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Vegetable biology and breeding in the genomics era

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Science China(life Sciences) 2023年第2期66卷 226-250页

作者： hongbo Li Xueyong Yang Yi Shang Zhonghua Zhang Sanwen Huang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Yunnan Key Laboratory of Potato Biology The CAAS-YNNU-YINMORE Joint Academy of Potato SciencesYunnan Normal UniversityKunming 650500China Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province College of HorticultureQingdao Agricultural UniversityQingdao 266109China Chinese Academy of Tropical Agricultural Sciences Haikou 571101China

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize,thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

关键词： vegetable genomics multi-omics gene discovery molecular breeding

Local high-temperature phenomena within magnetic clouds

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Science China Earth Sciences 2021年第1期64卷 177-184页

作者： Jiemin WANG Hengqiang FENG hongbo Li Yan ZHAO Institute of Space Physics Luoyang Normal UniversityLuoyang 471934China Henan Key Laboratory of Electromagnetic Transformation and Detection Luoyang Normal UniversityLuoyang 471934China

In this study,three methods were used to analyze 17 large-scale local high-temperature regions with durations exceeding 2 h within magnetic clouds(MCs)observed by advanced composition explorer from 1998 to 2008.Results show that five of these large-scale regions may have been caused by flare heating;seven of the regions may have been caused by nonuniform expansion when MCs propagated in the solar-terrestrial space;four large-scale high temperature regions may likely result from combined non-uniform expansion and flare heating;and only one large-scale local high-temperature region was not related to either flare heating nor non-uniform expansion.No evidence indicated that magnetic reconnection occurred or had occurred within the high-temperature regions.Based on our results,we infer that such local high-temperature phenomena within MCs are caused primarily as a result of flare heating and non-uniform expansion,either separately or jointly,and that magnetic reconnection plays only a minor role in the formation of high-temperature regions.

关键词： Magnetic cloud High-temperature regions Flare heating Non-uniform expansion

Approximate Optimal Filter Design for Vehicle System through Actor‑Critic Reinforcement Learning

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Automotive Innovation 2022年第4期5卷 415-426页

作者： Yuming Yin Shengbo Eben li Kaiming Tang Wenhan Cao Wei Wu hongbo Li School of Mechanical Engineering Zhejiang University of TechnologyHangzhou 310023China School of Vehicle and Mobility Tsinghua UniversityBeijing 100084China Beijing Geekplus Tech.Co. LtdBeijingChina

Precise state and parameter estimations are essential for identification,analysis and control of vehicle engineering problems,especially under significant model and measurement uncertainties.The widely used filtering/estimation algorithms,such as Kalman series like Kalman filter,extended Kalman filter,unscented Kalman filter,and particle filter,generally aim to approach the true state/parameter distribution via iteratively updating the filter gain at each time step.However,the optimal-ity of these filters would be deteriorated by unrealistic initial condition or significant model error.Alternatively,this paper proposes to approximate the optimal filter gain by considering the effect factors within infinite time horizon,on the basis of estimation-control duality.The proposed approximate optimal filter(AOF)problem is designed and subsequently solved by actor-critic reinforcement learning(RL)method.The AOF design transforms the traditional optimal filtering problem with the minimum expected mean square error into an optimal control problem with the minimum accumulated estimation error,in which the estimation error is used as the surrogate system state and the infinite-horizon filter gain is the control input.The estimation-control duality is proved to hold when certain conditions about initial vehicle state distributions and policy structure are maintained.In order to evaluate of the effectiveness of AOF,a vehicle state estimation problem is then demonstrated and compared with the steady-state Kalman filter.The results showed that the obtained filter policy via RL with different discount factors can converge to theoretical optimal gain with an error within 5%,and the average estimation errors of vehicle slip angle and yaw rate are less than 1.5×10–4.

关键词： Vehicle state estimation Kalman filter Estimation-control duality Reinforcement learning

Revisiting the efficacy of weak consistencies: a study of forward checking

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Science China(Information Sciences) 2021年第7期64卷 233-235页

作者： Zhe li Zhezhou YU hongbo Li Jinsong GUO Zhanshan li Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Computer Science and Technology Jilin University College of Information Science and Technology Northeast Normal University Department of Computer Science University of Oxford

Dear editor,Arc consistency (AC)[1] is currently the most popular local consistency for solving constraint satisfaction problems(CSP). To solve CSPs more efficiently, extensive work [2–4]has been done to find local c... 详细信息

关键词： Constraint Satisfaction Problem Arc Consistency Forward Checking Stronger Consistency Weaker Consistency

Analyzing space-time evolution of rural transition in a rapidly urbanizing region:A case study of Suzhou,China

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Journal of Geographical Sciences 2022年第7期32卷 1343-1356页

作者： ZHANG Ruoyan li hongbo YUAN Yuan Institute of Geographic Sciences and Natural Resources Research CASBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China School of Geographical Science Nanjing Normal UniversityNanjing 210023China School of Public Administration Hohai UniversityNanjing 211100China

Influenced by globalization,rural transition in developed Western countries has experienced processes of productivism,post-productivism,and multifunctional development.By contrast,rural transition in most developing countries has been accompanied by rapid urbanization,which has become a core topic in geography research.As the world’s largest developing country,China has undergone profound development since the reform and opening-up.Moreover,rural spaces in some eastern coastal areas have entered the stage of reconstruction after decades of industrialization and urbanization.This paper takes Suzhou as the case area and measures the process of rural transition from 1990 to 2015 by constructing an index system.It then analyzes the characteristics of space-time evolution using exploratory spatial data analysis(ESDA)methods to reveal the influence of economic and social development on rural transition.The results show that rural transition,which generally entails the weakening of rurality and enhancing of urbanity on a macro scale,tends to be heterogeneous across different regions on a micro scale.This paper argues that multifunctionality will be the main future trend of rural transition in rapidly urbanizing areas.The experience in Suzhou could provide an example for establishing policies on sustainable development in rural spaces and achieving urban-rural co-governance.

关键词： rural transition multifunctionality rural revitalization Suzhou space-time evolution exploratory spatial data analysis(ESDA)

Metal-Organic Frameworks-Based Fluorescent Nanocomposites for Bioimaging in living Cells and in vivo

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Chinese Journal of Chemistry 2021年第2期39卷 473-487页

作者： Meijia liu Xiangling Ren Xianwei Meng hongbo Li Experimental Center of Advanced Materials School of Materials Science&EngineeringBeijing Institute of TechnologyBeijing100081 China Laboratory of Controllable Preparation and Application of Nanomaterials Technical Institute of Physics and ChemistryChinese Academy of SciencesBeijing100190 China

Metal-organic frameworks(MOFs)as a class of porous functional materials have attracted more and more attention for biomedical applications.To date,MOFs have been developed for bioimaging based on a series of advantages such as the large surface areas,high porosity,fluorescence functionalities and good biocompatibility.It is worth noting that organic or inorganic fluorescent materials such as fluorescent dyes,quantum dots,metal nanoclusters and nanosheets can combine MOFs or be encapsulated in MOFs to form fluorescent nanocomposites for excellent imaging function.Importantly,excellent imaging capabilities are of great significance in living cells and in vivo for detection,diagnosis and cancer therapy.In this review,we focus on the recent research of the bioimaging in living cells and in vivo based on various MOF-based nanocomposites and their potential biological clinical applications.

关键词： Metal-organic frameworks Fluorescent material Nanostructures Fluorescence Bioimaging

B-SPliNE PATCHES AND TRANSFINITE INTERPOLATION METHOD FOR PDE CONTROLLED SIMULATION

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Journal of Systems Science & Complexity 2012年第2期25卷 348-361页

作者： Yuanjie liU hongbo Li Institute of Systems Science Academy of Mathematics and Systems ScienceChinese Academy of Sciences Graduate School of the Chinese Academy of Sciences

This paper is to discuss an approach which combines B-spline patches and transfinite interpolation to establish a linear algebraic system for solving partial differential equations and modify the WEB-spline method developed by Klaus Hollig to derive this new idea.First of all,the authors replace the R-function method with transfinite interpolation to build a function which vanishes on boundaries. Secondly,the authors simulate the partial differential equation by directly applying differential operators to basis functions,which is similar to the RBF method rather than Hollig’s method.These new strategies then make the constructing of bases and the linear system much more straightforward.And as the interpolation is brought in,the design of schemes for solving practical PDEs can be more flexible. This new method is easy to carry out and suitable for simulations in the fields such as graphics to achieve rapid rendering.Especially when the specified precision is not very high,this method performs much faster than WEB-spline method.

关键词：控制模拟插值方法超限插值 EB样条补丁 PDE 偏微分方程线性系统

Influences of the heterogeneity of viscoelastic medium on postseismic deformation of the 2008 M_(W) 7.9 Wenchuan earthquake

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Geodesy and Geodynamics 2022年第1期13卷 1-10页

作者： Feng li Peng Zhai Jinshui Huang hongbo Tan Mengcheng National Geophysical Observatory School of Earth and Space SciencesUniversity of Science and Technology of ChinaHefei230026China Earthquake Administration of Jiangsu Province Nanjing210014China CAS Center for Excellence in Comparative Planetology Hefei230026China

The study of postseismic deformation is important for constraining the viscoelastic properties of the Earth and inverting the post-earthquake process.The levelling survey revealed that the area near Bei-chuan elevated 5.3 cm about two years after the M_(W) 7.9 Wenchuan earthquake(05/12/2008),during which the area underwent significant downward movement.The GPS horizontal displacements showed a non-monotonic variation after the Wenchuan earthquake.In this study,a 3-D viscoelastic finite element model is employed to simulate the coseismic and postseismic deformation of the Wenchuan earthquake.The numerical simulations show that the lateral heterogeneity across the Longmenshan fault plays an important role in the postseismic displacements.The results reveal that the coseismic defor-mation is not sensitive to the horizontal heterogeneity,but the postseismic deformation is sensitive to it.The postseismic deformation of the horizontally heterogeneous model is generally consistent with the observations of all geodetic surveys,such as GPS,InSAR and levelling,but not for the horizontally homogenous model.We also find that the non-monotonous variation of the postseismic deformation of the Wenchuan earthquake could be explained by a viscoelastic relaxation model with lateral heterogeneous medium across the Longmenshan fault.

关键词： M_(W)7.9 Wenchuan earthquake Postseismic deformation Viscoelastic relaxation Horizontal heterogeneity Three-dimensional finite element

Impaired SWEET-mediated sugar transportation impacts starch metabolism in developing rice seeds

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The Crop Journal 2022年第1期10卷 98-108页

作者： Pei li lihan Wang hongbo Liu Meng Yuan National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Huazhong Agricultural UniversityWuhan 430070HubeiChina

Sugar transportation and sugar-to-starch metabolism are considered important processes in seed development and embryo viability.A few plant SWEET proteins acting as sugar transporters have been reported to function in inflorescence and/or seed development.Here,we identified seven members of the 21 Os SWEET genes in rice that play essential roles in sugar transportation and sugar-to-starch conversion in seed development.Nineteen Os SWEET genes exhibiting different expression patterns during inflorescence and seed development were knocked out individually by CRISPR/Cas9.One third of the mutants showed decreased fertile pollen viability and shriveled mature caryopses,resulting in weakened seed traits.Grain fill-related genes but not representative grain shape-regulating genes showed attenuated expression in the mutants.Seed of each of these mutants accumulated more sucrose,glucose or fructose but less starch.Among all Os SWEET genes,Os SWEET4 and Os SWEET11 had major effects on caryopsis development.The sugar-to-starch metabolic pathway was significantly altered in ossweet11 mutants based on differential expression analysis in RNA sequencing assays,confirming that Os SWEET11 functions as a sugar transporter with a key role in seed development.These results help to decipher the multiple functions of Os SWEET genes and to show how they might be used in genetic improvement of rice.

关键词： Oryza sativa Sugar transporter SWEET Sugar Starch