cassava/soybean intercropping patterns were compared, and the impacts of cassava/soybean intercropping patterns on the continuous cropping soil of cassava were explored; the differences in plant height, stem thickness, yield, and photosynthetic characteristics between the two planting patterns were compared too, and the correlation between soil physical and chemical properties, microbial species diversity, community structure, and plant height, stem thickness, yield, and photosynthetic characteristics of cassava were analyzed to clarify the impact and mechanism of cassava/soybean intercropping patterns on the growth of cassava. 【Result】 (1) In a 3-year trial, compared with the continuous monoculture of cassava, soil pH, porosity, organic matter content, alkali-hydrolyzable nitrogen content, bacterial number, fungal number, plant height, yield, photosynthetic rate, and transpiration rate under the cassava/soybean intercropping pattern increased year by year, while soil bulk density decreased year by year, and the differences in these indicators reached significant levels in the second or third year of the trial. (2) Cassava/soybean intercropping had little effect on the species diversity of bacteria and fungi in the continuous cropping soil of cassava, but had a significant impact on the composition and relative abundance of dominant bacterial communities in the continuous cropping soil of cassava, among which the impact on the abundance of the beneficial fungus Trichoderma was the most significant. (3) Soil pH showed a significantly positively correlated with the transpiration rate of cassava leaves; Soil organic matter content showed a significantly positively correlated with plant height, photosynthetic rate and transpiration rate of cassava leaves; Soil porosity and alkali-hydrolyzable nitrogen content both showed a significantly positively correlated with the photosynthetic rate and transpiration rate of cassava leaves; The relative abundance of Trichoderma showed a significantly positively correlated with the stem diameter, plant height, yield, photosynthetic rate and transpiration rate of cassava leaves. 【Conclusion】 The cassava/soybean intercropping pattern could improve the pH, porosity, organic matter content, and alkali-hydrolyzable nitrogen content of the continuous cropping soil of cassava, regulate the soil microbial community structure, recruit a large number of potential beneficial fungi Trichoderma, and alleviate the adverse factors, such as soil acidification, hardening, and nutrient decline in the continuous cropping soil of cassava, thereby promoting the growth of cassava and having a relieving effect on the obstacles of cassava continuous cropping.

A Review of Soil Carbon Sequestration and Greenhouse Gas Emissions Quantification in Cropland

SUN JianFei, CHENG Kun

Scientia Agricultura Sinica. 2025, 58(11): 2190-2205. doi:10.3864/j.issn.0578-1752.2025.11.009

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As significant sources and sinks of greenhouse gases in terrestrial ecosystems, cropland can effectively mitigate climate change through scientific management practices. Developing methods for quantifying soil carbon sequestration and greenhouse gas emissions is crucial for accurately measuring the contribution of agriculture to carbon neutrality strategies. These methods are also essential for greenhouse gas inventory preparation, evaluating carbon sequestration and emission reduction effects, voluntary emission reduction trading, and carbon-related certification. This paper systematically reviewed the methods for quantifying soil carbon sequestration and greenhouse gas emissions in cropland, comparing the differences among various methods in terms of data requirements, acquisition costs, estimation accuracy, and the challenges faced. It focused on the applicability of these methods in different scenarios and their optimization pathways. The methods discussed for soil carbon sequestration and greenhouse gas emissions included the Two-Period Difference Method (for soil carbon sequestration only), Data Integration Method (for soil carbon sequestration only), Parameter Method/Emission Factor Method, Empirical Models, and Process Models. The Two-Period Difference Method and Data Integration Method estimate changed in soil organic carbon using empirical data, but their accuracy was directly affected by the matching of datasets and the amount of data. The Parameter Method/Emission Factor Method estimated soil carbon sequestration and greenhouse gas emissions with minimal data requirements, but its accuracy depended on the localization and refinement of parameters/emission factors. Due to these limitations, the Parameter Method/Emission Factor Method was more suitable for low-resolution estimates at regional scales and could not accurately capture high-resolution spatial variations. Empirical Models and Process Models considered the effects of meteorological, soil, and management factors on soil carbon sequestration and greenhouse gas emissions, making them suitable for high-resolution spatial simulations and field-scale measurements. The performance of empirical models depended on the quantity, quality, and accuracy of variable selection in the modeling database. In contrast, Process-based Models could capture the spatiotemporal dynamics of soil organic carbon and greenhouse gases under complex conditions, but required local parameter optimization for accurate performance. Given the challenges of different methods, this paper highlighted the importance of balancing data requirements, costs, and estimation accuracy in specific-scenarios. It noteed that model simulation methods would become the main trend in future agricultural carbon quantification. Addressing how to balance data requirements, acquisition costs, and estimation accuracy for different scenarios was a significant challenge. Future research should focus on building comprehensive field monitoring networks, promoting standardized database construction and sharing, deepening the localization and refinement of emission factors, and exploring innovative applications of machine learning in multi-algorithm integration and process model parameter adjustment.

Research on the Spatio-Temporal Evolution and Differentiated Improvement Path of Low-Carbon Utilization Efficiency of Cultivated Land Under the Background of New and Old Kinetic Energy Conversion——A Case Study of Guangdong Province

ZHU QingYing, HE GengYi, SUN Ping

Scientia Agricultura Sinica. 2025, 58(11): 2206-2224. doi:10.3864/j.issn.0578-1752.2025.11.010

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【Objective】 To scientifically reveal the spatio-temporal evolution characteristics of the low-carbon use efficiency of cultivated land under the background of new and old kinetic energy conversion, and deeply analyze the differentiated configuration paths for improving the low-carbon use efficiency of cultivated land, so as to provide decision-making basis for the efficient and sustainable use of cultivated land, the cultivation of new agricultural productive forces, and even the high-quality development of agriculture.【Method】 Based on defining the connotation of the low-carbon use efficiency of cultivated land under the background of new and old kinetic energy conversion and constructing a theoretical framework for its configuration path, using the panel data of 21 prefecture-level cities in Guangdong Province from 2010 to 2021, the Super-SBM model with undesired outputs was adopted to evaluate the low-carbon use efficiency of cultivated land under the background of new and old kinetic energy conversion and depict the spatio-temporal evolution characteristics, and the fuzzy-set qualitative comparative analysis (fsQCA) was used to explore the differentiated configuration paths for improving the low-carbon use efficiency of cultivated land. 【Result】 (1) From the perspective of temporal characteristics, the low-carbon use efficiency of cultivated land in Guangdong Province showed a slow upward trend with fluctuations from 2010 to 2021, with an average value of 0.947; the evolution characteristics of the Pearl River Delta and Northern Guangdong were similar to those at the provincial level, Eastern Guangdong had small fluctuations, while Western Guangdong showed a downward trend with fluctuations, and only the Pearl River Delta had an average efficiency value greater than 1; from the perspective of spatial distribution, the spatial differentiation characteristics of the low-carbon use efficiency of cultivated land in Guangdong Province were significant, showing a multi-core and contiguous distribution of high and low efficiency areas, especially the prominent phenomena of high efficiency in the Pearl River Delta and low efficiency in Northern Guangdong. (2) The paths for improving the low-carbon use efficiency of cultivated land in Guangdong Province could be summarized into three types of configuration paths: single-factor dominated by socio-economic or government support, two-factor dominated by technological empowerment-government support or socio-economic-government support, and multi-factor dominated by resource endowment-socio-economic-government support. (3) The level of socio-economic development and the degree of government support were the most universal factors affecting the low-carbon use efficiency of cultivated land, while the influence of cultivated land resource endowment conditions and the level of agricultural technology investment was relatively weak. These factors could undergo equivalent substitution under specific conditions, and cultivated land resource endowment could be replaced by other three types of factors alone or in combination, forming the "same goal through different paths" for improving the low-carbon use efficiency of cultivated land.【Conclusion】 The low-carbon use of cultivated land is a configuration problem affected by the interaction of factors in the "resource-economy-technology-policy" complex system. In practice, attention should be paid to the overall planning of the design of improvement paths and policy implementation according to local conditions. At present, the quantity of cultivated land is under serious threat, and continuous efforts in socio-economic development, financial support for agriculture, and the level of agricultural production technology should become the long-term direction for promoting the low-carbon and efficient use of cultivated land.

The Influence of Nitrogen Application Under Aerated Drip Irrigation on the Hydraulic Characteristics and Photosynthetic Capacity of Tomato

LI XiaoYan, DU YaDan, HU XiaoTao, LU YiNing, GU XiaoBo

Scientia Agricultura Sinica. 2025, 58(11): 2225-2238. doi:10.3864/j.issn.0578-1752.2025.11.011

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【Objective】 The objective of this study is to investigate the effect of water and nitrogen coupling on tomato yield and water use efficiency (WUE) under aerated drip irrigation, and to provide a scientific basis for water and nitrogen management for tomato cultivation in Northwest China.【Method】 Two greenhouse experiments were carried out in 2023 and 2024, and three irrigation levels W1 (50% ET_C), W2 (75% ET_C) and W3 (100% ET_C) were set under aerated drip irrigation with micro and nano bubble generating devices (ET_C is the actual crop evaptranspiration). Three nitrogen application levels were N1 (0), N2 (150 kg·hm^-2) and N3 (250 kg·hm^-2), and W3 (100% ET_C) N3 (250 kg·hm^-2) under traditional drip irrigation was used as control treatment (CK). The effects on soil moisture content, hydraulic characteristics, photosynthetic characteristics and yield of tomato were studied.【Result】 Aerated drip irrigation promoted the uptake and utilization of soil water in tomato, improved plant hydraulic characteristics and leaf photosynthetic characteristics, and increased yield and WUE by 1.21% to 1.84% and 1.84% to 2.25%, respectively. Optimized water and nitrogen management under aerated drip irrigation could further promote tomato growth and yield. Soil moisture content increased with increasing irrigation but decreased with increasing nitrogen application, reaching a maximum in the W3N1 treatment, which was 0.31% to 19.37% higher than other treatments; tomato stem water potential, Pn, Gs, and SPAD all increased with increasing irrigation and nitrogen application, reaching maximum values in the W3N3 and W2N3 treatments, respectively, and increasing by 0.95% to 104.86% compared with other treatments. PLC decreased with the increase of irrigation water and N application and decreased to the minimum value in W3N3 treatment, which was 11.27% to 69.24% lower than other treatments. Nitrogen application under deficit irrigation alleviated water stress in tomato plants, and soil moisture content, stem water potential, PLC, Pn, Gs and SPAD were significantly improved by 17.37% to 21.16% under deficit irrigation W2 compared with W1. Yields of both spring-summer and autumn-winter tomato reached the maximum in the W2N3 treatment, WUE reached the maximum in the W2N3 and W1N3 treatments, respectively, and autumn-winter tomato WUE was increased by 1.02% in the W1N3 treatment compared with W2N3, but yield was significantly decreased by 15.25%. Path analysis revealed that the direct effect coefficient of soil moisture content on yield under aerated drip irrigation was 0.439, while the indirect effect coefficients of soil moisture content on yield through stem water potential, PLC, Pn and Gs were 0.952, 0.852, 0.582 and 0.494, respectively.【Conclusion】 Nitrogen application under aerated drip irrigation can improve the hydraulic characteristics of tomato under different irrigation conditions, enhance the photosynthetic capacity of leaves, and then improve the tomato yield. Considering the yield and WUE, the appropriate irrigation volume and nitrogen application rate for tomato in Northwest China are 75% ET_C and 250 kg·hm^-2, respectively.

Heat Resistance Analysis of Meiosis Related Gene BrASY2 in Chinese Flowering Cabbage

PANG QiangQiang, SUN XiaoDong, CHEN YiSong, ZHOU Man, WANG YaQiang, SHI GuoBin

Scientia Agricultura Sinica. 2025, 58(11): 2239-2252. doi:10.3864/j.issn.0578-1752.2025.11.012

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【Objective】 Chinese flowering cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) was a heat-resistant and enjoy cold vegetable, high temperature is one of the main problems faced in the production of summer and autumn vegetable production. In the early stage, we discovered a gene fragment that may be closely related to the response to heat stress in the transcriptome database of Chinese flowering cabbage, named BrASY2. By studying its physicochemical properties, protein structure, systematic evolution, and expression characteristics, and exploring its function in heat tolerance regulation, this study provides a reference for molecular breeding of heat-resistant. 【Method】 The BrASY2 gene sequence was obtained by whole gene synthesis, the physicochemical properties, signal peptides, protein structure, and cis acting elements of BrASY2 were analyzed using ExPASy ProtParam, ProtScale, SignalP-5.0, SOPMA, Swiss Model, and PlantCARE, respectively. Construct phylogenetic tree using MEGA 6.0, and the expression characteristics under heat stress were analyzed using real-time fluorescence quantitative PCR (qRT-PCR) method. Construct yeast heterologous overexpression vector pYES2-NTB-BrASY2 and gene silencing vector pK7GWIWG2(I)-BrASY2, respectively, to obtain transgenic yeast and silenced expression cabbage plants, and perform heat tolerance functional analysis.Cytological observation of meiotic chromosome behavior in BrASY2 silenced plant cells using anther pressing method.【Result】BrASY2 with an ORF of 852 bp was obtained, encoding 283 amino acids, the relative molecular weight was 69.16 kDa with a theoretical isoelectric point being 5.09. The results of gene structure analysis indicate that it contains abundant alpha helices and random coi. Signal peptide prediction revealed that BrASY2 was a hydrophilic protein without signal peptides. Evolutionary analysis revealed that BrASY2 had the closest genetic relationship with Chinese cabbage and Brassica napus. Transcriptome data showed that the BrASY2 gene expression levels were low in both the heat sensitive material CX7-3 and the heat-resistant material CX1-7 before high temperature stress (0 h), and the expression level was rapidly increased in CX1-7 after 6 h of heat stress, however, there was no significant change in CX7-3. qRT-PCR results showed that the expression level of BrASY2 gene in the leaves of heat-resistant inbred line CX1-7 showed an upregulation trend with the prolongation of heat stress treatment time, the highest expression level was occurred at 24 h. However, in the thermosensitive inbred line CX7-3, the relative expression level remained in a low-level expression state with no significant change. Analysis of heterologous overexpression of yeast revealed that overexpression of yeast pYES2-NTB-BrASY2 was tolerant to high temperatures and can help the yeast overcome heat stress.The silencing results showed that the expression of BrHsfA2, BrHsp90, and BrMn-SOD in the silenced plants were inhibited after heat stress compared with the control plants, and the plant leaves color became lighter, chlorophyll content decreased, relative conductivity and H₂O₂ content increased, and SOD activity decreased. The cytological observation results of meiosis showed that, compared with the control plants, the chromosome behavior of BrASY2 silenced plants at all stages was normal, and there was no significant difference in the proportion of balanced splits cells and quaternary inmeiosis anaphase.【Conclusion】 This study successfully obtained the BrASY2 gene in Chinese flowering cabbage, and it plays a positive regulatory role in response to heat stress.

Construction and Evaluation of a PK15 Cell Line Stably Expressing Porcine CD163 Protein

ZHAO QingYang, ZHANG XiaoXiao, GUO ChunHe

Scientia Agricultura Sinica. 2025, 58(11): 2253-2264. doi:10.3864/j.issn.0578-1752.2025.11.013

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【Background】 CD163 is an important transmembrane protein that plays a key role in host immune regulation, inflammatory response, and the infection process of various pathogens. Studies have shown that CD163, as a host receptor, not only influences cell signaling pathways but also regulates host susceptibility to foreign pathogens. Since the receptor-pathogen interaction mechanisms involving CD163 are not yet fully elucidated, establishing a cell model stably expressing CD163 is of great significance for related research. Porcine reproductive and respiratory syndrome virus (PRRSV) is an important model for studying the CD163-mediated viral entry mechanism. However, the primary target cells of PRRSV—porcine alveolar macrophages (PAMs)—cannot proliferate continuously in vitro, which limits their application in pathogenetic research. Therefore, the monkey-derived cell line MARC-145 is commonly used for PRRSV in vitro culture, but its non-porcine origin may affect the biological relevance of experimental results. 【Objective】 This study aimed to construct a porcine cell line stably expressing porcine CD163 protein and to evaluate its susceptibility to PRRSV infection.【Method】 This study was conducted at the Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology from June 2022 to November 2023. The porcine CD163 gene was cloned, and two strategies were employed to express this gene in the porcine kidney cell line (PK15). Firstly, recombinant plasmid transient transfection was attempted, but due to the low transient transfection efficiency of PK15 cells, a stably expressing cell line could not be obtained. To optimize the expression strategy, lentiviral vector-mediated gene transduction was further applied, followed by screening for stable cell lines. Lentiviral packaging was performed using 293T cells, and the resulting virus was transduced into PK15 cells. Positive clones were screened using puromycin to ensure stable integration and long-term expression of the exogenous gene. CD163 mRNA and protein expression levels were detected by RT-qPCR and Western blot, and passage experiments were further conducted to evaluate the stability of CD163 expression, ensuring the long-term application potential of the cell line. 【Result】 A recombinant lentiviral vector carrying the CD163 gene was successfully constructed, and a stably expressing PK15 cell line, named PK15-CD163, was obtained through lentiviral transduction. RT-qPCR and Western blot results showed that the expression levels of CD163 mRNA and protein in PK15-CD163 cells were significantly higher than those in normal PK15 cells and remained stable after multiple passages. However, PRRSV infection experiments indicated that PRRSV N protein expression could not be detected by either RT-qPCR or Western blot, suggesting that PRRSV replication might be restricted in this cell line.【Conclusion】 This study successfully established a PK15-CD163 cell line, providing an important experimental tool for further investigation of CD163’s biological functions in host cells. Although PRRSV infection in PK15-CD163 cells did not yield significant results, this cell line could still be used to explore CD163-mediated immune regulation, receptor function, and other pathogen infection mechanisms. Additionally, it provided a potential platform for antiviral drug screening.

Effects of β-mercaptoethanol on Rapamycin Induced Autophagy, Apoptosis and Steroid Hormone Synthesis in Buffalo Granulosa Cells

XU YuanYuan, HUANG LiQing, LU XingRong, FENG Chao, SHANG JiangHua

Scientia Agricultura Sinica. 2025, 58(11): 2265-2274. doi:10.3864/j.issn.0578-1752.2025.11.014

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【Objective】 The development of mammalian follicles involves a series of complex processes, which is regulated by various factors, among which granulosa cells (GCs) play an important role. The proliferation and differentiation of granulosa cells directly affect the development of follicles. Autophagy is a crucial biological process in the development of granulosa cells, and β-Mercaptoethanol (2-ME) is often used as an antioxidant to optimize the in vitro maturation culture system of domestic animal oocytes, but there is currently a lack of systematic research on its effects on the growth and development of buffalo follicular granulosa cells. In view of this, the aim of this study was to investigate the effects of 2-ME on rapamycin induced autophagy, apoptosis, and steroid hormone secretion in buffalo follicular granulosa cells. 【Method】 Buffalo ovaries were collected, and GCs were isolated and cultured in vitro. After the cells were passaged, the different concentrations of 2-ME and Rapamycin were added exogenously to measure the cell viability by CCK8 method. And then, the optimal concentrations of 2-ME and Rapamycin were selected to treat GCs. Real-time fluorescence quantitative PCR was used to detect the effects of 2-ME on the gene expression of Rapamycin induced autophagy, apoptosis and steroid hormone secretion in buffalo granulosa cells. In addition, contents of estradiol (E2) and progesterone (P4) were detected by ELISA. And the expression levels of autophagy and apoptosis related proteins in granulosa cells under different treatments were detected by Western blotting. 【Result】 The optimal treatment concentrations for 2-ME and Rapamycin were 50 and 25 µmol·L^-1, respectively. Overactivation of autophagy could extremely significantly upregulate the expression of autophagy related genes ATG5, LC3, and Beclin1 (P<0.01), while the expression of all three genes was down regulated after the addition of 2-ME and Rapamycin simultaneously. Overactivation of autophagy could extremely significantly upregulate the expression of Bax and Caspase3 (P<0.01) and significantly upregulate the expression of Bcl2 (P<0.05). However, the addition of 2-ME and Rapamycin at the same time restored the expression of Bax and Caspase3 genes. Overactivation of autophagy could reduce the expression of CYP19A1 and CYP11A1 genes, while adding 2-ME and Rapamycin simultaneously increased the expression levels of CYP19A1 and CYP11A1 genes. Overactivation of autophagy could significantly reduce the secretion levels of E2 and P4 in granulosa cells (P<0.05), while adding 2-ME after activating autophagy can increase the secretion levels of E2 and P4. Autophagy could upregulate the expression levels of LC3, Beclin1 and Caspase3 proteins. However, the expression levels of all three proteins decreased to varying degrees after the addition of 2-ME and Rapamycin simultaneously. 【Conclusion】 Autophagy could promote the apoptosis of granulosa cells in buffalo follicles and inhibit their ability to secrete E2 and P4. However, 2-ME could alleviate cell apoptosis caused by autophagy in granulosa cells and restore the ability of granulosa cells to secrete E2 and P4 reduced by autophagy. In conclusion, 2-ME played an important role in maintaining autophagy homeostasis of buffalo granulosa cells.

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