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PlantCaFo:An efficient few-shot plant disease recognition method based on foundation models

植物表型组学（英文） 2025年第1期7卷 248-259页

作者： Xue Jiang Jiashi Wang Kai Xie Chenxi Cui Aobo Du Xianglong Shi Wanneng Yang Ruifang Zhai College of Informatics Huazhong Agricultural UniversityWuhan 430070PR China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhan 430070PR China College of Informatics Huazhong Agricultural UniversityWuhan 430070PR China Engineering Research Center of Intelligent Technology for Agriculture Ministry of EducationHuazhong Agricultural UniversityWuhan 430070PR China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070PR China

Although plant disease recognition is highly important in agricultural production,traditional methods face challenges due to the high costs associated with data collection and the scarcity of ***-shot plant disease identification tasks,which are based on transfer learning,can learn feature representations from a small amount of data;however,most of these methods require pretraining within the relevant ***,foundation models have demonstrated excellent performance in zero-shot and few-shot learning *** this study,we explore the potential of foundation models in plant disease recognition by proposing an efficient few-shot plant disease recognition model(PlantCaFo)based on foundation *** model operates on an end-to-end network structure,integrating prior knowledge from multiple pretraining ***,we design a lightweight dilated contextual adapter(DCon-Adapter)to learn new knowledge from training data and use a weight decomposition matrix(WDM)to update the text *** test the proposed model on a public dataset,PlantVillage,and show that the model achieves an accuracy of 93.53％in a"38-way 16-shot"*** addition,we conduct experiments on images collected from natural environments(Cassava dataset),achieving an accuracy improvement of 6.80％over the *** validate the model's generalization performance,we prepare an out-of-distribution dataset with 21 categories,and our model notably increases the accuracy of this *** experiments demonstrate that our model exhibits superior performance over other models in few-shot plant disease identification.

关键词： Plant disease recognition Few-shot learning Foundation models Efficient funning

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A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification

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Plant Communications 2024年第2期5卷 261-278页

作者： Ning Guo Shenyun Wang Tianyi Wang Mengmeng Duan Mei Zong Liming Miao Shuo Han Guixiang Wang Xin Liu Deshuang Zhang Chengzhi Jiao Hongwei Xu Liyang Chen Zhangjun Fei Jianbin Li Fan Liu State Key Laboratory of Vegetable Biobreeding National Engineering Research Center for VegetablesBeijing Key Laboratory of Vegetable Germplasm ImprovementKey Laboratory of Biology and Genetics Improvement of Horticultural Crops(North China)Beijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijing 100097China Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Vegetable Research InstituteJiangsu Academy of Agricultural ScienceNanjingJiangsuChina Smartgenomics Technology Institute Tianjin 301700China Boyce Thompson Institute IthacaNYUSA

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ *** we report a graph-based pan-genome of *** constructed from high-quality genome assemblies of different *** pan-genome harbors over 200 structural variant hotspot regions enriched in auxin-andflowering-related *** genomic analyses revealed that early domestication of *** focused on leaf or stem *** resulting from agricultural practices and variety improvement were detected among different ***-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAV-ATA3/ESR-RELATED family gene as crucial players in leaf–stem differentiation during the early stage of *** domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels *** pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization andflowering characteristics among different morphotypes,and variations in thefirst intron of BoFLC3 are involved infine-tuning theflowering process in *** study provides a comprehensive understanding of the pan-genome of *** and sheds light on the domestication and differential organ development of this globally important crop species.

关键词： Brassica oleracea graph-based pan-genome structural variants SV domestication morphotype diversification

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AutoGP:An intelligent breeding platform for enhancing maize genomic selection

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Plant Communications 2025年第4期6卷 20-29页

作者： Hao Wu Rui Han Liang Zhao Mengyao Liu Hong Chen Weifu Li Lin Li College of Informatics Huazhong Agricultural UniversityWuhan 430070China Engineering Research Center of Intelligent Technology for Agriculture Ministry of EducationWuhanChina National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Hubei Hongshan Laboratory HubeiChina

In the face of climate change and the growing global population,there is an urgent need to accelerate the development of high-yielding crop *** this end,vast amounts of genotype-to-phenotype data have been collected,and many machine learning(ML)models have been developed to predict phenotype from a given ***,the requirement for high densities of single-nucleotide polymorphisms(SNPs)and the labor-intensive collection of phenotypic data are hampering the use of these models to advance ***,recently developed genomic selection(GS)models,such as deep learning(DL),are complicated and inconvenient for breeders to navigate and optimize within their breeding ***,we present the development of an intelligent breeding platform named AutoGP(http://***),which integrates genotype extraction,phenotypic extraction,and GS models of genotype-to-phenotype data within a user-friendly web *** has three main advantages over previously developed platforms:1)an efficient sequencing chip to identify high-quality,high-confidence SNPs throughout gene-regulatory networks;2)a complete workflow for extraction of plant phenotypes(such as plant height and leaf count)from smartphone-captured video;and 3)a broad model pool,enabling users to select from five ML models(support vector machine,extreme gradient boosting,gradient-boosted de-cision tree,multilayer perceptron,and random forest)and four commonly used DL models(deep learning genomic selection,deep learning genomic-wide association study,deep neural network for genomic pre-diction,and SoyDNGP).For the convenience of breeders,we use datasets from the maize(Zea mays)com-plete-diallel design plus unbalanced breeding-like inter-cross population as a case study to demonstrate the usefulness of *** show that our genotype chips can effectively extract high-quality SNPs asso-ciated with days to tasseling and plant *** models show reliable predictive accuracy on di

关键词： smart breeding genomic selection phenotypic extraction deep learning maize breeding platform

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Characterization of mulberry leaf instant tea and evaluation of its hypolipidemia effect via regulation of intestinal microbiota

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Food Science and Human Wellness 2024年第3期13卷 1348-1357页

作者： Xiaoyun Han Yunlong Bai Xiaoxin Feng Baochang Du Baojiang Zheng Qingshen Sun Engineering Research Center of Agricultural Microbiology Technology Ministry of Education&Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold RegionKey Laboratory of Molecular Biology&Key Laboratory of MicrobiologyCollege of Heilongjiang Province&School of Life SciencesHeilongjiang UniversityHarbin 150080China Gannan Forest Farm Qiqihaer 162100China College of Life Sciences Northeast Forestry UniversityHarbin 150040China

The purpose of this study was to characterize mulberry leaf instant tea(MLIT)powder prepared from the'Longsang No.1'(Morus abla *** 1)mulberry leaves in Heilongjiang Province(China)and assess its obesity-preventing/relieving effects.A total of 174 compounds including quercetin,chlorogenic acid,1-deoxyecomycin(1-DNJ)related to antihyperlipidemia effects were identified from the MLIT *** treatment reversed the Lee's index,fat coefficient,and serum biochemical parameters in both the obesity relieving and obesity preventing mice fed with high-fat *** the obesity relieving experiment,the relative abundance of Desulfovibrio in mouse feces decreased after both 0.5%and 1%MLIT *** obesity preventing experiments,mouse with different amount of MLIT treatments showed increased relative abundance of Akkermansia,Bifidobacterium and Lactobacillus,while Deferribacteres,Desulfobacterota *** beneficial bacteria in the intestinal tract of mice treated with MLIT *** study proved that MLIT had antihyperlipidemia potential via modulating intestinal microbiota in mice.

关键词： Mulberry leaf instant tea Liquid chromatography-mass spectrometry(LC-MS) Antihyperlipidemia Intestinal microbiota

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Universal chimeric Fcγreceptor T cells with appropriate affinity for IgG1 antibody exhibit optimal antitumor efficacy

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Acta Pharmaceutica Sinica B 2023年第5期13卷 2071-2085页

作者： Wen Zhu Yang Wang Liangyin Lv Hui Wang Wenqiang Shi Zexin Liu Mingzhe Zhou Jianwei Zhu Huili Lu Engineering Research Center of Cell and Therapeutic Antibody Ministry of EducationSchool of PharmacyShanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Genetic Engineering School of Life ScienceFudan UniversityShanghai 200433China

Developing universal CARs with improved flexible targeting and controllable activities is urgently *** several studies have suggested the potential of CD16a in tandem with monoclonal antibodies to construct universal CAR-T cells,the weak affinity between them is one of the limiting factors for ***,we systematically investigated the impact of Fcγreceptor(FcγR)affinity on CAR-T cells properties by constructing universal CARs using Fcγreceptors with different affinities for IgG1 antibodies,namely CD16a,CD32a,and *** demonstrated that the activities of these universal CAR-T cells on tumor cells could be redirected and regulated by IgG1 *** xenografted mice,64CAR chimeric Jurkat cells with the highest affinity showed significant antitumor effects in combination with herceptin in the HER2 low expression U251 MG ***,in the CD20 high expression Raji model,64CAR caused excessive activation of CAR-T cells,which resulted in cytokine release syndrome(CRS)and the decline of antitumor activity,and 32CAR with a moderate affinity brought the best *** work extended the knowledge about FcγR-based universal CAR-T cells and suggested that only the FcγRCAR with an appropriate affinity can offer the optimal antitumor advantages of CAR-T cells.

关键词： Universal CAR-T cells Fcγreceptor CD16a CD32a CD64 Affinity IgG1 antibody CRS

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PCMD:A multilevel comparison database of intraand cross-species metabolic profiling in 530 plant species

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Plant Communications 2024年第10期5卷 33-44页

作者： Yue Hu Yao Ruan Xin-Le Zhao Feng Jiang Dongxu Liu Qiang Zhu Qing-Ye Zhang Qing-Yong Yang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070HubeiChina Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Yazhouwan National Laboratory Sanya 572024China

Comparative metabolomics plays a crucial role in investigating gene function,exploring metabolite evolution,and accelerating crop genetic ***,a systematic platform for intra-and crossspecies comparison of metabolites is currently ***,we report the Plant Comparative Metabolome Database(PCMD;http://***/PCMD),a multilevel comparison database based on predicted metabolic profiles of 530 plant *** PCMD serves as a platform for comparing metabolite characteristics at various levels,including species,metabolites,pathways,and biological *** database also provides a number of user-friendly online tools,such as species comparison,metabolite enrichment,and ID conversion,enabling users to perform comparisons and enrichment analyses of metabolites across different *** addition,the PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite *** PCMD is the most speciesrich comparative plant metabolomics database currently available,and a case study demonstrates its ability to provide new insights into plant metabolic diversity.

关键词： comparative metabolomics plant database multilevel comparison metabolite characteristics

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Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related genes

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 573-588页

作者： Yan Zhang Jingwen Zhang Wei Zhang Mohan Wang Shuangqi Wang Yao Xu Lun Zhao Xingwang Li Guoliang Li National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data 3D Genomics Research CenterHuazhong Agricultural UniversityWuhan 430070China

Studies on the lung cancer genome are indispensable for developing a cure for lung ***-genome resequencing,genome-wide association studies,and transcriptome sequencing have greatly improved our understanding of the cancer ***,dysregulation of longrange chromatin interactions in lung cancer remains poorly *** better understand the three-dimensional(3D)genomic interaction features of the lung cancer genome,we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase II(RNAPII),CCCTC-binding factor(CTCF),enhancer of zeste homolog 2(EZH2),and histone 3 lysine 27 trimethylation(H3K27me3)using long-read chromatin interaction analysis by paired-end tag sequencing(ChIA-PET).Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes,either through loops or domains,and their distributions along the genome were distinct from and complementary to those associated with ***-related genes were highly enriched with chromatin interactions,and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes,such as additional repressive interactions on FOXO4 and promoter–promoter interactions between NF1 and *** of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes,suggesting that chromatin interactions are essential for proper expression of lung cancer-related *** findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.

关键词： Lung cancer 3D genome ChIA-PET Chromatin interaction Dysregulation

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Maturity Classification of Rapeseed Using Hyperspectral Image Combined with Machine Learning

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Plant Phenomics 2024年第1期6卷 269-280页

作者： Hui Feng Yongqi Chen Jingyan Song Bingjie Lu Caixia Shu Jiajun Qiao Yitao Liao Wanneng Yang National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan430070 HubeiPR China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityWuhan430070 HubeiPR China College of Engineering Huazhong Agricultural UniversityWuhan430070 HubeiPR China

Oilseed rape is an important oilseed crop planted *** classification plays a crucial role in enhancing yield and expediting breeding *** methods of maturity classification are laborious and destructive in *** this study,a nondestructive classification model was established on the basis of hyperspectral imaging combined with machine learning ***,hyperspectral images were captured for 3 distinct ripeness stages of rapeseed,and raw spectral data were extracted from the hyperspectral *** raw spectral data underwent preprocessing using 5 pretreatment methods,namely,Savitzky-Golay,first derivative,second derivative(D2nd),standard normal variate,and detrend,as well as various combinations of these ***,the feature wavelengths were extracted from the processed spectra using competitive adaptive reweighted sampling,successive projection algorithm(SPA),iterative spatial shrinkage of interval variables(IVISSA),and their combination algorithms,*** classification models were constructed using the following algorithms:extreme learning machine,k-nearest neighbor,random forest,partial least-squares discriminant analysis,and support vector machine(SVM)algorithms,applied separately to the full wavelength and the feature wavelengths.A comparative analysis was conducted to evaluate the performance of diverse preprocessing methods,feature wavelength selection algorithms,and classification models,and the results showed that the model based on preprocessing-feature wavelength selection-machine learning could effectively predict the maturity of *** D2nd-IVISSA-SPA-SVM model exhibited the highest modeling performance,attaining an accuracy rate of 97.86%.The findings suggest that rapeseed maturity can be rapidly and nondestructively ascertained through hyperspectral imaging.

关键词： learning image with classification combined hyperspectral machine maturity rapeseed using

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Role of cancer stem cell ecosystem on breast cancer metastasis and related mouse models

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Zoological research 2024年第3期45卷 506-517页

作者： Xilei Peng Haonan Dong Lixing Zhang Suling Liu Fudan University Shanghai Cancer Center&Institutes of Biomedical Sciences/State Key Laboratory of Genetic Engineering/Cancer Institutes/Department of Oncology/Key Laboratory of Breast Cancer in Shanghai/Shanghai Key Laboratory of Medical Epigenetics/Shanghai Key Laboratory of Radiation Oncology/International Co-laboratory of Medical Epigenetics and Metabolism Ministry of Science and Technology/Shanghai Medical College/Fudan UniversityShanghai 200032China

Breast cancer metastasis is responsible for most breast cancer-related deaths and is influenced by many factors within the tumor ecosystem,including tumor cells and *** cancer stem cells(BCSCs)constitute a small population of cancer cells with unique characteristics,including their capacity for self-renewal and *** have shown that BCSCs not only drive tumorigenesis but also play a crucial role in promoting metastasis in breast *** tumor microenvironment(TME),composed of stromal cells,immune cells,blood vessel cells,fibroblasts,and microbes in proximity to cancer cells,is increasingly recognized for its crosstalk with BCSCs and role in BCSC survival,growth,and dissemination,thereby influencing metastatic ***,a thorough understanding of BCSCs and the TME is critical for unraveling the mechanisms underlying breast cancer *** this review,we summarize current knowledge on the roles of BCSCs and the TME in breast cancer metastasis,as well as the underlying regulatory ***,we provide an overview of relevant mouse models used to study breast cancer metastasis,as well as treatment strategies and clinical trials addressing BCSC-TME interactions during ***,this study provides valuable insights for the development of effective therapeutic strategies to reduce breast cancer metastasis.

关键词： Breast cancer Metastasis Cancer stem cell Ecosystem Tumor microenvironment Mouse model

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A putative E3 ubiquitin ligase substrate receptor degrades transcription factor SmNAC to enhance bacterial wilt resistance in eggplant

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园艺研究（英文） 2024年第1期11卷 109-121页

作者： Shuangshuang Yan Yixi Wang Bingwei Yu Yuwei Gan Jianjun Lei Changming Chen Zhangsheng Zhu Zhengkun Qiu Bihao Cao Key Laboratory of Biology and Genetic Improvement of Horticultural Crops Ministry of Agriculture and Rural Affairs/Guangdong Vegetable Engineering and Technology Research CenterGuangdong Provincial Key Laboratory of Postharvest Science of Fruits and VegetablesCollege of HorticultureSouth China Agricultural UniversityGuangzhou 510642China

Bacterial wilt caused by Ralstonia solanacearum is a severe soil-borne disease globally,limiting the production in Solanaceae *** negatively regulated eggplant resistance to Bacterial wilt(BW)though restraining salicylic acid(SA)***,other mechanisms through which SmNAC regulates BW resistance remain ***,we identified an interaction factor,SmDDA1b,encoding a substrate receptor for E3 ubiquitin ligase,from the eggplant cDNA library using SmNAC as ***1b expression was promoted by *** inoculation and exogenous SA *** virus-induced gene silencing of the SmDDA1b suppressed the BW resistance of eggplants;SmDDA1b overexpression enhanced the BW resistance of tomato ***1b positively regulates BW resistance by inhibiting the spread of *** within *** SA content and the SA biosynthesis gene ICS1 and signaling pathway genes decreased in the SmDDA1b-silenced plants but increased in SmDDA1b-overexpression ***,SmDDB1 protein showed interaction with SmCUL4 and SmDDA1b and protein degradation experiments indicated that SmDDA1b reduced SmNAC protein levels through proteasome ***,SmNAC could directly bind the SmDDA1b promoter and repress its ***,SmDDA1b is a novel regulator functioning in BW resistance of solanaceous crops via the SmNAC-mediated SA *** results also revealed a negative feedback loop between SmDDA1b and SmNAC controlling BW resistance.

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