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Functional genomics of Brassica napus:Progresses,challenges,and perspectives

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Journal of Integrative Plant Biology 2024年第3期66卷 484-509页

作者： Zengdong Tan Xu Han Cheng Dai Shaoping Lu Hanzi He Xuan Yao Peng Chen Chao Yang Lun Zhao Qing-Yong Yang Jun Zou Jing Wen Dengfeng Hong Chao Liu Xianhong Ge Chuchuan Fan Bing Yi Chunyu Zhang Chaozhi Ma Kede Liu Jinxiong Shen Jinxing Tu Guangsheng Yang Tingdong Fu Liang Guo Hu Zhao national key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Yazhouwan national laboratory Sanya 572025China

Brassica napus,commonly known as rapeseed or canola,is a major oil crop contributing over 13%to the stable supply of edible vegetable oil worldwide.Identification and understanding the gene functions in the B.napus genome is crucial for genomic breeding.A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B.napus.In this review,we present an overview of the progress made in the functional genomics of B.napus,including the availability of germplasm resources,omics databases and cloned functional genes.Based on the current progress,we also highlight the main challenges and perspectives in this field.The advances in the functional genomics of B.napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B.napus and will expedite the breeding of high quality,high resistance and high yield in B.napus varieties.

关键词： accelerate breeding Brassica napus functional genomics high resistance high yield

Broadband high-efficiency plasmonic metalens with negative dispersion characteristic

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Photonics Research 2024年第4期12卷 813-820页

作者： YONG-QIANG LIU YONG ZHU HONGCHENG YIN JINHAI SUN YAN WANG YONGXING CHE national key laboratory of Scattering and Radiation Beijing 100854China

Controlling the dispersion characteristic of metasurfaces(or metalenses) along a broad bandwidth is of great importance to develop high-performance broadband metadevices. Different from traditional lenses that rely on the material refractive index along the light trajectory, metasurfaces or metalenses provide a new regime of dispersion control via a sub-wavelength metastructure, which is known as negative chromatic dispersion.However, broadband metalenses design with high-performance focusing especially with a reduced device dimension is a significant challenge in society. Here, we design, fabricate, and demonstrate a broadband highperformance diffractive-type plasmonic metalens based on a circular split-ring resonator metasurface with a relative working bandwidth of 28.6%. The metalens thickness is only 0.09λ0(λ0is at the central wavelength),which is much thinner than previous broadband all-dielectric metalenses. The full-wave simulation results show that both high transmissive efficiency above 80%(the maximum is even above 90%) and high average focusing efficiency above 45%(the maximum is 56%) are achieved within the entire working bandwidth of 9–12 GHz.Moreover, an average high numerical aperture of 0.7(NA = 0.7) of high-efficiency microwave metalens is obtained in the simulations. The broadband high-performance metalens is also fabricated and experimental measurements verify its much higher average focusing efficiency of 55%(the maximum is above 65% within the broad bandwidth) and a moderate high NA of 0.6. The proposed plasmonic metalens can facilitate the development of wavelength-dependent broadband diffractive devices and is also meaningful to further studies on arbitrary dispersion control in diffractive optics based on plasmonic metasurfaces.

关键词： resonator dispersion high

Learnware:small models do big

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Science China(Information Sciences) 2024年第1期67卷 39-50页

作者： Zhi-Hua ZHOU Zhi-Hao TAN national key laboratory for Novel Software Technology Nanjing University

There are complaints about current machine learning techniques such as the requirement of a huge amount of training data and proficient training skills,the difficulty of continual learning,the risk of catastrophic forgetting,and the leaking of data privacy/proprietary.Most research efforts have been focusing on one of those concerned issues separately,paying less attention to the fact that most issues are entangled in practice.The prevailing big model paradigm,which has achieved impressive results in natural language processing and computer vision applications,has not yet addressed those issues,whereas becoming a serious source of carbon emissions.This article offers an overview of the learnware paradigm,which attempts to enable users not to need to build machine learning models from scratch,with the hope of reusing small models to do things even beyond their original purposes,where the key ingredient is the specification which enables a trained model to be adequately identified to reuse according to the requirement of future users who know nothing about the model in advance.

关键词： artificial intelligence machine learning learnware

Epigenetic control on transcription of vernalization genes and whole-genome gene expression profile induced by vernalization in common wheat

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Plant Diversity 2024年第3期46卷 386-394页

作者： Yunzhen Li Liujie Jin Xinyu Liu Chao He Siteng Bi Sulaiman Saeed Wenhao Yan national key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Vernalization is necessary for winter wheat to flower.However,it is unclear whether vernalization is also required for spring wheat,which is frequently sown in fall,and what molecular mechanisms underlie the vernalization response in wheat varieties.In this study,we examined the molecular mechanisms that regulate vernalization response in winter and spring wheat varieties.For this purpose,we determined how major vernalization genes(VRN1,VRN2,and VRN3)respond to vernalization in these varieties and whether modifications to histones play a role in changes in gene expression.We also identified genes that are differentially regulated in response to vernalization in winter and spring wheat varieties.We found that in winter wheat,but not in spring wheat,VRN1 expression decreases when returned to warm temperature following vernalization.This finding may be associated with differences between spring and winter wheat in the levels of tri-methylation of lysine 27 on histone H3(H3K27me3)and tri-methylation of lysine 4 on histone H3(H3K4me3)at the VRN1 gene.Analysis of winter wheat transcriptomes before and after vernalization revealed that vernalization influences the expression of several genes,including those involved in leucine catabolism,cysteine biosynthesis,and flavonoid biosynthesis.These findings provide new candidates for further study on the mechanism of vernalization regulation in wheat.

关键词： Wheat Vernalization VRN1 Histone modification Regulate network

Modulation of starch synthesis in Arabidopsis via phytochrome B-mediated light signal

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Journal of Integrative Plant Biology 2024年第5期66卷 973-985页

作者： Qingbiao Shi Ying Xia Na Xue Qibin Wang Qing Tao Mingjing Li Di Xu Xiaofei Wang Fanying Kong Haisen Zhang Gang Li national key laboratory of Wheat Improvement College of Life SciencesShandong Agricultural UniversityTai'an 271018China national key laboratory of Wheat Improvement College of AgronomyShandong Agricultural UniversityTai'an 271018China

Starch is a major storage carbohydrate in plants and is critical in crop yield and quality.Starch synthesis is intricately regulated by internal metabolic processes and external environmental cues;however,the precise molecular mechanisms governing this process remain largely unknown.In this study,we revealed that high red to far-red(high R:FR)light significantly induces the synthesis of leaf starch and the expression of synthesis-related genes,whereas low R:FR light suppress these processes.Arabidopsis phytochrome B(phyB),the primary R and FR photoreceptor,was identified as a critical positive regulator in this process.Downstream of phyB,basic leucine zipper transcription factor ELONGATED HYPOCOTYL5(HY5)was found to enhance starch synthesis,whereas the basic helix-loop-helix transcription factors PHYTOCHROME INTERACTING FACTORs(PIF3,PIF4,and PIF5)inhibit starch synthesis in Arabidopsis leaves.Notably,HY5 and PIFs directly compete for binding to a shared G-box cis-element in the promoter region of genes encoding starch synthases GBSS,SS3,and SS4,which leads to antagonistic regulation of their expression and,consequently,starch synthesis.Our findings highlight the vital role of phyB in enhancing starch synthesis by stabilizing HY5 and facilitating PIFs degradation under high R:FR light conditions.Conversely,under low R:FR light,PIFs predominantly inhibit starch synthesis.This study provides insight into the physiological and molecular functions of phyB and its downstream transcription factors HY5 and PIFs in starch synthesis regulation,shedding light on the regulatory mechanism by which plants synchronize dynamic light signals with metabolic cues to module starch synthesis.

关键词： Arabidopsis thaliana HY5 light signal phyB PIFs starch synthesis

Robust cooperative multi-agent reinforcement learning via multi-view message certification

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Science China(Information Sciences) 2024年第4期67卷 131-145页

作者： Lei YUAN Tao JIANG Lihe LI Feng CHEN Zongzhang ZHANG Yang YU national key laboratory for Novel Software Technology Nanjing University Polixir Technologies

Many multi-agent scenarios require message sharing among agents to promote coordination,hastening the robustness of multi-agent communication when policies are deployed in a message perturbation environment. Major relevant studies tackle this issue under specific assumptions, like a limited number of message channels would sustain perturbations, limiting the efficiency in complex scenarios. In this paper,we take a further step in addressing this issue by learning a robust cooperative multi-agent reinforcement learning via multi-view message certification, dubbed CroMAC. Agents trained under CroMAC can obtain guaranteed lower bounds on state-action values to identify and choose the optimal action under a worst-case deviation when the received messages are perturbed. Concretely, we first model multi-agent communication as a multi-view problem, where every message stands for a view of the state. Then we extract a certificated joint message representation by a multi-view variational autoencoder(MVAE) that uses a product-of-experts inference network. For the optimization phase, we do perturbations in the latent space of the state for a certificate guarantee. Then the learned joint message representation is used to approximate the certificated state representation during training. Extensive experiments in several cooperative multi-agent benchmarks validate the effectiveness of the proposed CroMAC.

关键词： multi-agent reinforcement learning robust communication adversarial training multi-view learning message certification

Establishment of a humanized ST6GAL1 mouse model for influenza research

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Animal Models and Experimental Medicine 2024年第3期7卷 337-346页

作者： Lyu Chao Han Feng Gao Qian Lv Limin Lu Ziwei Lu Shuangshuang Li Xiaoyan Hu Yuechao Yang Mengjie Zhao Yingze Liu Jun Lu Xuancheng Duo Shuguang national key laboratory of Intelligent Tracking and Forecasting for Infectious Diseases Chinese Center for Disease Control and PreventionBeijingChina Institute of Zoology Chinese Academy of SciencesBeijingChina NHC key laboratory of Biosafety National Key Laboratory of Intelligent Tracking and Forecasting for Infectious DiseasesNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina Zhejiang Provincial key laboratory of Medical Genetics Key Laboratory of Laboratory MedicineMinistry of EducationSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhouChina

Background:This study aimed to construct and characterize a humanized influenza mouse model expressing hST6GAL1.Methods:Humanized fragments,consisting of the endothelial cell-specific K18 promoter,human ST6GAL1-encoding gene,and luciferase gene,were microinjected into the fertilized eggs of mice.The manipulated embryos were transferred into the oviducts of pseudopregnant female mice.The offspring were identified using PCR.Mice exhibiting elevated expression of the hST6GAL1 gene were selectively bred for propagation,and in vivo analysis was performed for screening.Expression of the humanized gene was tested by performing immunohistochemical(IHC)analysis.Hematologic and biochemical analyses using the whole blood and serum of humanized hST6GAL1 mice were performed.Results:Successful integration of the human ST6GAL1 gene into the mouse genome led to the overexpression of human SiaT ST6GAL1.Seven mice were identified as carrying copies of the humanized gene,and the in vivo analysis indicated that hST6GAL1gene expression in positive mice mirrored influenza virus infection characteristics.The IHC results revealed that hST6GAL1 was expressed in the lungs of humanized mice.Moreover,the hematologic and biochemical parameters of the positive mice were within the normal range.Conclusion:A humanized influenza mouse model expressing the hST6GAL1 gene was successfully established and characterized.

关键词： hST6GAL1 humanized mice influenza animal model

N-Heterocyclic carbene-catalyzed enantioselective(dynamic) kinetic resolutions and desymmetrizations

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Science China Chemistry 2024年第2期67卷 482-511页

作者： Yi Zhang Hui Cai Xiuhai Gan Zhichao Jin national key laboratory of Green Pesticide Key Laboratory of Green Pesticide and Agricultural BioengineeringMinistry of EducationGuizhou UniversityHuaxi DistrictGuiyang550025China

N-heterocyclic carbene-catalyzed enantioselective kinetic resolutions,dynamic kinetic resolutions,and desymmetrization reactions are systematically reviewed.The content is organized according to the activation modes involved in these transformations.Future advances within this highly active research field are discussed from our perspectives on the topic.

关键词： N-heterocyclic carbene kinetic resolution dynamic kinetic resolution desymmetrization organocatalysis

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

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Plant Diversity 2024年第3期46卷 372-385页

作者： Shanni Cao Xue Zhao Zhuojin Li Ranran Yu Yuqi Li Xinkai Zhou Wenhao Yan Dijun Chen Chao He State key laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China national key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific manner.Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings.This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets,addressing batch effects and conserving biological variance.This integration spans a broad spectrum of tissues,including both below-and above-ground parts.Utilizing a rigorous approach for cell type annotation,we identified 47 distinct cell types or states,largely expanding our current view of plant cell compositions.We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression.Taken together,our study not only offers extensive plant cell atlas exploration that serves as a valuable resource,but also provides molecular insights into gene-regulatory programs that varies from different cell types.

关键词： Arabidopsis Single cell transcriptome Gene regulatory network Data integration Plant cell atlas