农学最新文献

{"title":"Enhancing single-cell classification accuracy using image conversion and deep learning.","authors":"Bingxi Gao, Huaxuan Wu, Zhiqiang Du","doi":"10.16288/j.yczz.24-213","DOIUrl":"https://doi.org/10.16288/j.yczz.24-213","url":null,"abstract":"<p><p>Single-cell transcriptome sequencing (scRNA-seq) is widely used in the fields of animal and plant developmental biology and important trait analysis by obtaining single-cell transcript abundance data in high throughput, which can deeply reveal cell types, subtype composition, specific gene markers and functional differences. However, scRNA-seq data are often accompanied by problems such as high noise, high dimensionality and batch effect, resulting in a large number of low-expressed genes and variants, which seriously affect the accuracy and reliability of data analysis. This not only increases the complexity of data processing, but also limits the effectiveness of feature selection and downstream analysis. Although several statistical inference and machine learning methods have been used to address these challenges, the existing methods still have limitations in cell type identification, feature selection, and batch effect correction, which are difficult to meet the needs of complex biological research. In this study, we proposes an innovative single-cell classification method, scIC (single-cell image classification), which converts scRNA-seq data into image form and combines it with deep learning techniques for cell classification. Through this image conversion, we are able to capture complex patterns in the data more efficiently, and then construct efficient classification models using convolutional neural networks (CNN) and residual networks (ResNet). After testing scRNA-seq data from four cell types (mouse skin basal cells, mouse lymphocytes, human neuronal cells, and mouse spinal cord cells), the accuracy of the classification models exceeded 94%, with the mouse skin basal cell dataset achieving a classification accuracy of 99.8% when using the ResNet50 model. These results indicate that image transformation of scRNA-seq data and combining it with deep learning techniques can significantly improve the classification accuracy, providing new ideas and effective tools for solving key challenges in single-cell data analysis. The code for this study is publicly available at: https://github.com/Bingxi-Gao/SCImageClassify.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 3","pages":"382-392"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606515","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":"Thinking and practices of new methods for breeding wheat with improved nutrient use efficiency.","authors":"Yiping Tong, Wan Teng, Hongqing Ling, Aimin Zhang","doi":"10.16288/j.yczz.25-006","DOIUrl":"https://doi.org/10.16288/j.yczz.25-006","url":null,"abstract":"<p><p>In the early 1990s, based on China's basic national conditions, Li Zhensheng put forward the concept of sustainable agricultural development that took the path of resource-conserving and high-yield agriculture. He carried out breeding explorations on the efficient use of mineral nutrients by crops and pioneered a new direction for wheat breeding with the goals of \"less input, more output, environmental protection, and sustainable development\", mainly focusing on improving the absorption and utilization efficiency of phosphorus and nitrogen. He has led and greatly promoted \"the Second Green Revolution\" in China's agriculture. In September 2024, Academician Li Zhensheng was awarded the \"Medal of the Republic\". This review summarizes Academician Li Zhensheng's strategic considerations in advocating the new direction of breeding and how he arranged to conduct research on the physiological and genetic basis of phosphorus efficient use in wheat. By doing so, we pay tribute to the outstanding work done by Academician Li Zhensheng in the research field of nutrient-efficient use by crops, and it is expected to further demonstrate Li Zhensheng's academic approaches and spirit so as to provide references for those who come after him.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 3","pages":"300-307"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606559","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":"Differential transcriptome profiling of <i>Bartonella</i> spp. influenced by the species divergence factors.","authors":"Min Chen, Na Han, Yu Miao, Yujun Qiang, Wen Zhang, Pengbo Liu, Qiyong Liu, Dongmei Li","doi":"10.16288/j.yczz.24-201","DOIUrl":"https://doi.org/10.16288/j.yczz.24-201","url":null,"abstract":"<p><p>To reveal the differences in transcript levels of <i>Bartonella</i> spp. from different species and hosts and their impacts on phylogenetic relationships, we focus on 27 strains from four <i>Bartonella</i> species (<i>B. henselae</i>, <i>B. koehlerae</i>, <i>B. clarridgeiae</i> and <i>B. quintana</i>) and three hosts (<i>Felis catus</i>, <i>Homo sapiens</i> and <i>Macaca mulatta</i>) to conduct the transcriptome sequencing using Illumina high-throughput sequencing technology. Gene expression differences between strains from different species and hosts are analyzed, and the results of phylogenetic analysis at the transcriptome and genome levels are compared. The results show significant differences in gene transcription between strains from different species and hosts. Twelve genes are screened, including <i>virB10</i>, <i>bepC</i> and <i>virB4</i>, which may facilitate host-specific recognition. Furthermore, phylogenetic analysis based on SNPs within the core genes of the transcriptome demonstrate species-specific clustering patterns among strains. Further analysis indicate that host factors influence the genetic divergence of strains, while geographic factors exert a small impact on this process. These findings are congruent with the phylogenetic analysis of SNPs in the core genes of the genome. Our study uses differential transcriptome analysis to reveal the genetic divergence and phylogenetic relationships of <i>Bartonella</i> species. And the observed regular differences between strains from different species and hosts are found to correspond with the results of traditional genome analysis. Thus, our results indicate the utility of transcriptome data in efficiently investigating the genetic divergence between species.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 3","pages":"366-381"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606514","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":"Mining and analysis of key genes related to rice seed longevity in NJ9108 based on transcriptomics.","authors":"Chaofei Han, Ling Chen, Yuanxiu Wang, Qian Cheng, Sheng Zuo, Huabin Liu, Chengliang Wang","doi":"10.16288/j.yczz.24-243","DOIUrl":"https://doi.org/10.16288/j.yczz.24-243","url":null,"abstract":"<p><p>Seed longevity is the period over which seeds remain viable and capable of gemination, and is an important trait of seed quality. Longevity changes in seed directly affect the germination rate, seedling morphology, and storage time. Therefore, the identification of seed longevity genes has significant value for cultivating seeds that are storage-resistant and have long lifespan. The study found that NJ9108 seeds are a type of rice that is resistant to aging; Using transcriptomic technology, the annotated genes were subjected to mfuzz fuzzy clustering and divided into 6 subtypes, with a total of 8,384 genes upregulated/downregulated by aging induction. These differentially expressed genes are enriched into biological processes (BP), cellular components (CC), and molecular functions (MF), with 42 genes enriched in phenylpropanoid biosynthesis, 31 genes enriched in sugar signaling, and 42 genes enriched in plant hormone signaling pathways. They are the most important pathways involved in the aging resistance process of NJ9108. qRT-PCR results showed that compared with <i>ZH11</i>, <i>4CL5</i>, <i>CAD5</i>, <i>PRX3</i> and <i>PRX86</i> in the phenylpropanoid biosynthesis pathway were significantly upregulated in NJ9108 after aging; <i>BGLU18</i>, <i>BGLU22</i> and <i>TPP3</i> in the sugar signaling pathway were significantly upregulated in NJ9108; <i>RR12</i> and <i>SAPK5</i> involved in the plant hormone signaling pathway were significantly upregulated after aging, while <i>IAA12</i> and <i>IAA20</i> were significantly downregulated in NJ9108 seeds. The expression trends of these genes are consistent with transcriptomic results, suggesting that these genes regulating rice seed longevity. <i>BGLU18</i>, <i>BGLU22</i>, <i>OsRR12</i>, and <i>TPP3</i>, as the new identified seed longevity genes, can be further studied in the future. Above all, the experimental results provide a theoretical basis for understanding the regulatory network of rice seed longevity and for breeding rice varieties that are resistant to aging.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 3","pages":"351-365"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606552","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":"Environmental life cycle assessment and potential improvement measures in the shrimp and prawn aquaculture sector: A literature review","authors":"Mayra L. Pazmiño ,&nbsp;Leticia Chico-Santamarta ,&nbsp;Andrea Boero ,&nbsp;Angel D. Ramirez","doi":"10.1016/j.aaf.2024.06.003","DOIUrl":"10.1016/j.aaf.2024.06.003","url":null,"abstract":"<div><div>The shrimp and prawn aquaculture sector is a growing component of the global food supply. However, this ongoing growth can lead to environmental implications. Life Cycle Assessment (LCA) enables the assessment of these consequences by providing environmental information about the entire value chain. Furthermore, LCA highlights the improvements in environmental performance. This study aims to analyze the literature on LCA of shrimp production at different locations to assess methodological approaches such as functional unit and system boundaries, inventory data collection, impact categories evaluated, and main findings. A literature review in Scopus databases is performed to achieve this aim. Among the reviewed studies, it is observed that the scope of most of them encompasses everything from hatchery to farm gate. Some cases include packaging and transport to the point of destination. The consumption and waste treatment stages have been included in only two cases. The most analyzed impact categories are climate change, eutrophication, and acidification. The critical spots identified are feed formulation and farm energy use. The shrimp aquaculture sector could enhance its environmental performance by incorporating raw materials that replace the consumption of fishmeal and soybean meal in feeds with more sustainable alternatives. The adequate adjustment of the feed conversion ratio could support mitigating the amount of sediment and unconsumed feed, thereby reducing nutrient concentration in discharges. Renewable energy sources could be employed to cover the on-farm demands.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"10 2","pages":"Pages 183-201"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141707790","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":"Improvement of oilseed Brassica crops by Trichoderma use: Gene transfer and direct interaction","authors":"Tamara Sánchez-Gómez,&nbsp;Jorge Martín-García,&nbsp;Óscar Santamaría,&nbsp;Jorge Poveda","doi":"10.1016/j.ocsci.2025.02.001","DOIUrl":"10.1016/j.ocsci.2025.02.001","url":null,"abstract":"<div><div>Global agriculture must urgently adopt a new approach to ensure adequate food production for the increasing population in the current context of adverse conditions, while prioritizing environmental sustainability. This change requires innovative and environmentally conscious methods, such as symbiotic-microorganisms-based products. Among these organisms, the genus <em>Trichoderma</em> stands out, as these fungal endophytes reside within many plant species including those in the Brassicaceae family and interact with them positively. Brassicaceae encompass numerous taxa of special agricultural and food interest, such as those known as oilseed brassicas (OSBs). Among these group are crops for obtaining canola and mustard seeds, commonly used for oil and spices production, respectively. OSBs are of greater interest for food because they are rich source of vitamins and minerals, and have also a great antimicrobial, antioxidant and antitumor potential application. Therefore, the improvement of these plant species (or of their cultivation methods) may ultimately lead to an improvement in human food and, accordingly, human health. This progress could go hand in hand with the <em>Trichoderma</em> fungal genus, either based on transgenesis with some of their genes, or using these fungi to formulate and produce bioinoculants. In relation to transgenesis, the most widely studied are those based on <em>Trichoderma</em> genes encoding endochitinases and Kelch-like family proteins, in both cases to achieve an antifungal effect against pathogenic fungi. With regard to <em>Trichoderma</em>-based products, these can be aimed at promoting plant growth, protecting crops against pathogens by acting as biological control agents (BCAs), or even reducing contaminants in the soil, such as heavy metals. The purpose of the present literature review is to analyse and discuss most of the existing studies to date on the interaction between OSB crops and <em>Trichoderma</em> fungi.</div></div>","PeriodicalId":34095,"journal":{"name":"Oil Crop Science","volume":"10 1","pages":"Pages 51-63"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143682333","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":"Broadening the gene base of peanut breeding using incompatible wild species","authors":"Chunjiao Jiang,&nbsp;Jiakai Li,&nbsp;Haojie Sun,&nbsp;Zhiwei Wang,&nbsp;Zhen Yang,&nbsp;Chuantang Wang","doi":"10.1016/j.ocsci.2024.11.004","DOIUrl":"10.1016/j.ocsci.2024.11.004","url":null,"abstract":"<div><div>The cultivated peanut (<em>Arachis hypogaea</em> L.) is a significant edible oilseed crop. Although substantial progress has been made in breeding new peanut varieties through conventional methods, the narrow gene base of the cultivated peanut (stemming from six evolutionary bottlenecks) poses growing challenges for developing breakthrough varieties via intraspecific hybridization alone. Consequently, extensive efforts have been directed towards the utilization of incompatible wild <em>Arachis</em> species. In this study, we present the first genetic diversity assessment of 30 progenies derived from intersectional crosses between the high-oleic peanut cultivar Huayu 665 and two wild species, <em>A. paraguariensis</em> and <em>A. appresipilla</em>, alongside 32 cultivated materials and 29 wild accessions, using transposon element markers. The hybrids demonstrated greater genetic diversity than the cultivars, expanding the gene base for peanut breeding. Hybrid progenies with enhanced insect pest resistance and elevated levels of both oleic acid and oil/protein content were tentatively obtained. This work lays the groundwork for the future development of high-yielding, high-quality peanut varieties through the utilization of crop wild relatives.</div></div>","PeriodicalId":34095,"journal":{"name":"Oil Crop Science","volume":"10 1","pages":"Pages 44-50"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143682334","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":"Characterization of gill transcriptome, SSR/SNP markers and expression analysis of lysozyme LysC gene from Carassius auratus upon Aeromonas hydrophila infection","authors":"Meijuan Shi ,&nbsp;Xiucai Hu ,&nbsp;Rongrong Liu ,&nbsp;Yanjing Yang,&nbsp;Aijun Lv","doi":"10.1016/j.aaf.2023.08.011","DOIUrl":"10.1016/j.aaf.2023.08.011","url":null,"abstract":"<div><div>The gills are large mucosal surfaces and play primary roles in respiration and immune defences. However, the molecular mechanism for gills of fish needs still to be explored. In the present study, transcriptomic analysis and identification of SSR and SNP markers were performed in the gills of crucian carp <em>Carassius auratus</em>. The results showed a total of 84,259 unigenes were annotated to NCBI NR, KEGG and GO databases for 55,283, 39,303, 33,388, respectively. Enriched KEGG pathway analyses for the identified genes showed the mainly functional modules such as metabolism, cellular processes, environmental adaptation, genetic processing, organismal and immune systems. Moreover, 22,102 SSRs (simple sequence repeats) were potentially identified and 9776 (44.2%) were accounted for the most dinucleotides. Transition and transversion sites of SNPs (single nucleotide polymorphisms) were also observed. Tissue distribution showed that the expression level of lysozyme <em>LysC</em> gene was relatively high in intestine, liver, spleen and kidney tissues and up-regulated in gills, skin and brain after the <em>A. hydrophila</em> infection. We discovered the immune-related pathways through the transcriptome analysis in the gills of crucian carp, some potential SSR/SNP markers were identified, and lysozyme gene predominantly expressed in mucosal immune organs (eg., gills, skin, intestine) responded to <em>A. hydrophila</em> infection. To the best of our knowledge, this was the detailed report on the molecular characteristics in crucian carp gills with transcriptome analysis, which will not only provide a scientific reference for further understanding the local defense mechanism, but also lay a foundation for molecular marker-assisted breeding in fish.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"10 2","pages":"Pages 219-227"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134962148","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":"Protein requirements in Nile tilapia (Oreochromis niloticus) during production and reproduction phases","authors":"Fabio Meurer ,&nbsp;Jailson Novodworski ,&nbsp;Robie Allan Bombardelli","doi":"10.1016/j.aaf.2024.03.004","DOIUrl":"10.1016/j.aaf.2024.03.004","url":null,"abstract":"<div><div>The accelerated growth of global aquaculture has boosted the production chain of Nile tilapia (<em>Oreochromis niloticus</em>), currently the third most cultivated species worldwide. This fish plays a crucial role in global food security. Protein is the main fish diet nutrient, and its quality, as well as protein level variations, directly and significantly affect the productive chain of this species. In this study, we conducted a comprehensive review of protein requirements at different tilapia development stages, underscoring the fundamental importance of a balanced diet to promote efficient growth. The study identified protein requirement variations based on weight, age, and different tilapia farming systems. In addition, the challenges associated with formulating balanced diets are discussed, especially in the face of the scarcity of traditional protein sources, such as fishmeal. Several factors are considered in this review, including tilapia development stage, rearing system, stocking density, ingredient quality, specific tilapia nutritional requirements and strains, feed management, temperature, and water quality. A gradual decrease in protein requirements is observed as fish grow and reach a minimum point during the growth phase, followed by a slight increase during the subsequent fattening phase. Tilapia protein requirements are influenced by various factors, including growth phase and farming system characteristics. Identifying the ideal protein levels at each stage is crucial for guiding sustainable tilapia aquaculture practices and enhancing the overall production efficiency of the species.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"10 2","pages":"Pages 171-182"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140794975","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":"Improving crop image recognition performance using pseudolabels","authors":"Pengfei Deng,&nbsp;Zhaohui Jiang,&nbsp;Huimin Ma,&nbsp;Yuan Rao,&nbsp;Wu Zhang","doi":"10.1016/j.inpa.2024.02.001","DOIUrl":"10.1016/j.inpa.2024.02.001","url":null,"abstract":"<div><div>In crop image recognition, when faced with a large quantity of unlabeled data, the traditional manual labeling method requires a large amount of human and material resources. To solve this problem, this study proposes an image recognition method based on a pseudolabeling technique. First, the data are divided into labeled and unlabeled data. The initial network model is trained on labeled data. Then, pseudolabeling of the unlabeled data is predicted, and only the data that satisfy the confidence threshold are regarded as valid pseudolabeling. To convert the unlabeled data into supervised training data, the two types of data are mixed. The training is terminated when the number of remaining unlabeled data satisfies the end condition and when the fivefold cross-validation method is used to evaluate model performance. Compared with the traditional semisupervised method, the experimental method is simpler and more applicable. Experiments were conducted on rice growth stage recognition and crop weed seedling recognition tasks. The results showed that the proposed method achieved 99.17% accuracy in rice growth stage recognition and a high AUC value of 99.93% in crop weed seedling recognition, which demonstrated excellent performance. Compared with the traditional model, this method not only improves in accuracy but also has better stability and wider applicability and is expected to provide an efficient, accurate and scalable solution for crop image recognition.</div></div>","PeriodicalId":53443,"journal":{"name":"Information Processing in Agriculture","volume":"12 1","pages":"Pages 17-26"},"PeriodicalIF":7.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143534657","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}