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  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    LÜShuWei, TANGXuan, LIChen
    Scientia Agricultura Sinica. 2025, 58(1): 1-9. https://doi.org/10.3864/j.issn.0578-1752.2025.01.001

    Seed shattering is a major factor limiting rice production, and breeding new rice varieties with moderate seed shattering is a key challenge faced by rice breeders worldwide. Rice is the most important cereal crop in China, plays a vital role for national food security. Seed shattering is one of the most important traits during rice domestication, and the abscission zone is the important region to control seed shattering. Compared with wild rice, cultivar has eliminated the seed shattering with partially developed abscission layer. Seed shattering not only has a direct impact on the yield, but also affects the way of its mechanical harvest. In order to breed rice varieties with moderate seed shattering in agricultural production, it is necessary to mine and utilize important seed shattering genes and introduce them into excellent rice varieties for genetic improvement, so as to breed new rice varieties suitable for mechanical harvesting with moderate seed shattering. Several seed shattering genes had been identified by map-based cloning, such as SH4/SHA1, qSH1, OsSh1/ObSH3, and their functional mechanisms had been analyzed. At the same time, new rice materials with moderate seed shattering have been successfully developed through CRISPR/Cas9 gene editing technology, gamma ray mutagenesis technology and gene introduction methods. Seed shattering has an important effect on grain yield and rice harvesting methods, in this paper, we reviewed the methods, physiologic basis, the identification of seed shattering genes and genetic mechanism of seed shattering in rice. At the same time, it is proposed that by using the important genes in excellent rice germplasm resources, could provide reference for exploring the mechanism of rice seed shattering, and breed new rice varieties suitable for mechanical harvesting with moderate seed shattering.

  • ANIMAL SCIENCE·VETERINARY SCIENCE
    SUNYanYan, NIAiXin, YANGHanHan, YUANJingWei, CHENJiLan
    Scientia Agricultura Sinica. 2025, 58(5): 1017-1031. https://doi.org/10.3864/j.issn.0578-1752.2025.05.015

    Heterosis is a phenomenon where the offspring of genetically distinct populations exhibit superior vitality, reproductive capacity, and adaptability compared with the average of their parent populations, which is an important genetic resource. Heterosis plays a significant role in modern agriculture, contributing to increase yields and quality of livestock and crops, rapidly improve traits, accelerate the breeding of new varieties, and enhance genetic diversity, thereby efficiently boosting the production of animal husbandry and agriculture while reducing costs. Despite the discovery of heterosis is over a century ago, the elucidation of its genetic basis lags far behind its application in agricultural production. The study of the complex formation mechanism of heterosis is a classic and an active topic in the field of genetics and breeding, but the clear conclusions remain limited. In response to the characteristics of heterosis, scientists have successively proposed various hypotheses for its formation, such as the dominance hypothesis, overdominance hypothesis, and epistasis hypothesis, revealing that the genetic basis of heterosis was non-additive genetic effects. However, these hypotheses are based on the effects of single genes, which are overly idealized and simplistic. Explorations at different levels, such as DNA, RNA, and proteins, have successively discovered the coexistence of multiple genetic effects. Particularly in hybrid crops like rice and corn, the related researches have been continuously identified the loci of heterosis effects, enriched the understanding of the formation mechanism for heterosis in crops, and promoted the transformation of crop breeding technologies, such as precise molecular design breeding. Heterosis is also widely applied in the breeding of livestock and poultry. In developed countries with advanced animal husbandry, over 80% of commercial pork, chicken, and eggs are obtained from hybrid breeds. To efficiently apply heterosis in production for animal husbandry, it is necessary to predict heterosis in advance. New methods, such as the inter- and intra-group phenotypic variance ratio prediction, hybrid heritability prediction, and molecular marker prediction, have been developed to solve the long experimental cycle, environmental sensitivity, and high human and financial costs associated with traditional hybridization experiments for predicting heterosis. However, the accuracy of these prediction methods is limited. Heterosis involves in interaction of multiple levels, and because of the complex genetic background and long breeding cycle, it is still a big challenge for the study of the heterosis formation mechanism and accurate prediction methods. In recent years, the gradual application of sequencing technology has provided a new perspective for understanding the molecular regulatory network of heterosis in livestock and poultry. QTL mapping and genome-wide association study reveal the molecular mechanism of heterosis at the genomic level, and the identified molecular makers are applied in selection and breeding. Combined with multi-omics researches, such as transcriptomics and metabolomics, the key functional genes, variations, and metabolites affecting heterosis can be more precisely located, which facilitate hybrid improvement. This review elaborated the research progress in the formation mechanism and prediction methods for heterosis in the field of livestock and poultry. For looking forward to future, the researches will gradually clarify the complex mechanism of heterosis by integrating multi-omics sequencing data and bioinformatics analysis, in order to identify genes and molecular markers related to heterosis, and innovate new prediction methods, which will provide a more accurate direction for the utilization of heterosis.

  • TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY
    ZHANGSiJia, YANGJie, ZHAOShuai, LILiWei, WANGGuiYan
    Scientia Agricultura Sinica. 2025, 58(2): 238-251. https://doi.org/10.3864/j.issn.0578-1752.2025.02.003

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

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    XUYiHeng
    Scientia Agricultura Sinica. 2025, 58(5): 831-839. https://doi.org/10.3864/j.issn.0578-1752.2025.05.001

    Gene-edited crops, the product of the intersection between biotechnology and agricultural science, represent a crucial direction in the development of modern agriculture. With the rapid advancement of the CRISPR-Cas9 system, the scientific research and commercial development of crop trait improvement have gradually shifted towards a “technology-driven” path, which has not only overturned traditional crop cultivation methods but also fundamentally propelled humanity’s exploration of crop research. Nevertheless, the phenomenon of patenting fundamental research tools has sparked widespread controversy within academia and profoundly impacted the sharing and utilization of crop resources. Private entities patenting CRISPR-Cas9 technology restrict other researchers and farmers’ opportunities to explore and harness genetic resources. This practice not only hinders scientific progress but also violates the fundamental consensus that genetic resources should be shared by all humanity. The sharing and openness of crop resources are crucial for the sustainable development of global agriculture and ecological balance, serving as a necessary condition for safeguarding public interests. A key issue that the governance of biotechnology patents urgently needs to address is how to reasonably allocate benefits and risks among traditional communities, researchers, research investors, and the public. This is also essential for constructing a new scientific ethics framework and regulating emerging technologies. However, China’s policy responses in this area are still insufficient. To mitigate the negative effects stemming from the exclusivity of patents, it is imperative to reassess and reconstruct the framework of relevant systems. Firstly, we should adhere to the principle of moral utility, emphasizing the public nature of scientific research and its social responsibilities, while carefully considering the “harmful” nature of inventions to social morality. Secondly, implementing a mandatory disclosure system for biological genetic resources is a crucial step towards achieving transparency and fairness, with “applicants truthfully disclosing the actual origin of crop genes based on the principle of good faith” elevated to a mandatory norm. Lastly, the open licensing of fundamental patented technologies can draw inspiration from the experience of open-source software, encouraging more researchers to participate in the exploration of crop resources through the open sharing of research tools, thereby facilitating broader scientific collaboration and the transformation of research outcomes.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    WANGWei, WUChuanLei, HUXiaoYu, LIJiaJia, BAIPengYu, WANGGuoJi, MIAOLong, WANGXiaoBo
    Scientia Agricultura Sinica. 2025, 58(1): 10-29. https://doi.org/10.3864/j.issn.0578-1752.2025.01.002

    【Objective】Based on whole genome identification and analysis of soybean LOX gene family members, to understand the taxonomic evolutionary relationships of each member, to study the expression specificity of each gene member in different tissues and their response to abiotic stress, which provided a theoretical basis for further research on the molecular characteristics, evolutionary process, and function of the LOX gene family. 【Method】Based on the LOX protein sequences of rice and Arabidopsis species in Ensembl database, BLASTP alignment of homologous LOX protein sequences in soybean whole genome database was performed, and MEGA X software was used to construct a phylogenetic tree; Using website MEME for protein conserved motif analysis; Using online software GSDS 2.0 to analyze gene structure; Using TBtools for chromosome localization drawing; Analyze soybean LOX family replication genes using McscanX; Using the PlantCARE website to predict the promoter elements of soybean LOX gene family; Draw gene expression heatmaps of soybean under different tissues and abiotic stress using TBtools, and develop molecular markers for the excellent allele variant GmLOX15A1-G/A significantly correlated with 100-seed weight.【Result】A total of 43 LOX genes were identified in soybean, unevenly distributed on 13 chromosomes. Collinearity analysis indicates that the GmLOX gene has undergone extensive replication during the evolutionary process. Meanwhile, 39 different types of cis regulatory elements were detected in the LOX gene promoter, indicating that they may be involved in different pathways such as growth and development, light response, stress response, and hormone induction. Expression pattern analysis revealed that the LOX gene has different levels of expression in different tissues of soybean, indicating that members of this family have tissue and spatiotemporal expression specificity. Under drought stress conditions, the GmLOX gene was significantly differentially expressed in soybean roots and leaves (P<0.05). Among them, GmLOX3A3, GmLOX7A1, GmLOX20B1, GmLOX13A1, and GmLOX20A2 were significantly upregulated or downregulated in roots and leaves, suggesting that the GmLOX gene may play an important role in response to stress. At the same time, it was found that GmLOX15A1 is highly expressed in grain tissue and there is an excellent G/A allele variation in the seventh exon of the gene coding region. Molecular markers were developed for this variant site, and the correlation between different haplotypes of GmLOX15A1 and 100-seed weight was analyzed using 1 200 soybean germplasm resources from different ecological regions over a period of 2 years. The results showed that compared to the GmLOX15A1-A genotype, the average 100-seed weight of soybean germplasm carrying the GmLOX15A1-G allele gene increased by 2.33 g (P<0.001). 【Conclusion】A total of 43 members of the LOX family were identified in soybeans, which can be divided into 3 subfamilies. The promoter region of the GmLOX gene contains a large number of cis acting elements that respond to hormones and stress, playing different roles in drought stress response. Among them, GmLOX15A1 is highly expressed in grain tissue and there is an excellent G/A allele variation in the seventh exon of the coding region of this gene. Compared with the GmLOX15A1-A genotype, the average 100-seed weight of soybean germplasm carrying the GmLOX15A1-G allele gene is significantly increased by 2.33 g. This locus can be used as an excellent haplotype for genetic improvement of soybean grain size.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    DIAODengChao, LIYunLi, MENGXiangYu, JISongHan, SUNYuChen, MAXueHong, LIJie, FENGYongJia, LIChunLian, WUJianHui, ZENGQingDong, HANDeJun, $\boxed{\hbox{WANGChangFa}}$, ZHENGWeiJun
    Scientia Agricultura Sinica. 2025, 58(4): 617-634. https://doi.org/10.3864/j.issn.0578-1752.2025.04.001

    【Objective】The GRAS family constitutes a unique class of plant-specific transcription factors that play a pivotal role in plant development and stress response. To elucidate the function of GRAS family genes in wheat heat tolerance,which can provide genetic resources and theoretical foundation for wheat heat-resistant breeding.【Method】A potential heat stress-responsive transcription factor gene, TaGRAS34-5A, was identified through transcriptome analysis of TAM107 and Chinese spring wheat seedlings under high-temperature conditions. Subsequently, a bioinformatics analysis was performed on TaGRAS34-5A, and a phylogenetic tree was constructed to elucidate its molecular characteristics. The expression pattern of TaGRAS34-5A under various stresses, including high temperature, abscisic acid (ABA), ethylene (ETH), and salicylic acid (SA) treatments, were examined using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) method. The subcellular localization of the TaGRAS34-5A protein was determined using wheat protoplast transient expression technique. Furthermore, the heat tolerance function of TaGRAS34-5A was validated using the heterologous expression system of Saccharomyces cerevisiae and the BSMV:VIGS (Barley stripe mosaic virus: Virus-Induced Gene Silencing) silencing technique. potential interacting proteins of TaGRAS34-5A were screened using yeast two-hybrid technology, and the heat tolerance function was verified, providing preliminary insights into its heat tolerance mechanism.【Result】TaGRAS34-5A, equipped with a characteristic GRAS domain and belongs to the GRAS transcription factor family, is localized to both the cell nucleus and cytoplasm. Bioinformatics analysis indicates that the TaGRAS34-5A promoter contains a large number of hormone response elements and light response elements, and it is most closely related to TaSCL14, OsGRAS23, and AtSCL14 in terms of phylogenetic relationships, suggesting its potential function in responding to oxidative stress. Its expression is upregulated under high-temperature, ethylene (ETH), abscisic acid (ABA), and salicylic acid (SA) treatments, peaking at 4, 6, 0.5, and 12 hours post-treatment, respectively, with the most significant induction observed under heat stress and SA. Functional assays in yeast demonstrated that heterologous expression of TaGRAS34-5A enhances the heat tolerance of the yeast. The results of BSMV:VIGS transient silencing experiment showed that after the 42 ℃ high-temperature treatment, TaGRAS34-5A silenced plants exhibited decreased chlorophyll content, reduced POD enzyme activity, increased cellular peroxidation, and decreased heat tolerance compared to the control. Preliminary studies on the heat tolerance mechanism suggest that TaGRAS34-5A exhibits strong transcriptional self-activation activity.it may modulate wheat heat tolerance by interacting with proteins such as the bZIP family transcription factor HBP-1b and the E3 ubiquitin ligase hel2, thereby regulating cellular redox homeostasis and detoxification processes, positively influencing the heat tolerance of wheat.【Conclusion】TaGRAS34-5A is induced by heat, ABA, ETH, and SA, and its encoded protein is located in the nucleus and cytoplasm. It exhibits transcriptional activation activity. Heterologous overexpression of TaGRAS34-5A enhances the heat tolerance of Saccharomyces cerevisiae. Silencing TaGRAS34-5A in wheat plants increases cellular peroxidation, decreases chlorophyll content, and reduces heat tolerance. TaGRAS34-5A may regulate the heat tolerance of wheat by modulating cellular redox state and detoxification processes.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    LIYunLi, DIAODengChao, LIUYaRui, SUNYuChen, MENGXiangYu, WUChenFang, WANGYu, WUJianHui, LIChunLian, ZENGQingDong, HANDeJun, ZHENGWeiJun
    Scientia Agricultura Sinica. 2025, 58(9): 1663-1683. https://doi.org/10.3864/j.issn.0578-1752.2025.09.001

    【Objective】 Wheat is a cornerstone of global food security, with its production being pivotal in both China and the international community. With global climate change, the threat of high temperature has become increasingly prominent, posing a significant challenge to wheat cultivation. The strategic identification and selection of heat-tolerant germplasm, coupled with the exploration of genes associated with heat resistance, are crucial steps. These efforts are essential for broadening the genetic diversity of heat tolerance in wheat within China, providing prerequisites for breeding heat-tolerant wheat varieties and ultimately contributing to the safeguarding of our nation’s food security in the face of a warming climate. 【Method】 In this study, a natural population of 331 wheat accessions was utilized, and artificial climate chambers were employed to simulate high temperatures conditions. The heat tolerance of wheat seedlings was assessed by monitoring their survival rate under various durations of treatment, using heat resistance grade as the evaluative metric. Meanwhile, a genome-wide association study (GWAS) was conducted using the 55K SNP chip to identify genetic loci associated with heat tolerance. Expression data from multiple tissues, including roots, leaves under heat stress were analyzed, leading to the selection of genes related to heat tolerance. Subsequently, qPCR validation of candidate genes was performed using the extremely heat-tolerant accession Xinong 889 and the heat-sensitive accession Chinese Spring (CS) as materials. 【Result】 Under high-temperature stress, significant variations in survival rates were observed among different wheat accessions. The extremely heat-tolerant, moderately heat-tolerant, moderately heat-sensitive, and extremely heat-sensitive germplasm accounted for 110, 104, 110, and 7, respectively, representing 33.23%, 31.42%, 33.23%, and 2.12% of the total. Heat-tolerant germplasms, including Xinong 889, Zhengmai 7698, Zhongmai 895, Zhoumai 18, and Fengchan 3, were identified. Through GWAS, a total of 293 SNP loci significantly associated with the 12-hour survival rates (SR) and heat resistance grades (HRG) were detected, with the phenotypic variation explained ranging from 4.40% to 12.46%. Among these, 200 loci were related to the 12-hour survival rates, and 257 were related to the heat resistance grades, with 164 loci identified as the same heat-related loci. Based on significantly associated SNP markers, 313 heat-related genes were predicted. According to gene annotation information and expression data under heat stress, 23 heat tolerance candidates were selected, and after qPCR validation of differentially expressed candidate’s genes, 20 key heat tolerance candidate genes were identified. 【Conclusion】 At the seedling stage, 331 wheat germplasms were identified for heat tolerance. A rapid method was developed for determining the survival rate of wheat seedlings subjected to treatments of varying durations at 45 ℃ to assess their heat tolerance In total, 38 heat-tolerant germplasms and 293 loci significantly associated with seedling heat tolerance were screened. Also, TraesCS1A02G355900, TraesCS1A02G389500, TraesCS5A02G550700, TraesCS5D02G557100, TraesCS6D02G402500 and TraesCS7A02G232500 represented as candidate genes were filtered out.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    YUERunQing, LIWenLan, DINGZhaoHua, MENGZhaoDong
    Scientia Agricultura Sinica. 2025, 58(7): 1269-1283. https://doi.org/10.3864/j.issn.0578-1752.2025.07.002

    【Objective】To clarify the molecular characteristics and the effectiveness of target traits of transgenic maize LD05 with composite insect and herbicide resistance, and to provide data basis, technical support and product reserve for industrial application.【Method】Using biological information analysis, we designed and modified the proprietary insect-resistant fusion gene m2cryAb-vip3A, and selected BC4F3, BC4F4 and BC4F5 generations of the newly created transgenic hybrid insect-resistant and herbicide-tolerant maize LD05 to carry out experimental research. Specific PCR and Southern blot were used to analyze the stability of genomic integration. qRT-PCR and ELISA were used to analyze the expression stability. The resistance to target pests was evaluated by bioassay and field trials, and the herbicide tolerance was tested by field spraying of glufosinate. 【Result】A new insect-resistant fusion gene m2cryAb-vip3A with independent property right was discovered and designed, and a multivalent insect-resistant and herbicide resistant maize transformant LD05 was created. The exogenous T-DNA was integrated into the maize genome in the form of a single copy. The qRT-PCR results indicated that m2cryAb-vip3A and bar were both expressed in various tissues and organs across three generations, and the variation trend of expression quantities was largely consistent. Specifically, the expression level of m2cryAb-vip3A was the highest in the leaves at the seedling stage of the three consecutive generations, with an average expression quantity of 36.73, while the expression level was the lowest in the cob at the mature stage, with an average of merely 0.91. The expression pattern of bar was similar to that of m2cryAb-vip3A, with the highest expression level in the leaves at the seedling stage, averaging 7.35, and the expression level decreased after the jointing stage. The ELISA results demonstrated that M2CryAb-VIP3A could stably accumulate in different organs and at different periods in the three generations, and the protein accumulation amounts in different generations were similar. Among them, the accumulation amount was the highest in the leaves at the seedling stage of different generations, all exceeding 19.67 μg·g-1 fresh weight. The expression of the targeted protein at a relatively high level could be detected in different tissues of the PAT transgenic plants of three consecutive generations, and there was no significant difference in the expression quantity between different generations. Among them, the expression level was the highest in the leaves at the seedling stage of different generations, with an average content of 16.61 μg·g-1 fresh weight, while the accumulation amount was the lowest in the roots at the mature stage, with an average content of 0.30 μg·g-1 fresh weight. The bioassay result showed that the corrected mortality of Ostrinia furnacalis, Spodoptera fragiperda and Mythimna separata reached 100% after feeding on V5 maize leaf tissue of LD05 for 96 h, which was a high resistance level. The results of field trials showed that LD05 transformants had high resistance to Ostrinia furnacalis at V5 stage and silking stage, to Mythimna separata at V5 stage, and to Helicoverpa armigera at silking stage. The results of glufosinate tolerance test showed that transgenic maize LD05 could tolerate 4-fold glufosinate. Agronomic character investigation showed that there was no difference between transgenic maize LD05 and control maize Zheng 58.【Conclusion】A novel insect-resistant fusion gene m2cryAb-vip3A with independent property rights was developed, and a transgenic hybrid insect-resistant and herbicide-tolerant maize LD05 was created with clear molecular characteristics, genetic stability and outstanding functional traits.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    WANGHui, DINGBaoPeng, LIYuXian, RENQuanRu, ZHOUHai, ZHAOJunLiang, HUHaiFei
    Scientia Agricultura Sinica. 2025, 58(11): 2045-2061. https://doi.org/10.3864/j.issn.0578-1752.2025.11.001

    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.

  • SOIL & FERTILIZER·WATER-SAVING IRRIGATION·AGROECOLOGY & ENVIRONMENT
    ZHANGHaoXin, YUShengYue, LEIQiuLiang, DUXinZhong, ZHANGJizong, ANMiaoYing, FANBingQian, LUOJiaFa, LIUHongBin
    Scientia Agricultura Sinica. 2025, 58(8): 1564-1578. https://doi.org/10.3864/j.issn.0578-1752.2025.08.008

    【Objective】 This study explored the applicability of the RothC model for simulating soil organic carbon (SOC) dynamics in dryland and paddy fields in Northeast China and evaluated the impact of various calibration methods on simulation performance.【Method】 This study selected one typical dryland and one typical paddy field as long-term experimental sites. The dryland experiment was conducted at the Heilongjiang Agricultural Ecology Experimental Station of the Chinese Academy of Sciences (2004-2015), and the paddy field experiment utilized data from the 850 Farm (2010-2017). At each experimental site, two treatments were selected for model simulation validation and performance evaluation: one with fertilization only, without straw return (NPK), and the other with both fertilization and straw returning (NPKS). For the paddy field soil, in addition to the RothC model, two modified versions, including RothC_p and RothC_0.6, were also selected for suitability evaluation. Three different model calibration methods were employed: the equilibrium method, parameter optimization method, and transfer function method, to analyze the impact of these calibration methods on model simulation performance. Normalized root mean square error (nRMSE), mean difference (MD), and the index of agreement (d) were selected as model evaluation metrics. 【Result】At the Heilongjiang station, organic carbon input exhibited a significant fluctuating trend, with the average annual carbon input under NPK and NPKS treatments being 1.71 and 3.52 t·hm-⊃2;, respectively. In contrast, organic carbon input at the 850 Farm was relatively stable, with the average annual carbon input for NPK and NPKS treatments being 1.89 and 5.90 t·hm-⊃2;, respectively. The simulation validation results from the Heilongjiang station showed that, under different model calibration methods, the nRMSE was consistently below 5%, and the index of agreement (d) ranged from 0.60 to 0.74. This indicated that the model performance was excellent across all calibration methods, and RothC was able to accurately simulate the SOC stock changes for both NPK and NPKS treatments in the dryland. When using the M2 method, the nRMSE for NPK and NPKS was the smallest, at 3.46% and 3.09%, respectively. The simulation validation results for the 850 Farm showed that the MD for RothC and RothC_p ranged from -1.47 to -13.41, with nRMSE values between 2.90% and 26.48% and d-values all below 0.1. This indicated that both models significantly overestimated the increase in SOC stocks and were unable to accurately simulate the changes in SOC stocks in the paddy field. For the RothC_0.6 model under the NPK treatment, the MD ranged from -0.08 to 0.44, with nRMSE values between 0.24% and 0.85% and d-values ranging from 0.31 to 0.76. Under the NPKS treatment, the MD ranged from -5.71 to -6.22, with nRMSE values between 11.21% and 12.12% and d-values between 0.12 and 0.13. These results indicated that RothC_0.6 could accurately simulate the dynamic changes in SOC stocks under the NPK treatment but significantly overestimate the changes in SOC stocks under the NPKS treatment.【Conclusion】RothC and RothC_0.6 were suitable for studying the dynamic changes in SOC stocks under dryland and paddy field conditions without straw returning in the Northeast region, respectively, and could accurately simulate the trends in SOC stocks. The impact of different model calibration methods on simulation performance was not significant. However, the transfer function method was simpler to compute, saved model running time, and provided better simulation performance. Therefore, this study recommended prioritizing the use of the transfer function method for model calibration.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    WANGWeiMeng, WEIYunXiao, TANGYunNi, LIUMiaoMiao, CHENQuanJia, DENGXiaoJuan, ZHANGRui
    Scientia Agricultura Sinica. 2025, 58(8): 1479-1493. https://doi.org/10.3864/j.issn.0578-1752.2025.08.002

    【Background】 Cotton is one of the most important crops globally. The application of bioengineering technology has greatly improved the efficiency of molecular breeding. However, current cotton genetic transformation faces challenges such as genotype dependency, lengthy timelines, and limited transformation methods.【Objective】This study aims to establish an efficient Agrobacterium rhizogenes-mediated genetic transformation system for cotton to expand genetic breeding methodologies.【Method】Using the common cotton receptor varieties WC and R18 as primary materials and mRUBY as a reporter gene, the root inducing process mediated by A. rhizogenes was optimized through screening hormone combinations (types and concentrations), analyzing differences in explant types and genotype-specific rooting systems. A stable genetic transformation system was subsequently developed and applied to gene editing.【Result】The addition of naphthaleneacetic acid (NAA) and lovastatin to the root inducing medium (RIM) promoted more efficient root formation compared to NAA alone or combinations of NAA+indole-3-butyric acid (IBA) or NAA+Lovastatin+IBA. The optimal concentrations for inducing hairy roots were both 2 mg·L-1 for NAA and lovastatin. Cotyledons were the most effective explants for root induction: WC cotyledons, cotyledon nodes, and hypocotyls exhibited rooting efficiencies of 398%, 72%, and 39%, respectively. Cotyledons required the shortest induction time (7 d), 3 d shorter than cotyledon nodes and 8 d shorter than hypocotyls. Cotyledons were also the optimal explants for R18, their rooting capacity differed. Genotype comparisons revealed that 20 days post-infection (dpi), the rooting efficiencies per cotyledon were 398% (WC), 116% (R18), 199% (NDM8), 103% (XLZ61), 57% (Gb-1), and 0 (Gb-2). Upland cotton varieties (WC, R18, NDM8, and XLZ61) exhibited rooting efficiencies above 100%, while sea island cotton varieties (Gb-1, Gb-2) were below 100%. Notably, Gb-2 began to root at 35 dpi. Receptor varieties of upland cotton generally showed slightly higher rooting efficiency than production varieties. There was a certain difference between the positive rate of genetic transformation and the rooting rate. The positive rates of NDM8, XLZ61, Gb-1 and Gb-2 at 20 dpi were 59.8%, 16.0%, 38.5% and 0, respectively. Using positive roots as explants, non-embryogenic and embryogenic callus induction yielded transgenic mRUBY-expressing plants, establishing a complete genetic transformation system. The intensity of plant coloration correlated positively with mRUBY expression levels. Additionally, cotton plants with edited GhGI genes were successfully obtained.【Conclusion】The study optimized the A. rhizogenes-mediated root induction process in cotton and established a robust genetic transformation system. This system was successfully applied to gene editing, generating transgenic cotton plants expressing mRUBY and edited GhGI genes.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    DENGLiCheng, LICheng, HELei, ANHongQiang, WANGCaiLin, ZHANGYaDong, ZHAOChangJiang, LUKai
    Scientia Agricultura Sinica. 2025, 58(12): 2275-2290. https://doi.org/10.3864/j.issn.0578-1752.2025.12.001

    【Objective】Salt stress is one of the main environmental stresses that restrict rice production. Studying the physiological characteristics under salt stress and analysis the allelic variation and expression of salt-tolerance genes provide key gene resources and genetic materials for breeding salt-tolerance rice varieties. 【Method】This study first evaluated the salt-tolerance ability of the Nangeng series high-quality rice varieties/lines during the seedling stage, using survival rate as an indicator for screening salt-tolerance varieties, which physiological changes under salt stress were analyzed, including chlorophyll, Na+, K+, MDA, H2O2 and soluble sugar. The variation types and expression levels of salt-tolerance genes in rice varieties with resistance to high salt concentration were also analyzed to explaining their molecular mechanisms in response to salt stress. 【Result】Under the condition of treating with 140 mmol·L-1 NaCl for 6 days, the survival rates of NG9108, NG5718, and NGY1 were greater than 60%, with the highest survival rate among the tested varieties. Compared with Nipponbare, the seedlings of NG9108, NG5718, and NGY1 under salt stress had higher chlorophyll content and lower MDA content, indicating that salt stress caused less cell damage to the three varieties. The Na+/K+ values in the roots of NG9108, NG5718, and NGY1 were significantly higher than those in Nipponbare, while the Na+/K+ values in the aerial parts were significantly lower than those in Nipponbare, implying that the three varieties absorb or store more Na+ in roots, but transport less Na+ upwards, which is beneficial for maintaining cell ion balance and causing less ion toxicity and osmotic stress in aerial parts of the seedlings. The three salt-tolerance varieties have 94 SNPs or InDel sites, distributing in exons, introns, 5′UTR, and 3′UTR of the 23 salt-tolerance genes. 24 variation sites of 11 genes occur in the exons, including 7 genes with frameshift mutations or missense mutations which distributed in Os02g0813500 (OsGR2), Os05g0343400 (OsWRKY53), Os06g0685700 (OsRST1), Os07g0685700 (OsEIL2), Os10g0431000 (OsPQT3), Os11g044600 (OsRSS3), Os12g0150200 (P450). Salt stress significantly induces expression of OsSKC1, OsBAG4, OsGPX1, OsCCX2, OsGR3, OsDREB2a, OsRAB21, OsP5CS, OsbZIP23, OsAPX37 and OsLEA3, which help to enhance salt tolerance and reduce the adverse effects of salt damage on rice growth. 【Conclusion】NG9108, NG5718 and NGY1 showed strong salt tolerance phenotype during the seedling growth stage, which is closely related to the balance of sodium and potassium ions under salt stress, allelic variations of multiple salt tolerance genes, and gene expression levels. NG9108, NG5718 and NGY1 have pyramided multiple salt tolerant and high-quality genes, which can be used as backbone parents for genetic improvement and breeding.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    WENJin, NINGYanFang, QINXin, LIUYuan, ZHANGXiaoLing, ZHUYongHong, TIANShiMin, MAYanBin
    Scientia Agricultura Sinica. 2025, 58(12): 2291-2302. https://doi.org/10.3864/j.issn.0578-1752.2025.12.002

    【Objective】Cotton bollworm (Helicoverpa armigera) and field weeds are major constraints to high-yield cotton production. Existing varieties with single traits (insect resistance or herbicide tolerance) fail to meet the demands of efficient cultivation. Developing transgenic cotton varieties with combined insect resistance and glyphosate tolerance will provide high-efficiency germplasm resources for stress-resistant cotton breeding.【Method】The insect-resistant fusion gene cry1Ac-vip3Da and glyphosate-tolerant gene g10-epsps were introduced into cotton R15 through Agrobacterium-mediated method, regenerated transgenic plants were screened via PCR, positive lines underwent multi-generation self-pollination to achieve homozygosity, and stable lines with superior resistance were selected. The expression of target genes in different tissues of transgenic lines was analyzed using qRT-PCR and ELISA. Bioactivity assays and glyphosate tolerance tests were conducted to evaluate the genetic stability of insect resistance and herbicide tolerance across generations (T4-T6). Agronomic traits of transgenic lines were comprehensively assessed. 【Result】Eight positive transgenic lines with dual resistance were identified through PCR screening, and CA-6, CA-7 and CA-17 lines exhibited higher resistance. qRT-PCR revealed high expression of cry1Ac-vip3Da and g10-epsps in all tissues of these lines, and expression levels varied significantly among tissues. ELISA analysis demonstrated significant differences in Cry1Ac-Vip3Da and G10-EPSPS protein content across tissues of the three transgenic lines, with the highest levels observed in leaves. Protein accumulation gradually decreased during the developmental stages (from the four-leaf stage to boll-opening stage), but remained stable across T4-T6 generations. Bioactivity assays and glyphosate tolerance tests demonstrated that three transgenic cotton lines (T4-T6 generations) exhibited corrected mortality rates of 65.12%-82.75%, tolerated glyphosate at over four times the recommended dosage, and showed no attenuation of resistance across generations. There were no significant differences in plant height, number of fruit branches, number of bells per plant, bell weight, lint percentage, seed cotton yield, and lint cotton yield between transgenic lines and R15.【Conclusion】The exogenous genes cry1Ac-vip3Da and g10-epsps were stably inherited across generations in transgenic lines CA-6, CA-7, and CA-17, conferring dual insect resistance and glyphosate tolerance without compromising agronomic performance.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    LI Ning, GAO LiFeng, HUANG Xin, SHI HuaWei, YANG JinWen, SHI YuGang, CHEN Ming, JIA JiZeng, SUN DaiZhen
    Scientia Agricultura Sinica. 2025, 58(13): 2487-2503. https://doi.org/10.3864/j.issn.0578-1752.2025.13.001

    【Objective】 The excessive application of nitrogen fertilizers has led to ecological pollution and waste of agricultural resources. Developing nitrogen-efficient wheat varieties and improving nitrogen use efficiency are effective approaches for achieving sustainable agricultural development and environmental protection. Screening low-nitrogen-tolerant germplasm resources and identifying genetic loci and candidate genes associated with low-nitrogen tolerance can provide materials and theoretical foundations for breeding nitrogen-efficient wheat varieties. 【Method】 A natural population consisting of 389 wheat varieties was cultivated under high-nitrogen (HN) and low-nitrogen (LN) treatments in 10 field environments. Grain yield per plant (GYP) was measured to calculate the stress tolerance index (STI), thereby enabling the classification of varieties with differential low-nitrogen tolerance. Genome-wide association studies (GWAS) were conducted using 660K SNP array genotyping data to identify stable genetic loci associated with low-nitrogen tolerance. Candidate genes were prioritized through haplotype analysis, expression profiling, and functional annotation. 【Result】 Twelve wheat varieties with strong low-nitrogen tolerance were identified, including Zhongluo 08-1, Jimai 15, Jinghua 2, Kehong 1, Mianyang 19, Jimai 22, Zhenmai 4, Yumai 35, Fengkang 7, Mianyang 11, Jinmai 31, and Lumai 5. Fourteen loci significantly associated with STI were detected, among which four (qSTI1A.1, qSTI3B, qSTI6A, and qSTI7A.2) overlapped with previously reported low-nitrogen tolerance or yield-related QTLs. Notably, qSTI3B-replicated across three environments-was identified as a key locus governing low-nitrogen tolerance. Functional annotation revealed that its candidate gene, TraesCS3B02G042400, encodes an AP2/EREBP (APETALA2/ethylene-responsive element-binding protein) transcription factor. Haplotype analysis showed significant STI divergence among varieties carrying distinct haplotypes, while expression levels of TraesCS3B02G042400 exhibited nitrogen dose-responsive upregulation. 【Conclusion】 Twelve wheat varieties with strong low-nitrogen tolerance were screened. A stable genetic locus, qSTI3B, and a candidate gene, TraesCS3B02G042400, associated with low-nitrogen tolerance were identified.

  • TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY
    ZHANGYanJun, DAIJianLong, DONGHeZhong
    Scientia Agricultura Sinica. 2025, 58(10): 1908-1916. https://doi.org/10.3864/j.issn.0578-1752.2025.10.004

    With the advancement of agricultural supply-side structural reforms and the growing demand for high-quality, safe, and eco-friendly agricultural products in China, cotton production now faces the challenge of coordinating multiple objectives, including yield enhancement, quality optimization, simplified and efficient management, and environmental sustainability. To address these challenges, this paper proposes the novel concept of multi-objective collaborative cultivation (hereafter termed “collaborative cultivation”). We systematically elaborate on the theoretical foundations underpinning this approach, including mechanisms of precision sowing for robust seedling establishment, synergistic water-fertilizer management under partial root-zone irrigation, population regulation through high-density planting with chemical regulation and pruning-free canopy shaping, physiological mechanisms of defoliation-ripening for synchronized boll maturation, and compensatory growth strategies ensuring yield stability under abiotic stress. Building on these theorical bases and international research insights, we identify four core technologies of collaborative cultivation: (i) precision sowing coupled with stress-resilient seedling establishment under adversity, (ii) high-density planting with chemical regulation for canopy shaping, (iii) variable-rate drip irrigation with water-fertilizer synergy management, and (iv) synchronized maturation control technology. Empirical evaluations demonstrate that the integrated application of these technologies optimizes resource utilization, enhances productivity, and ensures fiber quality consistency, while reducing labor inputs and chemical usage. Case studies from major cotton-producing regions validate that collaborative cultivation achieves synergistic outcomes in productivity, sustainability, and economic viability, aligning with green agricultural development goals. Future research priorities include optimizing multi-objective trade-offs, deciphering genotype-environment-management interactions, enhancing stress compensation mechanisms, and extending collaborative principles to multi-cropping systems. Through interdisciplinary innovation and technology integration, this framework offers a systemic solution for high-quality cotton industry development, demonstrating significant potential to drive the sector's green transformation and sustainable advancement.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    ZHOUGuangFei, MALiang, MALu, ZHANGShuYu, ZHANGHuiMin, SONGXuDong, ZHANGZhenLiang, LUHuHua, HAODeRong, MAOYuXiang, XUELin, CHENGuoQing
    Scientia Agricultura Sinica. 2025, 58(3): 431-442. https://doi.org/10.3864/j.issn.0578-1752.2025.03.003

    【Objective】Husk is an important trait that affects the mechanical harvesting of maize grain, and identification of the genetic loci and candidate genes can provide theoretical basis for genetic improvement of maize husk traits. 【Method】To identify significantly associated single nucleotide polymorphisms (SNPs) and predict candidate genes for three husk traits, 251 maize inbred lines were used as plant materials and evaluated for husk number (HN), length (HL), and coverage (HC) in two environments. The genome-wide association study (GWAS) was conducted by multi-locus random-SNP-effect mixed linear model (mrMLM) with 32 853 SNPs across entire genome. 【Result】The three husk traits exhibited abundant variation among 251 maize inbred lines with 10.65%-40.60% of phenotypic variation coefficients. The variances of genotype, environment, and the genotype×environment interactions were significant at P<0.01 for each trait, and the broad-sense heritability for each trait was more than 80%. A total 92 SNPs significantly associated with three husk traits were identified in two environmental and best linear unbiased predictors (BLUP) across two environments values by GWAS. Among these SNPs, 35 SNPs were significantly associated with HN, and the phenotypic variance explained by single SNP ranged from 1.48% to 10.53%. 33 SNPs were significantly associated with HL, and the phenotypic variance explained by single SNP ranged from 1.61% to 21.69%. 24 SNPs were significantly associated with HC, and the phenotypic variance explained by single SNP ranged from 2.17% to 20.86%. However, none of SNP could be significantly associated with two husk traits. Five of 92 SNPs were stable, as they were repeatedly detected in two environments and BLUP, also they were novel loci for first reported in this study. Based on the five stable SNPs and qRT-PCR analysis for husk tissue of 17 maize inbred lines, three candidate genes (Zm00001d003850, Zm00001d033706 and Zm00001d025612) related to maize husk were screeded out, which encoded BOI-related E3 ubiquitin-protein ligase, GeBP transcription factor, and protein of unknown function, respectively. 【Conclusion】A total of 92 SNPs significantly associated with three husk traits were identified, including five stable SNPs. Three candidate genes were predicted that might be involved in maize husk growth and development.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    DUSiQi, WENYuLun, NINGLiXing, YINXiaoYu, WANGShuFen, SONGHaiYan, WANGZhaoHai, LIWeiXing, LIAOJiangLin
    Scientia Agricultura Sinica. 2025, 58(10): 1867-1877. https://doi.org/10.3864/j.issn.0578-1752.2025.10.001

    【Objective】 To elucidate the causes of high-temperature stress inducing rice floret infertility, the present study analyzed the effects of high-temperature stresses on pollen release related traits including pollen grain swelling, anther dehiscence, pollen grain residue in anther and pollen grain deposition on the stigma of the differential genotypes Indica at anthesis. 【Method】Indica germplasms were sown in batches and cultivated in the Nanchang region, Jiangxi Province, China. The rice plants flowering at natural high-temperature environments on early August with 36.5-37.8 ℃ canopy temperature was used as treatments, and the rice plants flowering at suitable environments on middle September with 30.8-32.5 ℃ canopy temperature were used as controls. The pollen release related traits, such as pollen grain swelling, anther dehiscence, pollen grain residue in anther and pollen grain deposition on the stigma from treatments and controls, were detected and analyzed. 【Result】 After flowering under high-temperature stress, the rice germplasms Jiangxijiansimiao, Yuexiangzhan and Huangguangyouzhan show high-temperature tolerant at anthesis, and the floret fertility rates are 91.6%, 89.2% and 87.9%, respectively; while the germplasms Zhenfu, Yuzhenxiang, IR64 and Miyang46 show high-temperature sensitive at anthesis, and the floret fertility rates are just 55.2%, 60.3%, 61.1% and 73.2%, which are very significantly or significantly lower than that of its corresponding controls. Under high-temperature environments, the pollen grain swelling rates for the high-temperature sensitive germplasms Zhenfu, Yuzhenxiang, IR64 and Miyang46 are just 1.99%, 1.16%, 1.12% and 2.70%, which are very significant smaller than that of its corresponding controls; while the pollen grain swelling rates of the other germplasms show no significant difference between treatment and its corresponding control. Under high-temperature environments, the rates of anther dehiscence length in total anther length for the high-temperature sensitive germplasms Zhenfu, Yuzhenxiang, IR64 and Miyang46 are respective 66.0%, 45.4%, 48.7% and 63.6%, which are very significantly or significantly shorter than that of the corresponding controls, and the pollen grain residue are obvious more than that of the corresponding controls; while the anther dehiscence length rates and the pollen grain residue from the other germplasms show no significant difference between treatments and controls. After flowering under high-temperature environments, the average pollen grain number deposited on one stigma of the sensitive germplasms were about 20, which were significant less than that of the controls; while the average pollen grain number deposited on one stigma of the other rice germplasms show no significant difference between treatments and controls. 【Conclusion】 The high-temperature stresses inhibit the pollen grain swelling, effect the anther normal dehiscence, increase the pollen viscidity to impede the pollen grain releasing from anther and decrease the pollen grain number scattering on the stigma, inducing rice floret infertility and decreasing the seed set.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    WEIPing, PANJuZhong, ZHUDePing, SHAOShengXue, CHENShanShan, WEIYaQian, GAOWeiWei
    Scientia Agricultura Sinica. 2025, 58(8): 1463-1478. https://doi.org/10.3864/j.issn.0578-1752.2025.08.001

    【Objective】 The AP2/ERF (APETALA2/ethylene responsive factor) superfamily is a group of transcription factors that play important regulatory roles in plant growth and development, as well as in response to adverse environmental stressors. The AP2/ERF transcription factors are widely present and have many members in plants. Exploring the function of AP2/ERF family gene on grain size provides important genetic resources for regulating grain shape in rice. 【Method】OsDREB1J gene (LOC_Os08g43200) was cloned by homologous recombination, and its basic characteristics, tissue expression characteristics, and the relative expression patterns under plant hormones were analyzed by bioinformatics and qRT-PCR. The transactivation activity and subcellular localization of OsDREB1J were analyzed by yeast heterologous expression, transient expression of rice protoplasts and tobacco. The overexpression and knockout mutant transgenic rice plants of OsDREB1J were obtained by genetic transformation system, and the grain size phenotypes were analyzed by phenotypic analysis technology. 【Result】Subcellular localization analysis showed that OsDREB1J was localized in the nucleus. Bioinformatics showed that the full-length coding sequence of OsDREB1J was 711 bp, encoding 236 amino acids. OsDREB1J protein had no transmembrane structure, and the molecular weight of 27.47 kDa, the theoretical isoelectric point of 5.54, and had a conserved AP2 domain unique to the AP2/ERF family. The cis-acting elements analysis of OsDREB1J promoter showed that the promoter contained cis-acting elements related to hormone response, light and stresses response. The qRT-PCR analysis showed that OsDREB1J was expressed in different tissues of rice with no tissue specificity, and the relative expression level in panicle was the highest. At the same time, OsDREB1J was induced or reduced by different hormone. Transcriptional activation analysis showed that the full-length of OsDREB1J has no transcriptional activity, but the C-terminal fragment was sufficient for the transactivation ability. Phenotypic analysis showed that the grain length, length-width ratio and thousand grain weight of osdreb1j mutant were significantly higher than those of ZH11, OsDREB1J overexpression transgenic rice plants displayed opposite phenotypes, while changing the expression of OsDREB1J did not affect rice grain width. These results show that OsDREB1J may affect grain size by regulating cell length rather than cell proliferation and cell expansion. 【Conclusion】In conclusion, OsDREB1J may be involved in regulating rice grain size through hormone signaling pathway.

  • PLANT PROTECTION
    CONGQiQi, ZHANGJingYi, MENGXiangLong, DAIPengBo, LIBo, HUTongLe, WANGShuTong, CAOKeQiang, WANGYaNan
    Scientia Agricultura Sinica. 2025, 58(3): 478-492. https://doi.org/10.3864/j.issn.0578-1752.2025.03.006

    【Objective】Apple ring rot is one of the serious fungal diseases in apple production caused by Botryosphaeria dothidea. The aim of this study is to obtain strains of B. dothidea with weak pathogenicity carrying dsRNA viruses, identify the types of viruses, and clarify the distribution of these viruses in China, so as to provide new biological control resources for the prevention and control of apple ring rot and new insights into the diversity and systematic evolution of fungal viruses. 【Method】Samples of branches with typical symptoms of apple ring rot were collected from across China, and pure cultures were obtained through tissue isolation and single-spore isolation. Virus-carrying strains were identified through dsRNA band analysis, and the types of dsRNA viruses carried by the virus-carrying strain WH-2L were identified using high-throughput sequencing and molecular cloning techniques. The presence of two types of dsRNA viruses in B. dothidea from six provinces (autonomous region) in China was determined by RT-PCR. Pathogenicity differences among representative strains carrying different viruses were clarified through pathogenicity tests. Finally, the transmission characteristics of the two viruses were revealed through analysis of vertical and horizontal transmission properties. 【Result】For the first time in apple-producing regions of China, strains of B. dothidea causing apple ring rot were found to be co-infected with two viruses: Botryosphaeria dothidea chrysovirus 1 (BdCV1), belonging to the family Chrysoviridae and genus Chrysovirus, and Botryosphaeria dothidea victorivirus 2 (BdVV2), belonging to the family Totiviridae and genus Victorivirus. It was clarified that BdCV1 and BdVV2 are widely distributed in B. dothidea causing apple ring rot in China. BdCV1 was detected in strains from Liaoning, Shandong, Henan, Hebei, Shaanxi, and Xinjiang, except for Yan’an in Shaanxi and Shijiazhuang in Hebei, with an average detection rate of 53.6%. BdVV2 occurred in Liaoning, Shandong, Henan, Hebei, and Shaanxi, but was not detected in Yan’an in Shaanxi, Shijiazhuang and Handan in Hebei, Aksu in Xinjiang, Taian and Qingdao in Shandong, with an average detection rate of 28.6%. It was clarified that the pathogenicity of strains with co-infection of the two viruses and single infection of BdCV1 on branches, apple fruits, and pear fruits was significantly reduced. The vertical transmission efficiency of BdCV1 and BdVV2 was 100%, and the horizontal transmission efficiency was 9% and 3%, respectively. 【Conclusion】The strain WH-2L of B. dothidea with weak pathogenicity carries two viruses, BdCV1 and BdVV2. The detection rates of BdCV1 and BdVV2 in B. dothidea causing apple ring rot in six apple-producing regions in China were 53.6% and 28.6%, respectively. Both viruses can cause reduced pathogenicity in their hosts, with high vertical transmission efficiency and certain horizontal transmission efficiency, and have potential for development as biological control resources for apple ring rot.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    XIONGJiaNi, LIZongYue, HUHengLiang, GUTianYu, GAOYan, PENGJiaShi
    Scientia Agricultura Sinica. 2025, 58(7): 1259-1268. https://doi.org/10.3864/j.issn.0578-1752.2025.07.001

    【Objective】Cadmium (Cd) is the predominant pollutant in China’s arable land, with rice cultivated on these contaminated soils being a significant dietary source of Cd for the population. This study aims to tissue-specifically express OsNRAMP5, a transporter responsible for the majority of Cd uptake in rice, to investigate strategies for developing low-Cd rice varieties and provide a reference for molecular design breeding to cope with Cd pollution. 【Method】To drive the expression of OsNRAMP5 in rice, we utilized a 2 500 bp sequence upstream of the OsLCT1 start codon as the promoter. The red fluorescent protein mRFP was fused to the C-terminus of OsNRAMP5 to visualize its tissue localization. After obtaining independent homozygous transgenic lines, the transcripts of the OsNRAMP5 were first detected using qRT-PCR, and its tissue localization in roots and nodes was observed via laser confocal microscopy. Subsequently, the accumulation and tolerance of Cd were evaluated in transgenic and wild-type rice under varying concentrations of Cd treatment. Furthermore, plants were grown in Cd-contaminated paddy soil, and the accumulation of Cd and other mineral elements in seeds and leaves, as well as related yield traits, were measured. 【Result】Under the drive of the OsLCT1 promoter, OsNRAMP5 was expressed mainly in the epidermis, exodermis and stele of roots, as well as in the phloem area of enlarged vascular bundles and diffuse vascular bundles in nodes, differing significantly from the native expression pattern of OsNRAMP5 in rice. Compared to wild-type rice, the transgenic lines exhibited increased Cd accumulation in roots, decreased Cd accumulation in shoots, and enhanced tolerance to Cd stress during the seedling stage. When cultivated in Cd-contaminated paddy soils, plant height and grain yield were unaffected by the ectopic expression of OsNRAMP5, while Cd accumulation in seeds and leaves significantly decreased in the transgenic lines. The Cd content in seeds decreased by over 80%, with a greater reduction ratio compared to that in leaves. Although the Mn content in seeds and leaves slightly decreased, the expression of OsNRAMP5 had little impact on the accumulation of other mineral elements such as Fe, Zn, and Cu. 【Conclusion】The expression of OsNRAMP5 driven by the OsLCT1 promoter greatly decreases the Cd migration toward rice seeds by reducing Cd transport to the aboveground parts from roots and increasing the Cd transporting to leaves at nodes. Therefore, the expression of OsNRAMP5 under the control of the OsLCT1 promoter is an effective strategy to reduce Cd accumulation in rice seeds.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    JINYaRu, CHENBin, WANGXinKai, ZHOUTianTian, LIXiao, DENGJingJing, YANGYuWen, GUODongShu, ZHANGBaoLong
    Scientia Agricultura Sinica. 2025, 58(6): 1052-1064. https://doi.org/10.3864/j.issn.0578-1752.2025.06.002

    【Objective】 Rice (Oryza sativa L.) is a staple cereal crop for about half of the global population, with protein being the second-most significant nutritional component in rice grains. The storage proteins in rice grains mostly consist of glutelin, prolamin, globulin, and albumin, among which the content of easy-to-digest glutelin is the highest. Consequently, common rice increases the burden of kidney and accelerates the progression of renal disorders. The method of generating low-glutelin rice germplasm will provide novel genetic material for the cultivation of functional rice cultivars suitable for individuals with kidney diseases. 【Method】 We utilized Suxiu 867 (SX867), an elite japonica rice cultivar appropriate for cultivation in Jiangsu province, as a transgenic recipient to delete a fragment of approximately 3 500 bp between the B subfamily glutelin-coding genes GluB4 and GluB5 using CRISPR/Cas9-mediated gene editing technology. The large fragment deletion was identified by PCR using the primers corresponding to the flanking sequence of gene editing target sites, while sequence-specific primers for Cas9 and hygromycin resistance gene cassettes were used to identify the low-glutelin rice mutant absent of transgenic elements. The protein component contents of homozygous low-glutelin mutants were analyzed qualitatively and quantitatively, and the expression levels of glutelin-coding genes in rice grains were detected by quantitative PCR. The agronomic traits and quality traits of homozygous low-glutelin mutants and recipient cultivar cultivated under the same cultivation conditions were measured. 【Result】 Homozygous mutants with a 3 448 bp deletion between GluB4 and GluB5 genes were generated successfully. In the mutants, the relative proportion of glutelin decreased significantly, while that of prolamin and globulin increased significantly. The glutelin content of homozygous mutants decreased to 45.54%-49.75% compared to recipient cultivar, and the reduction level is comparable to LGC-1, a low-glutelin rice germplasm commonly used as a donor of low-glutelin trait in commercialized rice cultivars. The expression levels of B subfamily glutelin-coding genes in homozygous mutant were decreased significantly, and the changing trends was consistent with that of LGC-1 derived rice cultivar. Except that plant height decreased and grain length increased significantly, other measured agronomic and quality traits of homozygous mutants were not changed significantly compared to recipient cultivar. 【Conclusion】 Using CRISPR/Cas9-mediated gene editing technology, rice mutants with significant lower glutelin content free from transgenic elements were obtained successfully providing a convenient and quick method to generate low-glutelin germplasm.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    LIULuPing, HUXueJie, QIJin, CHENQiang, LIUZhi, ZHAOTianTian, SHIXiaoLei, LIUBingQiang, MENGQingMin, ZHANGMengChen, HANTianFu, YANGChunYan
    Scientia Agricultura Sinica. 2025, 58(5): 840-850. https://doi.org/10.3864/j.issn.0578-1752.2025.05.002

    【Objective】Maturity time is an essential phenotypic measure of ecological adaptability of soybean and an important trait related to its yield formation. The study of promoters and expression patterns of major maturity genes E1 and E2 would provide basis for the study of gene function and molecular regulatory network of maturity time and lay foundation for adaptability improvement and yield increase in soybean.【Method】The promoter sequences of major maturity genes E1 and E2 were analyzed through the promoter cis-element analysis website PlantCARE, and the important regulatory elements were detected. The promoters of E1 and E2 were cloned, the GUS vectors were constructed, and transformation of Arabidopsis was performed to detect GUS activity in different tissues and organs of transgenic plants. Under low light and strong light conditions, the expression levels of E1 and E2 were compared between long day and short day conditions. The expression levels of E1 and E2 were detected in soybean varieties of different maturity groups, which is for the analysis of correlation between expression levels and maturity time of soybean varieties.【Result】Both E1 and E2 promoters contained multiple photoresponsive elements such as AE-box, Box4 and G-box, E1 promoter also contained auxin-response, abolic acid-response elements, and E2 promoter also contained low temperature-response, drought-response elements and meristem expression elements. In GUS activity detection of transgenic Arabidopsis, E1 promoter had strong transcriptional activity in all organs of the plant, and transcriptional activity of E2 promoter in fibrovascular tissues of seedling hypocotyl, leaf and root was relatively strong. Under both low light and strong light conditions, the expression level of E1 was significantly higher in long day than in short day. Under low light conditions, the expression level of E2 was higher in short day than in long day. Under strong light conditions, the expression level of E2 was higher in long day than in short day. With the increase of maturity time of different soybean varieties, expression level of E1 increased gradually, while E2 expression level did not change regularly.【Conclusion】The promoter of E1 gene was a widely expressed promoter, and its expression level was significantly regulated by photoperiod and significantly correlated with the maturity time of soybean varieties. The promoter of E2 was strongly expressed in vascular tissues of various organs, the photoperiodic regulation mode of this gene was different under strong light and low light conditions, and there was no significant correlation between expression level of E2 and maturity time.

  • TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY
    TANGYu, LEIBiXin, WANGChuanWei, YANXuanTao, WANGHao, ZHENGJie, ZHANGWenJing, MAShangYu, HUANGZhengLai, FANYongHui
    Scientia Agricultura Sinica. 2025, 58(6): 1083-1101. https://doi.org/10.3864/j.issn.0578-1752.2025.06.004

    【Objective】 Under the background of global warming, this paper explored the physiological mechanism of anthocyanin content in colored wheat in response to high temperature stress in the middle of grain filling, so as to lay a theoretical basis for further coping with the high-quality cultivation of functional colored wheat varieties under climate warming. 【Method】 The experiment was conducted in Hefei High-tech Agricultural Park in the 2022-2023 and 2023-2024 growing seasons. Six colored wheat varieties with different colors were selected and subjected to high temperature stress treatment (T) for 5 days at the middle stage of filling, with the same materials grown under ambient temperature as the controls (CK). 【Result】 Under high temperature stress after anthesis, the net photosynthetic rate, stomatal conductance, transpiration rate, relative chlorophyll content (SPAD), dry matter partition, soluble sugar content, sucrose synthase activity, anthocyanin content, anthocyanidin synthase activity, chalcone synthase activity and phenylalanine ammonia-lyase activity of colored wheat were significantly reduced, and the yield of six varieties of colored wheat decreased by 9.10% to 16.94%, 1000-grain weight decreased by 7.84% to 16.94%, and anthocyanin content decreased by 7.18% to 14.17%. The yield, photosynthetic intensity, SPAD value, dry matter partition, soluble sugar content, sucrose synthase activity, anthocyanin content, anthocyanidin synthase activity, chalcone synthase activity, and phenylalanine ammonia-lyase activity of different varieties of colored wheat were: Qinbai 1>Qinlü 3>Qinzi 1>Xinchun 36>Qinhe 2>Qinlan 1, and the anthocyanin content was: Qinhei 2>Xinchun 36>Qinzi 1>Qinlü 3>Qinlan 1>Qinbai 1. The yield of heat-resistant wheat varieties of Qinbai 1, Qinlü 3 and Qinzi 1 decreased significantly less than that of heat-sensitive wheat varieties Qinhei 2, Xinchun 36 and Qinlan 1. The decreases in photosynthetic intensity, SPAD value, dry matter fraction, soluble sugar content, sucrose synthase activity, anthocyanin content, anthocyanidin synthase activity, chalcone synthase activity and phenylalanine ammonia-lyase activity of color wheat varieties Qinhei 2, Xinchun 36 and Qinzi 1 with high anthocyanin content were smaller than those of Qinlü 3, Qinlan 1 and Qinbai 1 with low anthocyanin content. Correlation analysis showed that the yield of each color wheat variety was significantly positively correlated with 1000-grain weight, sucrose content, sucrose synthase activity, flag leaf net photosynthetic rate, stomatal conductance, transpiration rate and SPAD value, anthocyanin content was significantly positively correlated with soluble sugar content, and yield was negatively correlated with anthocyanins, but the correlation was not significant. After high temperature stress after anthesis, the decomposition of sucrose bound to free anthocyanins decreased, and the decomposition of anthocyanins in grains increased, which supplemented the growth and development of wheat.【Conclusion】 The antioxidant activity of anthocyanins helped crops resist external stress, and the decline of various indexes of color wheat varieties with higher anthocyanin content was comparable to that of color wheat varieties with lower anthocyanin content under high temperature stress after anthesis, the anthocyanin content was significantly positively correlated with soluble sugar content. In conclusion, the accumulation of anthocyanin content could respond to high temperature stress, reduce the decrease of soluble sugar content, and increase the heat resistance of colored wheat.

  • SOIL & FERTILIZER·WATER-SAVING IRRIGATION·AGROECOLOGY & ENVIRONMENT
    ZHANGYang, GAOYan, ZHANGYan, HUANGDanDan, CHENXueWen, ZHANGShiXiu, LIANGAiZhen
    Scientia Agricultura Sinica. 2025, 58(10): 1958-1968. https://doi.org/10.3864/j.issn.0578-1752.2025.10.008

    【Objective】 This study aimed to explore the effects of different residue return methods on nitrogen fractions, nitrogen mineralization and nitrogen-cycling genes in black soil of Northeast China, and to clear the soil nitrogen supply capacity and the change of soil nitrogen cycling gene community structure under long-term residue return. 【Method】 Based on the long-term experiment of black soil in Northeast China, the residue incorporated into soil (RI) and the residue covered on soil surface (RC) under monoculture maize were selected, with residue removed as control (CK). Nitrogen content in soil fractions were measured, soil nitrogen mineralization incubation was conducted by using leaching incubation at intervals, and fluorescence quantitative PCR (qPCR) was used to determine the copy number of nitrogen-cycling genes in soil. 【Result】 After 8-year experiment, compared with CK, RC significantly increased the content of particulate organic nitrogen (PON)(0.21 g·kg-1) and mineral-associated organic nitrogen (MAON) (0.27 g·kg-1) in surface (0-5 cm) soil, whereas RI only increased the content of MAON (0.13 g·kg-1) in soil (P<0.05). Residue return (RI and RC) markedly increased the microbial biomass nitrogen (MBN) in soil by 1.4-2.8 times (P<0.05), the RI had higher content of ammonium nitrogen (NH4+) and dissolved organic nitrogen (DON), while the RC had the lowest content of nitrate nitrogen (NO3-). In comparison with CK, residue return significantly enhanced soil nitrogen mineralization amount by 25.3%-83.2% (P<0.05), taking the descending order of RC>RI>CK. Residue return remarkably increased the potential of soil nitrogen mineralization (N0) and mineralization rate constant (k) (P<0.05) by using a first-order reaction kinetics model, both showing the highest values under RC, with N0 and k reached 199.8 mg·kg-1 and 0.31 mg·kg-1·d-1, respectively. Random forest analysis indicated that PON, MBN, and NO3- had greater impacts on N0. In addition, the abundance of nifH, AOB and nirS genes under residue return were enhanced and the abundance of AOA and nirK genes under residue return were declined in comparison with residue removed (P<0.05), which indicated that residue return could change the structure of soil nitrogen-cycling genes communities. Redundancy analysis (RDA) result showed that the changes of soil microbial community structure were affected by different nitrogen fractions under different residue return methods. 【Conclusion】 Long-term residue covered on soil surface had the highest organic nitrogen content and nitrogen mineralization potential in soil. It was beneficial to improve soil nitrogen pools and to ensure the supply of nitrogen required for plant growth, which provided greater possibility for reducing the application of chemical nitrogen fertilizer in cropland in black soil of Northeast China.

  • TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY
    ZHANGHongCheng, XINGZhiPeng, ZHANGRuiHong, SHANXiang, XIXiaoBo, CHENGShuang, WENGWenAn, HUQun, CUIPeiYuan, WEIHaiYan
    Scientia Agricultura Sinica. 2025, 58(5): 864-876. https://doi.org/10.3864/j.issn.0578-1752.2025.05.004

    【Objective】The aim of this study was to provide the theoretical and technical support for the innovation of green, high-yield, high-quality and high-efficient unmanned cultivation technology system of wheat. 【Method】 According to the situation of accelerating land transfer and large-scale operation, decreasing labor force engaged in agricultural production, and more efficient and comfortable farming methods, the integrated unmanned cultivation technology of wheat was put forward through the integration study of “agronomy-machinery-intelligence”, that is, using new technology, new product and new equipment to simplify and integrate the whole process of wheat production, and complete wheat production with the least number of operations, the least number of machines and unmanned operations. On the basis of exploratory experimental research, the integrated unmanned cultivation technology of wheat (IU) and conventional mechanized high-yield cultivation techniques of wheat in experimental area (CK) were set up as treatments in Dazhong Farm of Yancheng, Jiangsu Province in 2019-2020, 2020-2021 and 2021-2022, to study the traits and differences of wheat yield formation among different technology treatments, analyze the high-yield traits of IU, and put forward the technical approaches of IU. 【Result】 The IU increased wheat yield by 3.0%-5.9% compared with CK, and significant differences were observed between treatments of some varieties or some growing seasons. In terms of yield components, the spike number was IU>CK (significant differences were observed between treatments of some varieties or some growing seasons), the grains per spike were IU>CK (P>0.05), the total grains were IU>CK (P<0.05), and the 1000-kernels weight was IU<CK (P>0.05), indicating that the IU increased wheat yield by stabilizing the grains per spike and 1000-kernels weight, and increasing the spike number. In the production of photosynthetic matter, the culm number, leaf area index, dry matter accumulation at the main growth stages, the leaf area duration and crop growth rate in the main growth periods, and the culm fertility and grain leaf ratio were all expressed as IU>CK (significant differences were observed between treatments of some varieties or some growing seasons), which laid a material foundation for the yield increase of the IU. This paper not only summarized the technical approaches and basic technologies of IU but also discussed the development of IU from the aspects of integrated cultivation, unmanned cultivation, “agronomy-machinery-intelligence” fusion degree, key agronomy technology and comprehensive evaluation. 【Conclusion】 The yield under IU was equivalent or significantly increased to that under CK. And the high-yield cultivation of wheat was realized with less agricultural machinery and labor and unmanned operation, which was an effective way for the development of agricultural modernization production. In the future, multi-faceted collaborative innovation and investment should be strengthened to accelerate the application and large-scale promotion of this technology.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    LILu, XIEZhuang, XIEKeYing, ZHANGHan, ZHAOZhuoWen, XIANGAoNi, LIQiaoLong, LINGYingHua, HEGuangHua, ZHAOFangMing
    Scientia Agricultura Sinica. 2025, 58(3): 401-415. https://doi.org/10.3864/j.issn.0578-1752.2025.03.001

    【Objective】Rice grain size is a quantitative trait controlled by multiple genes. They can be dissected into a single segment substitution line (SSSL), which is of great significance for their genetic mechanism study and breeding by design. 【Method】Z492, a chromosome segment substitution line in the genetic background of Nipponbare, was used as material to dissect QTL for rice grain size by mixed linear model (MLM) method. 【Result】The F2 population was constructed from Nipponbare/Z492 to identify four QTL for grain size, including qGL6 and qGL7 for grain length and qRLW7 and qRLW12 for rate of grain length to width. Then three single-segment substitution lines (SSSL, S1-S3) and 3 dual-segment substitution lines (DSSL, D1-D3) carrying these QTL were further constructed. And the SSSL were then used to detect eight QTL for grain size, including qGL6, qGL7 and six newly identified QTL (qGW6, qRLW6, qGW7, qGWT7, qGL12, qGW12). Simultaneously, the genetic model of different QTL in 3 DSSL were analyzed. The results showed that interaction of qGL6 (a=0.26 mm) and qGL7 (a=0.21 mm) produced -0.21 mm of grain length epistatic effect, which resulted in the genetic effect (0.26 mm) of D1 equal to the additive effect of each QTL. Thus, the grain length (7.98 mm) of D1 displayed no difference from those (7.89 and 7.98 mm) of S2 with qGL7 and S1 containing qGL6, while significantly longer than that (7.47 mm) of Nipponbare. The result indicated that it is not necessary to pyramid qGL6 and qGL7 in breeding by design for increasing grain length. qGW6 (a=0.07 mm) and qGW12 (a=0.06 mm) belonged to independent inheritance in D2, thus, the genetic effect (0.13 mm) after pyramiding of qGW6 and qGW12 caused the grain width (3.65 mm) of D2 broader significantly than any of the SSSL with the single QTL. So, qGW6 and qGW12 can be selected to increase grain width in breeding by design. Interaction of qGW7 (a=0.11 mm) and qGW12 (a=0.06 mm) yielded -0.10 mm of epistatic effect, causing the grain width genetic effect (0.07 mm) of D3 parallel to the additive effect of qGW12. Thus, the grain width (3.59 mm) of D3 exhibited no difference with that (3.56 mm) of S3 carrying qGW12, while wider significantly than that (3.44 mm) of Nipponbare and narrower significantly than that (3.66 mm) of S2. 【Conclusion】It is very necessary for breeding by design to identify QTL for different important traits using SSSL and DSSL. Pyramiding different QTL produce various genetic models. Some display independent inheritance, and others exhibit various epistatic effects. In addition, to cross with S1 and S3 can realize the goal of longer, wider and heavier rice grain, and to cross with S1 and S2 can reach the target of heavier grain weight, while to cross with S2 and S3 have no any effects in grain size.

  • TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATIONTECHNOLOGY
    WANGRuiZhi, LITao, QIANXiangLing, ZHANGYa, YANGXiaoZhuo, LIGuangYan, WEIHaiYan, ZHANGHongCheng, LIUGuoDong
    Scientia Agricultura Sinica. 2025, 58(12): 2316-2332. https://doi.org/10.3864/j.issn.0578-1752.2025.12.004

    【Objective】Nitrogen panicle fertilizer is one of the key factors affecting rice yield and quality. Studying its impact on the yield, quality, and aroma of aromatic japonica rice in southern China could provide a theoretical basis for high-yield and high-quality cultivation of southern japonica rice. 【Method】 Conducted from 2022 to 2023, this study used Nanjing 9108, a representative variety of aromatic japonica rice in southern China, as the material, and three nitrogen application modes were set up: no nitrogen fertilizer (N0), no panicle fertilizer (N1), and conventional application of panicle fertilizer (N2, with 70% base and tillering fertilizer + 30% panicle fertilizer). In addition, the experiment of applying ear fertilizer at different leaf age stages, including the top sixth leaf, fifth leaf, fourth leaf, third leaf, second leaf and first leaf just after emerging from the sheath (designated as L6, L5, L4, L3, L2, and L1), was conducted to study the synergistic regulation mechanism of nitrogen panicle fertilizer on yield, quality, and aroma of Nanjing 9108.【Result】Compared with no nitrogen fertilizer application and no panicle fertilizer application, the application of panicle fertilizer could significantly increase the effective panicle number per unit area and grains per panicle of aromatic japonica rice, thereby enhancing its yield. As the period of panicle fertilizer application was delayed, the yield first increased and then decreased, reaching a maximum at the treatment of applying fertilizer at the fourth leaf from the top (counted downwards from the flag leaf). The application of panicle fertilizer improved rice processing quality, appearance quality, and aroma quality. The period of panicle fertilizer application had an impact on these qualities of aromatic japonica rice. With the delay in the period of panicle fertilizer application, the milled rice rate of Nanjing 9108 showed an increasing trend, but the chalkiness degree increased, leading to a deterioration in appearance quality. Simultaneously, the amylose content decreased while the protein content increased, resulting in a decline in taste value and eating quality. The content of 2-acetyl-1-pyrroline (2-AP), as the main component of aroma, also decreased with the delay in the period of panicle fertilizer application. The application of panicle fertilizer significantly increased the proline content and proline dehydrogenase activity in grains. Advancing the period of panicle fertilizer application had a significant promoting effect on proline accumulation during the rice filling stage, and proline dehydrogenase activity also increased, which was conducive to maintaining higher proline content and proline dehydrogenase activity in grains during the maturity stage, thereby promoting the synthesis of 2-AP in rice grains. Based on a comprehensive evaluation of the effects of panicle fertilizer application period using indicators, such as actual yield, milled rice rate, chalkiness degree, taste value, and grain 2-AP content, it was found that the treatment of applying fertilizer at the fourth leaf from the top had the highest comprehensive score. 【Conclusion】Under the experimental conditions of this study, the application of panicle fertilizer contributed to the synergistic improvement of yield and quality. On the basis of ensuring stable yield, the application of panicle fertilizer at the fourth leaf from the top achieved the best overall benefits in terms of yield, taste, and aroma.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    JINYiDan, HENiQing, CHENGZhaoPing, LINShaoJun, HUANGFengHuang, BAIKangCheng, ZHANGTao, WANGWenXiao, YUMinXiang, YANGDeWei
    Scientia Agricultura Sinica. 2025, 58(6): 1043-1051. https://doi.org/10.3864/j.issn.0578-1752.2025.06.001

    【Objective】 Rice blast is one of the most devastating diseases of rice production. A broad-spectrum disease resistance gene Pigm-1 was identified but its functional pathway and interactors are unknown. The screening and identification of key proteins in the Pigm-1 signaling pathway will provide an important theoretical basis for rice disease resistance breeding. 【Method】 In this study, the decoy protein pGBKT7-Pigm-1-CC1-576 vector was constructed to detect the decoy protein self-activation, and the toxicity of the decoy protein was detected by separately transforming the plasmid pGBKT7 and pGBKT7-Pigm-1-CC1-576 into Y2H Gold yeast. The rice disease resistance R protein Pigm-1 was screened by cDNA expression yeast library induced by rice blast fungus. The sequencing results were compared and annotated by Rice Information GateWay (RIGW). The interaction of OsbHLH148 protein was verified by Luc, Co-IP and yeast two-hybrid assays, and the tissue expression of the corresponding gene of the interaction protein OsbHLH148 was analyzed by qRT-PCR. 【Result】 The self-activation test showed that the decoy protein pGBKT7-Pigm-1-CC1-576 did not self-activate when cotransformed with the AD plasmid, and the toxicity analysis showed that the decoy protein had little or no toxicity to yeast cells. A total of 124 proteins that may interact with Pigm-1 were obtained by screening the yeast library, and among these proteins, there are ethylene synthesis related, gibberellin synthesis related, active oxygen species clearly related, enzyme metabolism related, and some function unknown. The interaction between Pigm-1-CC1-576 and OsbHLH148 was verified by Luc, Co-IP and yeast two-hybrid methods. Further analysis showed that OsbHLH148 can be induced by blast fungus infection, and the tissue expression analysis showed that OsbHLH148 expression level was the highest in rice leaves at 6 weeks. 【Conclusion】 In this study, 124 proteins that may interact with Pigm-1 were obtained. One of these proteins, OsbHLH148, was selected and verified to interact with Pigm-1-CC1-576. Suggesting that OsbHLH148 may be involved in Pigm-1 mediated resistance of rice blast.

  • FOOD SCIENCE AND ENGINEERING
    ZHANGTao, WANGHuan, XIEHongKai, CHENYinJi
    Scientia Agricultura Sinica. 2025, 58(5): 1004-1016. https://doi.org/10.3864/j.issn.0578-1752.2025.05.014

    【Objective】This study aimed to investigate the impact of wheat bran polysaccharide on the physical properties and microstructure of surimi gel, and to elucidate the mechanism by which the concentration of wheat bran polysaccharide affects surimi gel characteristics, so as to provide the theoretical support for enhancing surimi gel quality through the utilization of wheat bran by-products.【Method】Different concentrations of wheat bran polysaccharide were added to threadfin bream (Nemipterus virgatus) surimi to prepare composite gels. The effects of wheat bran polysaccharide on the characteristics and structures of surimi gel were investigated using texture analysis, rheological test, molecular interaction measurement, Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM).【Result】The impact of wheat bran polysaccharide on the macroscopic physical properties and microstructures of surimi gel exhibited a pronounced concentration dependence. As the amount of wheat bran polysaccharide increased, the rheological parameters (G' and G" values), water holding capacity, texture profile analysis (TPA) values, gel strength, and water distributions of the blended system were all initially elevated and then declined, achieving the maximum improvement at the addition level of 1.0%. FTIR revealed that the secondary structure of proteins during the heat-induced gelation of surimi was closely related to the polysaccharide content: with increasing polysaccharide content, the α-helix content gradually decreased, while β-turn and β-sheet content showed an upward trend (P<0.05). However, when the polysaccharide addition exceeded 1.0%, the α-helix content gradually increased again, while β-turn and β-sheet content exhibited downtrends. This may be due to the concentration-dependent effect of polysaccharides on the disulfide bonds and electrostatic interactions, which were the primary intermolecular forces within the protein gel, leading to the changes in its secondary structure. SDS-PAGE electrophoresis showed that when the polysaccharide addition was over 1.0%, the actin (AC) and myosin heavy chain (MHC) bands became significantly lighter, with dark bands accumulating at the top of the stacking gel. SEM observations of the microstructure of surimi gels revealed that as the polysaccharide added, the pore size within the surimi gel network gradually reduced. When the polysaccharide addition reached 1.0%, the surimi gel network structure was the most compact, with the fractal dimension (Df) reaching a maximum value of 2.8657. Further addition of the polysaccharide leaded to phase separation in the gel system, and extensive self-aggregation of polysaccharides disrupted the surimi protein gel network, resulting in a decrease of Df.【Conclusion】Wheat bran polysaccharide with the concentration of 1.0% to the surimi could be used as a filler as well we water retention agent in the three-dimensional network structure of surimi protein, and induce the formation of a more uniform and dense gel matrix, which could effectively improve the gel quality of surimi.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    LÜTao, SUNGuoQing, GUODongCai, CHENQuanJia, CAIYongSheng, FANBiaoXing, QUYanYing, ZHENGKai
    Scientia Agricultura Sinica. 2025, 58(9): 1684-1701. https://doi.org/10.3864/j.issn.0578-1752.2025.09.002

    【Objective】 The objective of this study is to develop InDel molecular markers for Island cotton, which is characterized by its superior fiber quality, particularly the fiber tensile strength-a key indicator of cotton fiber quality. The study aims to validate these markers using RIL (Recombinant Inbred Line) populations and resource materials, thereby providing a theoretical foundation for breeding new varieties of Island cotton with enhanced fiber quality. 【Method】 Utilizing a previously established population of 213 Pima S-7 and 5917 F5:6 RILs, we conducted QTL (Quantitative Trait Locus) mapping to identify the locus regulating fiber strength in Island cotton, designated qFS-chr17-1. InDel markers were designed based on whole genome sequencing (WGS) data of the parental lines, followed by the identification of polymorphic markers. Preliminary validation of these markers was performed using 40 extreme family materials selected based on phenotypic data. Genotyping was carried out on both the 213 RIL population and the 213 Island cotton resource population, alongside multi-year fiber quality data to assess the markers' effectiveness. 【Result】 The genotyping of the RIL and Island cotton resource populations with the two developed InDel markers indicated a close linkage to fiber strength phenotypic data, with significant differences observed in fiber strength traits among the differentiated materials. The analysis of genotypic combinations revealed an upward trend in fiber strength across four combination types, with materials exhibiting the Hap3 (B/A) and Hap4 (B/B) genotypes demonstrating significantly greater fiber strength than those with Hap1 (A/A) and Hap2 (A/B). Furthermore, the InDel-3L2 marker showed significant correlations with fiber length, fiber uniformity, and spinning consistency index, consistent with the observed phenotypic trends. Analysis of multi-year fiber quality data from two experimental sites revealed environmental variability in fiber quality, while temperature data indicated that the developed molecular markers are minimally influenced by environmental factors. Clustering analysis of fiber quality data from 213 Island cotton resource materials, combined with molecular marker genotyping, identified eight materials exhibiting superior fiber quality. 【Conclusion】 This study successfully developed two InDel molecular markers closely linked to the fiber strength QTL (qFS-chr17-1), which maintain their effectiveness upon combination. The InDel-3L2 marker demonstrates significant correlations with fiber length, fiber uniformity, and spinning consistency index. These markers can efficiently and accurately identify high-strength fiber resources in Island cotton, contributing to the breeding of improved fiber quality. Additionally, eight materials with excellent fiber quality have been identified.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    CAOShiLiang, ZHANGJianGuo, YUTao, YANGGengBin, LIWenYue, MAXueNa, SUNYanJie, HANWeiBo, TANGGui, SHANDaPeng
    Scientia Agricultura Sinica. 2025, 58(2): 203-213. https://doi.org/10.3864/j.issn.0578-1752.2025.02.001

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

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    QIAOZhengYan, YUMiao, TANGYuJie, SHIGuiShan, LIUXinYu, LIUXiaoHan, WANGXinDing, LIYang, WANGNai, CHENBingRu
    Scientia Agricultura Sinica. 2025, 58(1): 30-42. https://doi.org/10.3864/j.issn.0578-1752.2025.01.003

    【Objective】This study was conducted to screen the concentration of soda saline-alkali stress solution and the determination index of saline-alkali tolerance, to establish the identification method of saline-alkali tolerance to large-scale identification of sorghum germplasms. The saline-alkali tolerance of the core germplasms of grain sorghum were comprehensively evaluated, and the saline-alkali tolerant germplasms were identified and selected to provide a germplasm basis for further breeding of saline-alkali tolerant parents and hybrids.【Method】The main components of saline-alkali soil of in The Songnen Plain are Na2CO3 and NaHCO3. This experiment used 50 mmol·L-1 NaHCO3﹕Na2CO3=9﹕1 as a stress solution to simulate the moderate saline-alkali environment in Songnen Plain, the pH is 9.19, Salinity is 0.21%. Eight traits, including seedling height, root length, seedling fresh weight, root fresh weight, seeding dry weight, root dry weight, root-shoot ratio fresh weight and root-shoot ratio dry weight were used as measurement indexes and the saline-alkali tolerance characteristics of 285 sorghum core germplasms at seedling stage were identified. Principal component analysis was used to screen the salt-alkali tolerance identification indexes of grain sorghum at seedling stage and establish a mathematical model for salt-alkali tolerance evaluation at seedling stage. The saline-alkaline tolerance of 285 sorghum germplasms was classified by cluster analysis, and the germplasms with strong saline-alkaline tolerance were screened.【Result】50 mmol·L-1saline-alkali stress showed inhibitory effects on 8 indexes of 285 sorghum germplasms, the average values of saline -alkali resistance coefficients are 0.794, 0.785, 0.565, 0.554, 0.802, 0.638, 0.978, and 0.841.Under saline alkali stress, 8 indexes showed significant positive correlations; the seedling height and root fresh weight could be used as the indexes for the identification and evaluation of soda saline-alkali stress in sorghum seedling stage by principal component analysis; The evaluation model of saline-alkali tolerance characteristics of sorghum seedlings was summarized by multiple linear regression analysis Y=0.097X4+0.171X2+0.201X6+0.157X1+0.105X3- 0.147, it can be used for comprehensive evaluation of multiple indicators. 285 grain sorghum core collections were divided into 5 grades by cluster analysis, strong saline-alkali tolerance, saline-alkali tolerance, intermediate type, sensitive type and extremely sensitive type, Among them, there were 8 strong salt-tolerant germplasms, 8 salt-tolerant germplasms, 112 intermediate germplasms, 134 sensitive germplasms and 23 extremely sensitive germplasms. The saline-alkali tolerant germplasm and extremely sensitive germplasm were planted in the moderate saline-alkali soil (pH 8.5-9.5, Salinity 0.3%) for verification in Zhenlai County of western Jilin Province. The average seedling emergence rate of strong saline-alkali tolerant germplasm was 45.4%, and the average seedling height was 23 cm. The average seedling emergence rate of salt-tolerant germplasm was 31.3%, and the average height was 20.9 cm. The average emergence rate of extremely sensitive germplasm was 20%, and the average seedling height was 12.3 cm.【Conclusion】8 strong soda saline-alkali tolerant germplasms and 8 saline-alkali tolerant germplasms were screened out from 285 sorghum germplasms resources with 50 mmol·L-1 soda saline-alkali concentration (NaHCO3﹕Na2CO3=9﹕1). The seedling height and root fresh weight could be used as the preferred evaluation indexes for the identification of saline-alkali tolerance at seedling stage.

  • SOIL & FERTILIZER·WATER-SAVING IRRIGATION·AGROECOLOGY & ENVIRONMENT
    LIShaoXing, SONGWenFeng, WEIZeYu, ZHOUYuLing, SONGLiXia, RENKe, MAQun, WANGLongChang
    Scientia Agricultura Sinica. 2025, 58(8): 1591-1603. https://doi.org/10.3864/j.issn.0578-1752.2025.08.010

    【Objective】 This study aimed to explore the effects of straw and green manure mulching on soil fertility and crop yield on the dryland in southwest China, so as to provide the theoretical basis and practical guidance for exploring reasonable, efficient and ecologically healthy conservation tillage measures in southwest China. 【Method】 The sweet potato field in the "broad bean/maize/sweet potato" dry three-crop intercropping mode in southwest China was selected as the research object, and four treatments were set up: no mulching (CK), straw mulching (S), straw and milk vetch mulching (S+M), and milk vetch mulching (M). The effects of different treatments on soil characteristics and soil fertility, sweet potato dry matter content in the sweet potato field were studied. 【Result】(1) Compared with no-mulching treatment, straw and milk vetch mulching could improve the physical and chemical properties and biological characteristics of soil in sweet potato field. Among them, straw and milk vetch mulching had the best effect. (2) The comprehensive evaluation of soil fertility based on principal component analysis showed that soil fertility under straw and milk vetch mulching treatment was higher than that under no mulching treatment, and the comprehensive scores of straw and milk vetch mulching treatment were the highest in both rhizosphere and non-rhizosphere soil. (3) S+M treatment significantly improved the dry matter quality of various organs of sweet potato and sweet potato yield, the yield of sweet potato under S+M, S and M treatment was 34.53%, 14.60% and 11.55% higher than that under CK treatment, respectively.【Conclusion】Straw and milk vetch mulching in the dryland, triple cropping systems of southwest China, could effectively improve the physical and chemical properties and biological characteristics of soil, enhance soil fertility, and improve dry matter quality and yield.

  • PLANT PROTECTION
    ZHAOYuMeng, LIGuangXu, DAIQiDong, LIUJiaCheng, ZHAOHaiJuan, ZHANGYuJun, YANGHua, LIUShuo
    Scientia Agricultura Sinica. 2025, 58(12): 2358-2370. https://doi.org/10.3864/j.issn.0578-1752.2025.12.007

    【Objective】Plum cultivation is an important industry in Liaoning region, while the large-scale epidemic of bacterial shot hole has seriously affected the sustainable development of plum cultivation. The purpose of this paper is to clarify the pathogenic bacteria species of plum bacterial shot hole in Liaoning, and to explore the toxicity of different agents against the pathogenic bacteria, so as to provide a theoretical basis for the prevention and control of the disease.【Method】From 2023 to 2024, the occurrence of plum bacterial shot hole was investigated in 10 plum production areas of Liaoning Province. By collecting 20 disease samples of leaves, fruits, and twigs with typical symptoms, a total of 30 pathogenic bacteria were isolated, purified and preserved. The characteristics of these colonies including morphology, color, size and edge morphology were observed and recorded. Transmission electron microscopy was employed to further observe their morphology and the Gram staining was performed. The bacterial 16S rDNA universal primer 27F/1492R and multiple gene loci were used for amplification. The sequencing result was compared by BLASTn analysis in the NCBI database and the reference sequences of the corresponding genera were downloaded. Then, a multi-gene joint phylogenetic tree was constructed using the maximum likelihood method on the website of GIPRES Science Gateway. Subsequently, the leaves of ‘Qiu Ji’ plum were inoculated with pathogenic bacteria by the stab inoculation of bacterial suspension, and then cultivated at 28 ℃ under high humidity. The disease occurrence of the leaves was regularly observed and recorded. Furthermore, the pathogenic bacteria were re-isolated from the disease-health junction of the leaves to complete the verification of the whole Koch’s postulates. The sensitivities of pathogenic bacteria to 0.15% tetramycin, 80% ethylicin, 3% benziothiazolinone, 1.8% octylamine, 3% zhongshengmycin and 6% kasugamycin were determined by the inhibition zone method, respectively.【Result】Based on morphological observation and molecular biology identification, the pathogenic bacteria were identified as Xanthomonas arboricola pv. pruni (Xap) (36.67%, 11 strains) and Pantoea vagans (63.33%, 19 strains). The sensitivity results demonstrated that the best inhibitory activities were achieved by 0.15% tetramycin and 80% ethylicin, with the EC50 of 0.15% tetramycin being 0.026 and 0.502 μg·mL-1 for Xap and P. vagans, respectively, and that of 80% ethylicin being 1.162 and 25.643 μg·mL-1, respectively. The second was 3% benziothiazolinone, and its EC50 values against Xap and P. vagans were correspondingly 5.200 and 96.075 μg·mL-1, followed by EC50 of 1.8% octylamine against Xap and P. vagans of 176.008, 273.072 μg·mL-1, and 3% zhongshengmycin against Xap and P. vagans of 621.697 and 72.270 μg·mL-1. As for 6% kasugamycin, it had an EC50 of 886.467 μg·mL-1 for P. vagans and was less effective in inhibiting Xap.【Conclusion】The pathogens causing plum bacterial shot hole in Liaoning were identified as Xap and P. vagans. Moreover, the 0.15% tetramycin and 80% ethylicin were screened and selected as exerting better inhibitory effects on these two pathogens. The results of the study will provide a theoretical basis for the precise prevention and control of plum bacterial shot hole in the field.

  • TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY
    ZHAOYao, CHENGQian, XUTianJun, LIUZheng, WANGRongHuan, ZHAOJiuRan, LUDaLei, LICongFeng
    Scientia Agricultura Sinica. 2025, 58(7): 1296-1310. https://doi.org/10.3864/j.issn.0578-1752.2025.07.004

    【Objective】Increasing planting density is a key agronomic strategy to enhance maize yield; however, excessive density may result in an imbalanced population structure, reduced utilization efficiency of limited resources (e.g., light), and suppressed yield potential. Gene editing can optimize canopy architecture through targeted improvement of maize plant type, thereby enhancing adaptability to high-density planting and boosting yield. Elucidating the effects of plant type improvement on root-shoot characteristics, grain yield, and density response in spring maize, as well as the underlying mechanisms, will provide theoretical and technical foundations for optimizing plant type and achieving high-yield dense planting in spring maize.【Method】The field experiment was conducted at Gongzhuling farm in Jilin, China. In this study, two maize hybrids, includding Jingke 968 and the improved plant types Jingke Y968, were grown with 60 000 plants/hm2 (D1), 75 000 plants/hm2 (D2) and 90 000 plants/hm2 (D3) in 2019 and 2020, respectively. The effects of two plant types of spring maize of the same genetic background on the root-canopy characteristics and yield of spring maize were studied.【Result】Under normal density conditions (D1), there were no significant differences in leaf area index (LAI), net photosynthetic rate (Pn), PAR utilization (PUE), dry matter accumulation and grain yield between the two different plant types spring maize cultivars. However, compared with Jingke 968, under D3 conditions, the improved plant type Jingke Y968 had a relatively high number of main roots (7.2%) and a relatively large weight of root dry matter (6.0%), which promoted the absorption of nutrients; furthermore, under D2 and D3 conditions, Jingke Y968 significantly improved the canopy structure of maize, so that the upper, middle and lower parts had relatively low leaf angles, higher leaf orientation and LAI, and the excellent canopy structure increased the Pn of mid-to-late ear leaves of (7.5% (D2) and 7.7% (D3)) and PUE (4.3% (D2) and 10.8% (D3)). The structural equation results showed that higher leaf direction values and LAI could positively and directly increase the accumulation of dry matter in the aboveground, thereby increasing grain yield (8.7% (D2) and 11.2% (D3)).【Conclusion】In summary, the improvement of plant type enabled Jingke Y968 to have higher main root number and larger root dry matter weight under high-density conditions, which was conducive to nutrient absorption in the underground part. Meanwhile, its leaves were more compact, Pn was significantly increased, PUE was effectively improved, and root-canopy characteristics were more reasonable, which promoted dry matter accumulation in the above-ground part. Thus, the relatively high grain yield could be obtained.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    SHIShunYu, YANGTao, PANGBo, LIJing, LINYiFeng, WANGZhengRui, FULinCheng, ABUDUBEKZalgamali, GAOWenWei, WUPengHao
    Scientia Agricultura Sinica. 2025, 58(10): 1878-1895. https://doi.org/10.3864/j.issn.0578-1752.2025.10.002

    【Objective】 Chlorophyll, as the core pigment of plant photosynthesis, directly affects the photosynthetic efficiency and yield of plants. By mining molecular markers and candidate genes related to chlorophyll in Sea-island cotton, we can provide a theoretical basis for the improvement of Sea-island cotton varieties. 【Method】 Using 203 sea-island cotton varieties as research objects, the chlorophyll content of sea-island cotton in three stages (budding stage, flowering stage, and boll stage) was measured in 4 environments (2 points in 2 years), and the chlorophyll content of sea-island cotton in 4 environments was measured. Correlation analysis was performed on the chlorophyll content, and the whole-genome resequencing data and the BLUP value of the chlorophyll content were used for genome-wide correlation analysis to screen candidate genes related to chlorophyll content. 【Result】 Descriptive statistics of chlorophyll content in the four environments showed that the chlorophyll content at bud stage, flowering stage and bell stage were normally distributed across years and locations, indicating that the trait is a quantitative trait controlled by multiple genes. Chlorophyll content varied significantly across growth periods and was significantly affected by environment, with correlation coefficients of 0.021-0.287 for chlorophyll content at bud stage, 0.017-0.180 at flowering stage and -0.118-0.212 at bell stage. GWAS research results screened out a total of 52 significant SNPs sites. Among them, 20, 20 and 12 significant SNP sites were screened in the bud stage, flowering stage and boll stage respectively, mainly distributed on chromosomes such as A05, A06, D05, D06 and D10. By annotating significant sites, a total of 80 candidate genes were annotated, including GB_A05G0103, GB_A05G0104, GB_A05G0105, GB_A05G0106, GB_A05G0107, GB_A05G0108, GB_A05G0109, GB_A05G0110, GB_A05G0111 and GB_A 05G0112 and other 10 genes are in type I (4 environments) The flowering stage and the flowering stage of type Ⅱ (two environments in northern Xinjiang) are all annotated. GB_A06G1512 and GB_A06G1513 are annotated in the flowering stage and boll stage of typeⅠand the flowering stage of typeⅡ. GB_D09G0836, GB_D09G0837 and GB_D09G0838 are annotated in the florescence and boll stage of typeⅠand typeⅡ. The flowering stages are all annotated. Nine genes related to chlorophyll content were identified through relative expression analysis. Among them, genes such as GB_A05G0097, GB_A05G0093 and GB_D05G0109 play important roles in chlorophyll metabolism, photosynthesis and plant stress resistance. 【Conclusion】 There are significant differences in the chlorophyll content of sea-island cotton at different growth stages, and are significantly affected by the environment. A total of 52 loci related to the chlorophyll content of sea-island cotton were detected, and nine genes were found to be candidate genes for chlorophyll in sea-island cotton.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    LUOZhengYing, HUXin, WUZhuanDi, QIANZhenFeng, TIANChunYan, LIUXinLong, LIFuSheng
    Scientia Agricultura Sinica. 2025, 58(5): 851-863. https://doi.org/10.3864/j.issn.0578-1752.2025.05.003

    【Objective】 Erianthus fulvus, serving as a crucial wild resource for sugarcane, is capable of enhancing the stress tolerance and yield of varieties. In order to utilize E. fulvus for sugarcane breeding, it is important to systematically identify and develop simple sequence repeat (SSR) loci in the E. fulvus genome, screen for polymorphic SSR markers, analyse the genetic diversity characteristics of E. fulvus resources and then develop SSR markers associated with important traits. 【Method】Using the SSRminer module in the software TBtools, a comprehensive exploration of SSR loci was conducted on the diploid E. fulvus whole genome sequence. The obtained data were statistically analyzed to reveal their distribution patterns and regularities within the genome. The Batch Target Region Primer Design function was employed for batch designing SSR primers, and the specificity of the primers was evaluated using the Primer check tool. To comparethe SSR polymorphism betweenE. fulvus and sugarcane, amplification experiments were performed on 50 pairs of randomly synthesized SSR primers and 14 pairs of SSR primers sourced from sugarcane across 6 E. fulvus germplasms. 【Result】A total of 152 707 SSR loci, which were distributed on E. fulvus genome with an average density of 5.64 kb/locus, were identified. The majority were located in intergenic regions. In terms of SSR type distribution, mononucleotide, dinucleotide, and trinucleotide had the highest density. Dinucleotide SSR types exhibited the greatest variation in motif repeat numbers, while pentanucleotide motif repeat variations were the least. Across the entire genome, 883 distinct SSR motif repeat types were identified, with A/T and AT/TA being the most abundant. A total of 144 692 pairs of SSR primers, of which 85 025 pairs exhibited high specificity, were designed. These specific primers displayed a distribution characteristic of dense ends and sparse middles on the genome. Amplification experiments showed that 42 out of the 50 randomly synthesized SSR primer pairs yielded stable and clear bands in E. fulvus, with 32 exhibiting polymorphisms, yielding a polymorphism rate of 64.0%. In contrast to the 14 sugarcane SSR primers, the E. fulvus SSR primers demonstrated superior amplification efficacy and greater polymorphism. After screening, 16 pairs of SSR primers with good polymorphism and clear amplification bands were determined from the 32 effective SSR primer pairs. These 16 pairs of primers amplified a total of 72 bands, with polymorphism information content (PIC) ranging from 0.63 to 0.83, and an average PIC value of 0.74, indicating their effectiveness and practicality in polymorphism analysis and molecular marker research of E. fulvus germplasm resources. 【Conclusion】This study comprehensively identified SSR loci in the E. fulvus genome, revealing the high abundance and diversity of SSR distribution features. Sixteen pairs of highly specific and polymorphic SSR primers were successfully screened.

  • TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY
    LIUJing, WANGHong, ZHANGLei, XIAOJiuJun, WUJianGao, GONGMingChong
    Scientia Agricultura Sinica. 2025, 58(2): 252-265. https://doi.org/10.3864/j.issn.0578-1752.2025.02.004

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

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    CUIMengJie, SUNZiQi, QIFeiYan, LIUHua, XUJing, DUPei, HUANGBingYan, DONGWenZhao, HANSuoYi, ZHANGXinYou
    Scientia Agricultura Sinica. 2025, 58(12): 2303-2315. https://doi.org/10.3864/j.issn.0578-1752.2025.12.003

    【Objective】Aflatoxin contamination is one of the important factors that hinders sustainable development of the peanut industry. Precise evaluation of germplasm resources from China and abroad for resistance to A. flavus infection and creation of new resistant germplasms will facilitate the development of resistant cultivars. 【Method】The A. flavus infection index of 322 peanut germplasm lines were characterized following in-vitro inoculation of seeds harvested from 3 different “environments” (CA2020, CS2020, CS2021). Aspergillus flavus strain As 3.4408, known for its strong infectivity and high toxin production, was used as the inoculation strain. The botanical type, plant type and nutritional quality of kernels were measured and analyzed. Accessions exhibiting resistance with novel traits were comprehensively evaluated and screened. 【Result】Thirteen accessions with stable resistance were identified, accounting for 4.04% of the total germplasm lines evaluated, most of which belonged to var. hypogaea, including two with stable and high resistance (C203 and C206), while no accession was observed to be immune to Aspergillus flavus infection. The frequency distribution of infection index of 322 accessions exhibited continuous variation, with the broad-sense heritability exceeding 0.8, indicating that the A. flavus-resistance of kernels was significantly influenced by genotypes and “environments”, and the phenotypic variation was primarily controlled by genetic factors. Correlation analysis revealed significant positive correlation of infection index of accessions among the different “environments” (P<0.001), and the phenotype of each accession harvested from various “environments” was relatively consistent. Additionally, no significant correlation was found between nutritional quality and infection index. Comparative analysis of infection index among peanut accessions of different botanical and plant types revealed that var. hypogaea/prostrate-type peanuts were more likely to exhibit resistance to A. flavus infection within the existing peanut germplasm resources. 【Conclusion】The phenotypes of peanut germplasms harvested from different “environments” in response to A. flavus infection were relatively stable. Variation of kernels resistance to A. flavus infection was primarily controlled by genotype. Accessions C203 and C206, exhibiting stable and high resistance, can serve as excellent resistant parents for the mining of aflatoxin resistance genes and for the improvement of peanut varieties resistant to aflatoxin contamination.

  • TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY
    WANGJiaXin, HUJingYi, ZHANGWei, WEIQian, WANGTao, WANGXiaoLin, ZHANGXiong, ZHANGPanPan
    Scientia Agricultura Sinica. 2025, 58(3): 460-477. https://doi.org/10.3864/j.issn.0578-1752.2025.03.005

    【Objective】This study explored the effects of different mulching methods on the production of photosynthetic substances and water use of maize under the intercropping mode of maize and soybean, aiming to determine the suitable mulching method for maize and soybean plantation in dryland agriculture in northern Shaanxi, so as to provide a basis for high-yield and efficient production of maize and soybean and ecological environment protection. 【Method】This study was conducted in irrigated land and nonirrigated land in 2022, using 'Zhonghuang 30' soybean and 'Xianyu 335' maize as materials. The two-factor complete randomized design was carried out, and the control group combined single crop (maize “M”, soybean “S”) and film mulching (bare land, interbrane “J”), and the test group combined intercropping crop (maize “M”, soybean “S”) and film mulching (bare land, interbrane “J” and whole film “Q”), with a total of 13 treatment groups. The characteristics changes of growth, photosynthesis, and water use efficiency of intercropped maize under different mulching methods were studied. 【Result】 (1) From jointing to silking stage, the growth space of intercropped maize was limited, resulting in a disadvantage in aboveground biomass of intercropped maize compared with monoculture. The biomass during the jointing stage of S/MQ, SQ/MJ, and SQ/MQ was 5.1%, 6.3%, and 1.7% higher than that of monoculture M, respectively; under intercropping, SJ/MJ maize plants had the fastest growth rate and a sharp increase in growth. SQ/MQ S/M, S/MJ, SQ/MJ, and SJ/M in dry land had a better promoting effect on the photosynthetic products of maize during the silking stage, and the aboveground biomass was 0.6%-105.9% higher than that of monoculture M. (2) To some extent, intercropping and mulching treatments improved the photosynthetic characteristics of maize, and the net photosynthetic rate (Pn) content of paddy maize. There was a certain degree of positive relationship between stomatal conductance (Gs), cellular CO2 concentration (Ci) and transpiration rate (Tr). The photosynthetic parameters of SQ/MJ and SJ/MQ were relatively high, while SJ/M and SQ/MQ were lower than non film coated S/M; there was a weak negative correlation between Pn and Ci in dryland maize, and the effect of maize mulching was not significant among different treatments. The Gs of intercropping treatment was 5.7% -38.1% lower than that of monoculture M, and Tr was also reduced by 5.6% -25.6%. Only the Pn of SJ/M and SQ/M, as well as the Ci of SQ/MJ and S/M, were higher than monoculture M. (3) The intercropping film mulching had a significant impact on water use efficiency (WUE). The WUE of the intercropping treatment was 41.1% -74.0% higher than that of monoculture M, among which SJ/M, S/M and S/MJ were relatively high; among all treatments in arid land, SQ/MJ had the highest WUE (19.04 kg∙mm-1∙hm-2), followed by SJ/MJ (17.07 kg∙mm-1∙hm-2), and the WUE of SJ/M and SQ/M was significantly lower than that of monoculture M by 26.7% and 20.6%, respectively. (4) Compared with monoculture M, intercropping S/MJ between irrigated land and dry land SJ/M and SJ/MJ maize increased yields by 76.8%, 73.0%, and 72.3%, respectively, while soybean yield reduction was relatively less among all intercropping treatments, demonstrating higher economic benefits; dry land intercropping SJ/MJ and SJ/MQ maize increased production by 17.1% and 23.5%, respectively, while economic benefits decreased by 17.5% and 22.8%, respectively. 【Conclusion】Compared with single cropping M, SJ/MJ model improved the photosynthetic performance, biomass, and yield of maize in irrigated land, and improved system economic benefit and promoted water use efficiency. In dry land, through the complementary effect and resource allocation in the intercropping system, it maintained maize yield and improved water use efficiency, but the increase of total input in agricultural materials reduced the economic feasibility. Therefore, in the dryland agriculture of Northern Shaanxi, the intercropping planting pattern of maize with degradable film and soybeans with degradable film was recommended for both irrigated land and moderately irrigated dry farm, aiming to enhance water use efficiency, increase production and profitability, and promote sustainable ecological agriculture development.