农学最新文献

{"title":"Analysis of structure and function of phage community occurring in the abnormal fermentation of vinegar mash through virome sequencing.","authors":"Jia-Wen Ma, Xin-le Liang","doi":"10.16288/j.yczz.24-226","DOIUrl":"https://doi.org/10.16288/j.yczz.24-226","url":null,"abstract":"<p><p>In order to investigate the cues, which cause abnormal fermentation during the traditional Zhejiang rosy rice vinegar production, here, the Illumina Novaseq sequencing platform is adopted to decipher the abnormal phage community organization, structure, and related function annotation. The results show that the dominant viral families from the abnormal and the normal fermentation vinegar mash are inconsistency on known taxonomic identification information. Population network analysis and PCA (principal component analysis) indicate that the composition and structure of phage communities differ significantly between abnormal and normal fermentation vinegar mash. Only 3.29% VCs (viral clusters) simultaneously contain vOTUs (viral operational taxonomic units) from both fermentation situation. The abnormal phageome displays high network heterogeneity and dominant phage species at the genus level. Accompanied by the widespread distribution of phage-derived hydrolases that target bacterial cell wall, the lower proportion of lysogenic phages contributes to the phages of abnormal fermentation vinegar mash more inclined to lyse the hosts. Furthermore, the predicted bacterial host community coupling with the aberrant phage community is quite different from that in the normal vinegar fermentation. In conclusion, the abnormal structure and function of the phage community constitutes one of the primary reasons for the failure of traditional rosy vinegar fermentation. Phageome research has opened up a new approach for analyzing the causes of abnormal fermentation in traditional fermented foods as well as for regulating and transforming microbial communities.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 4","pages":"489-498"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application and research of genomic optical mapping technology in disease diagnosis.","authors":"Jing Quan, Yan-Qun Xiao, Da-Ru Lu, Yun Bao","doi":"10.16288/j.yczz.24-192","DOIUrl":"https://doi.org/10.16288/j.yczz.24-192","url":null,"abstract":"<p><p>In the continuous progression of genomic research, an increasing number of investigations have revealed that structural variations (SVs) hold a vital role in human evolution and the pathogenesis of diseases. Consequently, SVs have attracted extensive attention within the realm of clinical research.In recent years, optical genome mapping (OGM), which represents a high-resolution, ultra-long-read, automated, non-sequencing genomic detection technique, has exhibited remarkable advantages in the exploration of structural variations. When compared with karyotyping, fluorescence <i>in situ</i> hybridization (FISH), chromosomal microarray analysis (CMA), and high-throughput sequencing technologies, OGM is capable of detecting structural and numerical aberrations throughout the entire genome in a single assay. These encompass aneuploidy, insertions, deletions, duplications, inversions, balanced translocations, and complex structural variations. With a detection resolution reaching as high as 500 bp, OGM is alternatively designated as the next-generation cytogenetic technology due to its high-resolution and long-fragment analysis capabilities. This endows it with substantial practical value in the detection of genomic structural variations. In this review, we comprehensively summarize the application of OGM methods in the detection of disease-related SVs, with the intention of providing valuable references and profound insights for SVs research, especially in the domain of disease diagnosis.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 4","pages":"428-436"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interactive effect of potassium and zinc application on oil yield of sunflower","authors":"Farid Hellal,&nbsp;Doaa Abou Basha,&nbsp;Saied El Sayed,&nbsp;Hanan Abdelkader","doi":"10.1016/j.ocsci.2025.03.001","DOIUrl":"10.1016/j.ocsci.2025.03.001","url":null,"abstract":"<div><div>Several initiatives have been made in Egypt to increase the overall production of oil crops, especially sunflower and to close the gap between edible oil production and demand. Field experiments were conducted during the main seasons of 2022 and 2023 ​at the agricultural research station of National Research Centre, Nubaria, Egypt to investigate the effects of potassium nitrate (0, 20, 40, 60 ​kg K₂O fed⁻¹) (fed ​= ​feddan ​= ​2.4 ​ha) and zinc sulfate (0, 25, 50, 75 ​ppm Zn) on growth, oil yield, nutrients components and chemical composition of sunflower. Results indicated that application of potassium nitrate has a promoted effect on chlorophyll content, growth parameters (Head weight, head diameter and 100 seed weight), protein content, oil yield as well as nutrient content under all applied levels. The data also showed that the highest significant increase occurred with the soil application of 40 ​kg fed⁻¹ potassium nitrate combined with 75 ​ppm Zn foliar spray. Meanwhile, the lowest values were obtained at the control treatment. Therefore, the current study detected that potassium soil addition at 40 ​kg K₂O fed⁻¹, besides foliar application with 75 ​ppm Zn are important to improve the growth, macro-micronutrient, seeds and oil productivity of sunflower crops. Oil yield and nutrient content exhibit a strong positive correlation, with a correlation coefficient of 0.903 for N, 0.94 for P, 0.962 for K and 0.966 for Zn. This indicates that a higher nutrient percentage is associated with higher oil content of sunflower. Study underscores the importance of comprehending the interplay between potassium and zinc treatments in sunflower plants to enhance growth, yield, and oil production effectively. Understanding these relationships can lead to optimized cultivation practices and improved outcomes in sunflower farming.</div></div>","PeriodicalId":34095,"journal":{"name":"Oil Crop Science","volume":"10 2","pages":"Pages 79-86"},"PeriodicalIF":0.0,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143907930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Local and systemic transcriptome and spliceome reprogramming induced by the root-knot nematode <i>Meloidogyne incognita</i> in tomato.","authors":"","doi":"10.1093/hr/uhaf056","DOIUrl":"https://doi.org/10.1093/hr/uhaf056","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/hr/uhae206.].</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"12 3","pages":"uhaf056"},"PeriodicalIF":7.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11890024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Potassium stimulates fruit sugar accumulation by increasing carbon flow in <i>Citrus sinensis</i>.","authors":"","doi":"10.1093/hr/uhaf057","DOIUrl":"10.1093/hr/uhaf057","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/hr/uhae240.].</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"12 3","pages":"uhaf057"},"PeriodicalIF":7.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11890026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An automatic method for estimating insect defoliation with visual highlights of consumed leaf tissue regions","authors":"Gabriel S. Vieira ,&nbsp;Afonso U. Fonseca ,&nbsp;Naiane Maria de Sousa ,&nbsp;Julio C. Ferreira ,&nbsp;Juliana Paula Felix ,&nbsp;Christian Dias Cabacinha ,&nbsp;Fabrizzio Soares","doi":"10.1016/j.inpa.2024.03.001","DOIUrl":"10.1016/j.inpa.2024.03.001","url":null,"abstract":"<div><div>As an essential component of the architecture of a plant, leaves are crucial to sustaining decision-making in cultivars and effectively support agricultural processes. When the leaf area is constantly monitored, a plant’s health and productive capacity can be assessed to foment proactive and reactive strategies. Because of that, one of the most critical tasks in agricultural processes is estimating foliar damage. In this sense, we present an automatic method to estimate leaf stress caused by insect herbivory, including damage in border regions. As a novelty, we present a method with well-defined processing steps suitable for numerical analysis and visual inspection of defoliation severity. We describe the proposed method and evaluate its performance concerning 12 different plant species. Experimental results show high assertiveness in estimating leaf area loss with a concordance correlation coefficient of 0.98 for grape, soybean, potato, and strawberry leaves. A classic pattern recognition approach, named template matching, is at the core of the method whose performance is compared to cutting-edge techniques. Results demonstrated that the method achieves foliar damage quantification with precision comparable to deep learning models. The code prepared by the authors is publicly available.</div></div>","PeriodicalId":53443,"journal":{"name":"Information Processing in Agriculture","volume":"12 1","pages":"Pages 40-53"},"PeriodicalIF":7.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140084130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A deep learning framework for prediction of crop yield in Australia under the impact of climate change","authors":"Haydar Demirhan","doi":"10.1016/j.inpa.2024.04.004","DOIUrl":"10.1016/j.inpa.2024.04.004","url":null,"abstract":"<div><div>Accurate prediction of crop yields is essential to ensure food security. In this study, a new deep neural networks framework is developed to predict crop yields in Australia, considering the impact of climate change, fertilizer use, and crop area. It is implemented for oats, corn, rice, and wheat crops, and its forecasting performance is benchmarked against five statistical and machine learning methods. All the software codes for the implementation of the proposed framework are freely available. The proposed framework shows the highest forecasting performance for all the considered crop types. It provides 23%, 38%, 39%, and 40% lower average mean absolute error than the benchmark methods for oat, corn, rice, and wheat crops, respectively. The reductions in average root mean squared error are 19%, 25%, 37%, and 29% over the benchmark methods. Then, it is used to predict yields of the considered crops in Australia towards 2025 under six different climate change scenarios. It is observed that although climate change has some boosting impact on crop yield, it is not sustainable to meet the demand. However, it is possible to keep crop yields rising while mitigating climate change.</div></div>","PeriodicalId":53443,"journal":{"name":"Information Processing in Agriculture","volume":"12 1","pages":"Pages 125-138"},"PeriodicalIF":7.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140761172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Technologies, Protocols, and applications of Internet of Things in greenhouse Farming: A survey of recent advances","authors":"Khalid M. Hosny ,&nbsp;Walaa M. El-Hady ,&nbsp;Farid M. Samy","doi":"10.1016/j.inpa.2024.04.002","DOIUrl":"10.1016/j.inpa.2024.04.002","url":null,"abstract":"<div><div>Greenhouse farming is considered one of the precision and sustainable forms of smart agriculture. Although greenhouse gases can support off-season crops inside the indoor environment, monitoring, controlling, and managing crop parameters at greenhouse farms more precisely and securely is necessary, even in harsh climate regions. The evolving Internet of Things (IoT) technologies, including smart sensors, devices, network topologies, big data analytics, and intelligent decision-making, are thought to be the solution for automating greenhouse farming parameters like internal atmosphere control, irrigation control, crop growth monitoring, and so on. This paper introduces a comprehensive survey of recent advances in IoT-based greenhouse farming. We summarize the related review articles. The classification of greenhouse farming based on IoT (smart greenhouse, hydroponics greenhouse, and vertical farming) is introduced. Also, we present a detailed architecture for the components of greenhouse agriculture applications based on IoT, including physical devices, communication protocols, and cloud/fog computing technologies. We also present a classification of IoT applications of greenhouse farming, including monitoring, controlling, tracking, and predicting. Furthermore, we present the technical and resource management challenges for optimal greenhouse farming. Moreover, countries already applying IoT in greenhouse farming have been presented. Lastly, future suggestions related to IoT-based greenhouse farming have been introduced.</div></div>","PeriodicalId":53443,"journal":{"name":"Information Processing in Agriculture","volume":"12 1","pages":"Pages 91-111"},"PeriodicalIF":7.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140773497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A reliable, simple and cost-efficient UPLC-vwd method for simultaneously determining tocopherol and tocotrienol in peanut seeds","authors":"Zekai Tian ,&nbsp;Yue Zhang ,&nbsp;Chenshuo Sun ,&nbsp;Liying Yan ,&nbsp;Yanping Kang ,&nbsp;Dongxin Huai ,&nbsp;Yuning Chen ,&nbsp;Xin Wang ,&nbsp;Qianqian Wang ,&nbsp;Huifang Jiang ,&nbsp;Boshou Liao ,&nbsp;Zhihui Wang ,&nbsp;Yong Lei","doi":"10.1016/j.ocsci.2025.02.002","DOIUrl":"10.1016/j.ocsci.2025.02.002","url":null,"abstract":"<div><div>Vitamin E is an essential micronutrient that is abundant in peanut seeds. However, the absence of a rapid and reliable method for determining its content has impeded advancements in peanut quality improvement. In this study, we developed an efficient ultra-performance liquid chromatography variable wavelength detector (UPLC-vwd) method for quantifying vitamin E content in peanut seeds, capable of detecting four tocopherols and four tocotrienols. Compared to traditional methods, this approach is simpler, more efficient, and highly accurate. By comparing two sample preparation techniques, it was found that slicing better reflects the true vitamin E content than grinding, as it minimizes losses caused by mechanical pressure. The method demonstrated robust stability and accuracy in both repeatability tests and spiked recovery tests, showing no significant differences compared to the national standard method. The study revealed that the cotyledons of peanuts are the primary storage site for vitamin E, being rich in γ- and α-tocopherols, which together account for over 90°% of the total vitamin E content. In contrast, the vitamin E content in the seed coat is considerably lower. Therefore, the optimized detection method minimizes seed coat interference during sample preparation, ensuring the accuracy of the results. In summary, the UPLC-vwd method developed in this study is a promising tool for determining vitamin E content and supports the improvement of peanut quality.</div></div>","PeriodicalId":34095,"journal":{"name":"Oil Crop Science","volume":"10 1","pages":"Pages 70-78"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143760507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression analysis of cytochrome P450 gene family in Macrobrachium nipponense","authors":"Xiao Wu ,&nbsp;Zheyan Chen ,&nbsp;Yaoran Fan ,&nbsp;Jianbin Feng ,&nbsp;Jiale Li","doi":"10.1016/j.aaf.2023.12.004","DOIUrl":"10.1016/j.aaf.2023.12.004","url":null,"abstract":"<div><div>Cytochrome P450 (CYP450) is a superfamily widely found in various biological organisms, including animals, plants, and microorganisms. CYP450 is involved in the metabolism of endogenous and exogenous substances. In addition, a few CYP450 genes named as Halloween genes (CYP302a1, CYP307a1, etc.) are associated with the synthesis and secretion of ecdysone in Arthropods. <em>Macrobrachium nipponense</em> (Arthropoda, Crustacean) has many excellent breeding characteristics; for example, rapid growth rate, ability to survive in a variety of environments and high economic value. In order to further explored the structure and function of CYP450, a genome-wide analysis of CYP450 gene family was performed in <em>M. nipponense</em>. A total of 67 CYP450 genes were identified, and extensive bioinformatic analysis methods were conducted, including physicochemical property, sequence alignment, evolutionary tree construction, conserved sequence, chromosome localization, protein-protein interactions, and quantitative expression. The results showed that most CYP450 genes being around 500 amino acids, with 25 tandem repeats genes. The majority of CYP450 genes have the signature structure of the CYP450 gene family to ensure the stability of the spatial structure and the ability to bind substrates. The Halloween genes and CYP18a1 sequences are similar and occupy an importance role in <em>M. nipponense</em>. Finally, most CYP450 genes were up-regulated in gill and hepatopancreas of <em>M. nipponense</em> under acute high temperature stress, with significant up-regulation of Halloween gene expression. This study could further deepen the understanding of the structure and function of CYP450 in <em>M. nipponense</em> and investigate the role of CYP450 in freshwater crustaceans under high temperatures.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"10 2","pages":"Pages 228-237"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143715786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}