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| 1 | Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study显示文摘 | Quanxiu. Wang Weibo Xie Hongkun Xing Ju Yan Xiangzhou Meng Xinglei Li Xiangkui Fu Jiuyue Xu Xingming Lian Sibin Yu Yongzhong Xing Gongwei Wang | 2015 | Molecular Plant2015，8，6： | 20 |
| 2 | N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression,Plant Development, and Stress Responses显示文摘N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive.Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars,Nipponbare (Nip;Japonica)and 93-11 (Indica).Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis.We found that 6mA levels are positively correlated with the expression of key stressrelated genes,which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover,we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants. | Qian Zhang Zhe Liang Xuean Cui Changmian Ji Yun Li Pingxian Zhang Jingrong Liu Adeel Riaz Pu Yao Min Liu Yunpeng Wang Tiegang Lu Hao Yu Donglei Yang Hongkun Zheng Xiaofeng Gu | 2018 | Molecular Plant2018，11，12： | 18 |
| 3 | A Chromosome-Scale Genome Assembly of Paper Mulberry(Bmussonetia papyrifera)Provides New Insights into Its Forage and Papermaking Usage显示文摘Paper mulberry(Broussonetia papyrifera)is a well-known woody tree historically used for Cai Lun papermaking,one of the four great inventions of ancient China.More recently,Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents.In this study,we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches,including Illumina and PacBio sequencing platform as well as Hi-C,optical,and genetic maps.The assembled Paper mulberry genome consists of 386.83 Mb,which is close to the estimated size,and 99.25%(383.93 Mb)of the assembly was assigned to 13 pseudochromosomes.Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families,respectively,accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry.Moreover,the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine,forage,papermaking,and barkcloth making.We also identified the rootassociated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation.Collectively,these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition.Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making,and as forage.These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide. | Xianjun Peng Hui Liu Peilin Chen Feng Tang Yanmin Hu Fenfen Wang Zhi Pi Meiling Zhao Naizhi Chen Hui Chen Xiaokang Zhang Xueqing Yan Min Liu Xiaojun Fu Guofeng Zhao Pu Yao Lili Wang He Dai Xuming Li Wei Xiong Wencai Xu Hongkun Zheng Haiyan Yu Shihua Shen | 2019 | Molecular Plant2019，12，5： | 18 |
| 4 | Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies显示文摘Brassica rapa comprises several important cultivated vegetables and oil crops.Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous,thereby limiting extensive genetic and genomic analyses.Here,we report an improved assembly of the B.rapa genome(v3.0)using single-molecule sequencing,optical mapping,and chromosome conformation capture technologies(Hi-C).Relative to the previous reference genomes,our assembly features a contig N50 size of 1.45 Mb,representing a~30-fold improvement.We also identified a new event that occurred in the B.rapa genome~1.2 million years ago,when a long terminal repeat retrotransposon(LTR-RT)expanded.Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B.rapa genome.The B.rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B.rapa.This resource will facilitate breeding efforts in B.rapa,as well as comparative genomic analysis with other Brassica species. | Lei Zhang Xu Cai Jian Wu Min Liu Stefan Grob Feng Cheng Jianli Liang Chengcheng Cai Zhiyuan Liu Bo Liu Fan Wang Song Li Fuyan Liu Xuming Li Lin Cheng Wencai Yang Mai-he Li Ueli Grossniklaus Hongkun Zheng Xiaowu Wang | 2018 | Horticulture Research2018，5，1： | 10 |
| 5 | Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence显示文摘Rapeseed (Brassica napus),an important oilseed crop,has adapted to diverse climate zones and latitudes by forming three main ecotype groups,namely winter,semiwinter,and spring types. However,genetic variations underlying the divergence of these ecotypes are largely unknown. Here,we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions.A total of 5.56 and 5.53 million singlenucleotide polymorphisms (SNPs)as Well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of 'Darmor-bzh'and 'Tapidor,'respectively.We generated a map of allelic drift paths that shows splits and mixtures of the main populations,and revealed an asymmetric evolution of the two subgenomes of B.napus by calculating the genetic diversity and linkage disequilibrium parameters.Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses.A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups,and will facilitate screening of molecular markers for accelerating rapeseed breeding. | Dezhi Wu Zhe Liang Tao Yan Ying Xu Lijie Xuan Juan Tang Gang Zhou Ulrike Lohwasser Shuijin Hua Haoyi Wang Xiaoyang Chen Qian Wang Le Zhu Antony Maodzeka Nazim Hussain Zhilan Li Xuming Li Imran Haider Shamsi Ghulam Jilani Linde Wu Hongkun Zheng Guoping Zhang Boulos Chalhoub Lisha Shen Hao Yu Lixi Jiang | 2019 | Molecular Plant2019，12，1： | 10 |
| 6 | Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game显示文摘Crop weediness,especially that of weedy rice(Oryza sativa f.spontanea),remains mysterious.Weedy rice possesses robust ecological adaptability;however,how this strain originated and gradually formed proprietary genetic features remains unclear?Here,we demonstrate that weedy rice at Asian high latitudes(WRAH)is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice.We also identified novel quantitative trait loci underlying weedy-specific traits,and revealed that a genome block on the end of chromosome 1 is associated with rice weediness.To identify the genomic modifications underlying weedy rice evolution,we generated the first de novo assembly of a high-quality weedy rice genome(WR04-6),and conducted a comparative genomics study between WR04-6 with other rice reference genomes.Multiple lines of evidence,including the results of demographic scenario comparisons,suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication.A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity. | Jian Sun Dianrong Ma Liang Tang Minghui Zhao Guangchen Zhangh Wenjia Wang Jiayu Song Xiang Li Zimeng Liu Wenxing Zhang Quan Xu Yuncheng Zhou Jianzhong Wu Toshio Yamamoto Fei Dai Yan Lei Song Li Gang Zhou Hongkun Zheng Zhengjin Xu Wenfu Chen | 2019 | Molecular Plant2019，12，5： | 9 |
| 7 | Differentiation potential of bone marrow mesenchymal stem cells in duck显示文摘The bone marrow mesenchymal stem cells(MSCs) are multipotent stem cells which can differentiate into mesenchymal cells in vitro.In this study,MSCs in duck were isolated from bone marrow by density gradient centrifuge separation,purified and expanded in the me-dium.The primary MSCs were expanded for 11 passages.The different-passage MSCs were induced to differentiate into osteoblasts and neuron-like cells.Karyotype analysis indicated that MSCs kept diploid condition and the hereditary feature was stable.The different-passage MSCs expressed CD44,ICAM-1 and SSEA-4,but not CD34,CD45 and SSEA-1 when detected by immunofluorescence staining.There was no significant difference among the positive rates of passages 2,6 and 8(P > 0.05),but a significant difference existed among those of passages 2,6,8 and 11(P < 0.05).After the osteogenic inducement was added,the induced different-passage MSCs expressed high-level alkaline phosphatase(ALP),and are positive for tetracycline staining,Alizarin Red staining and Von Kossa staining.After the neural inducement was added,about 70% cells exhibited typical neuron-like phenotype,the induced different-passage MSCs expressed Nestin,neuron-specific enolase(NSE) and glial fibrillary acidic protein(GFAP) when detected by immunofluorescence staining.There was no significant difference among the positive rates of passages 3,4 and 6(P>0.05),but a significant difference existed among those of passages 3,4,6 and 8(P<0.05).These results suggest that MSCs in duck were capable of differentiating into osteoblasts and neuron-like cells in vitro. | Linfeng Li Xiujuan Bai Xuelian Gong Hongkun Liu Lina Chen Weijun Guan Yuehui Ma | 2009 | Journal of Genetics and Genomics2009，36，3： | 8 |
| 8 | Facile synthesis of poly(aroxycarbonyltriazole)s with aggregation-induced emission characteristics by metal-free click polymerization显示文摘Regioseletive 1,3-dipolar polycycloadditions of 4,4'-isopropylidenediphenyl dipropiolate (1) and tetraphenylethene (TPE)-containing diazides (2) are carried out in polar solvents such as DMF/toluene at a moderate temperature of 100℃ for 6 h,producing poly(aroxycarbonyltriazole)s (PACTs) P3 with high molecular weights (Mw up to 23900) and regioregularities (F1,4 up to ~90%) in high yields (up to ~99%).These metal-free click polymerizations can propagate smoothly in an open atmosphere without protection from oxygen and moisture.The obtained polymers are soluble in common organic solvents and thermally stable at temperatures up to 375℃.Thanks to their contained TPE moieties,the PACTs show aggregation-induced emission and can serve as fluorescent chemosensors for superamplified detection of explosives. | LI HongKun MEI Ju WANG Jian ZHANG Shuang ZHAO QiuLi WEI Qiang QIN AnJun SUN JingZhi TANG Ben Zhong | 2011 | Science China Chemistry2011，54，4： | 8 |
| 9 | Computer vision technology in agricultural automation--A review显示文摘Computer vision is a field that involves making a machine “see”.This technology uses a camera and computer instead of the human eye to identify,track and measure targets for further image processing.With the development of computer vision,such technology has been widely used in the field of agricultural automation and plays a key role in its development.This review systematically summarizes and analyzes the technologies and challenges over the past three years and explores future opportunities and prospects to form the latest reference for researchers.Through the analyses,it is found that the existing technology can help the development of agricultural automation for small field farming to achieve the advantages of low cost,high efficiency and high precision.However,there are still major challenges.First,the technology will continue to expand into new application areas in the future,and there will be more technological issues that need to be overcome.It is essential to build large-scale data sets.Second,with the rapid development of agricultural automation,the demand for professionals will continue to grow.Finally,the robust performance of related technologies in various complex environments will also face challenges.Through analysis and discussion,we believe that in the future,computer vision technology will be combined with intelligent technology such as deep learning technology,be applied to every aspect of agricultural production management based on large-scale datasets,be more widely used to solve the current agricultural problems,and better improve the economic,general and robust performance of agricultural automation systems,thus promoting the development of agricultural automation equipment and systems in a more intelligent direction. | Hongkun Tian Tianhai Wang Yadong Liu Xi Qiao Yanzhou Li | 2020 | Information Processing in Agriculture2020，7，1： | 8 |
| 10 | A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp.pekinensis)Selection显示文摘Chinese cabbage is the most consumed leafy crop in East Asian countries.However,premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution.In the past 40years,spring Chinese cabbage with strong winterness has been selected to meet the market demand.Here,we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes.In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China.We identified 23 genomic loci that underwent intensive selection,and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1(BrVIN3.1)and FLOWER LOCUS C 1(BrFLC1)is a determinant genetic source of variation during selection.Moreover,we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVlN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage.Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant Varieties by molecular-marker-assisted selection,transgenic or gene editingapproaches. | Tongbing Su Weihong Wang Peirong Li Bin Zhang Pan Li Xiaoyun Xin Honghe Sun Yangjun Yu Deshuang Zhang Xiuyun Zhao Changlong Wen Gang Zhou Yuntong Wang Hongkun Zheng Shuancang Yu Fenglan Zhang | 2018 | Molecular Plant2018，11，11： | 6 |
| 11 | Dual-shot dynamics and ultimate frequency of all-optical magnetic recording on GdFeCo显示文摘Although photonics presents the fastest and most energy-efficient method of data transfer,magnetism still offers the cheapest and most natural way to store data.The ultrafast and energy-efficient optical control of magnetism is presently a missing technological link that prevents us from reaching the next evolution in information processing.The discovery of all-optical magnetization reversal in GdFeCo with the help of 100fs laser pulses has further aroused intense interest in this compelling problem.Although the applicability of this approach to high-speed data processing depends vitally on the maximum repetition rate of the switching,the latter remains virtually unknown.Here we experimentally unveil the ultimate frequency of repetitive all-optical magnetization reversal through time-resolved studies of the dual-shot magnetization dynamics in Gd27 Fe63.87 C09.T3.Varying the intensities of the shots and the shotto-shot separation,we reveal the conditions for ultrafast writing and the fastest possible restoration of magnetic bits.It is shown that although magnetic writing launched by the first shot is completed after 100 ps,a reliable rewriting of the bit by the second shot requires separating the shots by at least 300 ps.Using two shots partially overlapping in space and minimally separated by 300 ps,we demonstrate an approach for GHz magnetic writing that can be scaled down to sizes below the diffraction limit. | Sicong Wang Chen Wei\Yuanhua Feng Hongkun Cao Wenzhe Li Yaoyu Cao Bai-Ou Guan Arata Tsukamoto Andrei Kirilyuk Alexey VKimel Xiangping Li | 2021 | Light(Science & Applications)2021，10，1： | 3 |
| 12 | Agronomic and physiological traits associated with genetic improvement of phosphorus use efficiency of wheat grown in a purple lithomorphic soil显示文摘Developing wheat that acquires and uses phosphorus(P)more efficiently is a promising and low-cost solution for increasing grain yield and reducing P-related environmental impacts.The present study identified agronomic and physiological traits that contribute to genetic variation in the P acquisition,remobilization,and utilization efficiency of 11 wheat cultivars from southwest China grown in P-deficient purple lithomorphic soil(Olsen P=4.7)with balanced(75 kg P ha^(−1))and excess P(120 kg P ha^(−1))supplies.On average,soil P deficiency(–P)reduced root P uptake(17.0%–60.8%),P remobilization(33.9%–52.8%),dry mass yield(11.5%–39.2%),and grain yield(17.7%–54.4%).Balanced P(+P)increased grain yield via increased plant biomass rather than increased HI.–P increased phosphorus uptake efficiency(PUpE,4.5-fold),phosphorus utilization efficiency(PUtE,1.25-fold),and phosphorus use efficiency(PUE,5.4-fold)compared with those under+P,and PUtE explained most(58.1%–60.8%)of the genetic variation in PUE under both–P and+P.The high root P uptake of P-efficient cultivars under–P was regulated by root surface area and root length density in the 0–10 cm soil layer but not in the 10–20 and 20–40 cm soil layers,suggesting that a topsoil foraging strategy is a more economical approach than deeper root exploration for increasing P uptake.Root P uptake before anthesis and P remobilization after anthesis were critical for increasing the PUtE of wheat,given that P-efficient cultivars showed higher Pn(net photosynthetic rate)and sucrose levels than P-inefficient cultivars.Pn reduction by–P resulted from decreased Gs and Ci,and high evapotranspiration under+P increased shoot P%by increasing root P uptake.Genetic variation in the source-to-sink ratio was observed in consequence of a+P-induced allometric increase in sucrose in leaves and kernels.Owing to these beneficial effects,+P increased the kernel N and P yields of the 11 cultivars by 9.9%–52.4%and 12.3%–48.8%,respectively.The findings of this study could help improve wheat in future breeding efforts and P management by identifying desirable Pefficient phenotypes in P-deficient farming systems. | Hongkun Yang Renhua Chen Yufeng Chen Han Li Ting Wei Wei Xie Gaoqiong Fan | 2022 | The Crop Journal2022，10，4： | 2 |
| 13 | Author Correction:Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies显示文摘Since the publication of this article,the authors have noticed that the total gene models(45,985),tandem arrays(2077),tandem genes(4963),redundancy removed(43,099),syntenic genes(39,858),nonsyntenic genes(3241),genes on chromosomes(45,411),genes on scaffolds(574)of B.rapa reference genome v3.0 were mistaken in the article. | Lei Zhang Xu Cai Jian Wu Min Liu Stefan Grob Feng Cheng Jianli Liang Chengcheng Cai Zhiyuan Liu Bo Liu Fan Wang Song Li Fuyan Liu Xuming Li Lin Cheng Wencai Yang Mai-he Li Ueli Grossniklaus Hongkun Zheng Xiaowu Wang | 2019 | Horticulture Research2019，6，1： | 2 |
| 14 | Visual detection of organophosphorus pesticides represented by mathamidophos using Au nanoparticles as colorimetric probe显示文摘 | Hongkun Li Jiajia Guo Hong Ping et al | 2011 | Talanta2011，87，： | 1 |
| 15 | Analysis of General Network Coding Conditions and Design of a Free-ride-oriented Routing Metric显示文摘 | Guo Bin Li Hongkun Zhou Chi | | 0，，04： | 1 |
| 16 | Pattern recognition on diesel engine working condition by using a novel methodology-Hilbert spectrum entropy显示文摘 | Li Hongkun Zhou Peilin Ma Xiaojiang | 2005 | Proceedings of the Institute of Marine Engineering Science and Technology2005，4，： | 1 |
| 17 | Pattern recognition of wearing of diesel engine piston and cylinder liner by using a novel methodology-hilbert spectrum entropy显示文摘 | Hongkun Li Peilin Zhou Xiaojiang Ma | 2005 | Proceedings of the Institute of Marine Engineering Science and Technology2005，6，： | 1 |
| 18 | Analysis of gener- al network coding conditions and design of a free-ride-oriented routing metric显示文摘 | Guo Bin Li Hongkun 2aaou Chi Cheng Yu | 2011 | 1EEE Transactions on Vehicular Technolo- gy2011，60，4： | 1 |
| 19 | Sensitive fluorescent detection of melamine in raw milk based on the inner filter effect of Au nanoparticles on the fluorescence of CdTe quantum dots显示文摘 | Zhang Minwei Cao Xianyi Li Hongkun | | 0，，： | 1 |
| 20 | Living biobank-based cancer organoids: prospects and challenges in cancer research显示文摘Biobanks bridge the gap between basic and translational research.Traditional cancer biobanks typically contain normal and tumor tissues,and matched blood.However,biospecimens in traditional biobanks are usually nonrenewable.In recent years,increased interest has focused on establishing living biobanks,including organoid biobanks,for the collection and storage of viable and functional tissues for long periods of time.The organoid model is based on a 3D in vitro cell culture system,is highly similar to primary tissues and organs in vivo,and can recapitulate the phenotypic and genetic characteristics of target organs.Publications on cancer organoids have recently increased,and many types of cancer organoids have been used for modeling cancer processes,as well as for drug discovery and screening.On the basis of the current research status,more exploration of cancer organoids through technical advancements is required to improve reproducibility and scalability.Moreover,given the natural characteristics of organoids,greater attention must be paid to ethical considerations.Here,we summarize recent advances in cancer organoid biobanking research,encompassing rectal,gastric,pancreatic,breast,and glioblastoma cancers.Living cancer biobanks that contain cancerous tissues and matched organoids with different genetic backgrounds,subtypes,and individualized characteristics will eventually contribute to the understanding of cancer and ultimately facilitate the development of innovative treatments. | Haixin Li Hongkun Liu Kexin Chen | 2022 | Cancer Biology & Medicine2022，19，7： | 1 |
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