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| 1 | A super pan-genomic landscape of rice显示文摘Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity.Using de novo longread assembly,we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.Our pan-genome reveals extensive structural variations(SVs)and gene presence/absence variations.Additionally,our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter-and intraspecific diversity.Moreover,we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes.We characterized genetic variants associated with submergence tolerance,seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice.This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species. | Lianguang Shang Xiaoxia Li Huiying He Qiaoling Yuan Yanni Song Zhaoran Wei Hai Lin Min Hu Fengli Zhao Chao Zhang Yuhua Li Hongsheng Gao Tianyi Wang Xiangpei Liu Hong Zhang Ya Zhang Shuaimin Cao Xiaoman Yu Bintao Zhang Yong Zhang Yiqing Tan Mao Qin Cheng Ai Yingxue Yang Bin Zhang Zhiqiang Hu Hongru Wang Yang Lv Yuexing Wang Jie Ma Quan Wang Hongwei Lu Zhe Wu Shanlin Liu Zongyi Sun Hongliang Zhang Longbiao Guo Zichao Li Yongfeng Zhou Jiayang Li Zuofeng Zhu Guosheng Xiong Jue Ruan Qian Qian | 2022 | Cell Research2022，32，10： | 3 |
| 2 | Genome-wide association study and transcriptome analysis reveal new QTL and candidate genes for nitrogen-deficiency tolerance in rice显示文摘The development of rice cultivars with improved nitrogen use efficiency(NUE)is desirable for sustainable agriculture.Achieving this goal depends in part on understanding how rice responds to low soil nitrogen(N)and identifying causative genes underlying this trait.To identify quantitative trait loci(QTL)or genes associated with low N response,we conducted a genome-wide association study(GWAS)using a diverse panel of 230 rice accessions and performed a transcriptomic investigation of rice accessions with differential responses to low N stress at two N levels.We detected 411 GWAS-associated genes in 5 QTL and 2722 differentially expressed genes in response to low N,of which 24 were identified by both methods and ranked according to gene annotations,literature queries,gene expression,and genetic diversity analysis.The large-scale datasets obtained from this study reveal low N-responsive characteristics and provide insights towards understanding the regulatory mechanisms of N-deficiency tolerance in rice,and the candidate genes or QTL would be valuable resources for increasing rice NUE via molecular biotechnology. | Qing Li Xueli Lu Changjian Wang Lan Shen Liping Dai Jinli He Long Yang Peiyuan Li Yifeng Hong Qiang Zhang Guojun Dong Jiang Hu Guangheng Zhang Deyong Ren Zhenyu Gao Longbiao Guo Qian Qian Li Zhu Dali Zeng | 2022 | The Crop Journal2022，10，4： | 3 |
| 3 | Multi-agent coverage control design with dynamic sensing regions显示文摘一个合作区域侦察问题在一组代理人被要求侦察的这份报纸被考虑兴趣的一个区域。这个问题的主要挑战是察觉到每个代理人的区域在高度限制以内与它的高度变化。同时,一个代理人的侦察能力被它的高度和光线的距离决定。首先,区域侦察作为一个有效范围问题被提出,它意味着在给定的区域的每个点应该被调查直到预设水平被完成。然后,一条有效范围控制法律被建议由调整一个代理人的高度最小化范围性能索引。最后,建议控制法律的有效性通过数字模拟被验证。 | Longbiao MA Fenghua HE Long WANG Yu YAO | 2018 | Control Theory and Technology2018，16，3： | 2 |
| 4 | Ultrasonic generation by exciting electric arc: A tool for grain refinement in welding process 显示文摘 | HE Longbiao LI Luming HAO Hongwei | 2006 | Applied Physics Letters2006，89，13： | 1 |
| 5 | Identifying candidate genes and patterns of heat-stress response in rice using a genome-wide association study and transcriptome analyses显示文摘Because high temperatures impair rice production,it is desirable to elucidate the regulatory mechanisms involved in rice response to heat stress.The objectives of this study were to identify candidate genes and characterize their response patterns during rice adaptation to high temperatures at the seedling stage.Ten heat-associated quantitative-trait loci were identified in a genome-wide association study.Comparison of transcript abundances in heat-sensitive and heat-tolerant rice pools under heat stress revealed approximately 400 differentially expressed genes.The expression of genes from heatsensitive accessions changed more than those from heat-tolerant accessions under heat stress.Alternative splicing(AS)events responded to heat stress in rice.The types of AS variants significant different between the heat-sensitive and heat-tolerant accessions.Expression patterns differing between the heat-sensitive and heat-tolerant accessions were identified for genes known to be involved in heat stress.We identified eleven genes associated with rice heat stress response.These genes could be pyramided to breed heat-tolerant rice accessions. | Yingxue Yang Chao Zhang De Zhu Huiying He Zhaoran Wei Qiaoling Yuan Xiaoxia Li Xu Gao Bin Zhang Hongsheng Gao Bo Wang Shuaimin Cao Tianyi Wang Yuhua Li Xiaoman Yu Longbiao Guo Guanjing Hu Qian Qian Lianguang Shang | 2022 | The Crop Journal2022，10，6： | 1 |
| 6 | A complete assembly of the rice Nipponbare reference genome显示文摘Dear Editor,In 2005,the current commonly used rice reference genome(Oryza sativa ssp.japonica cv.Nipponbare)was initially released by the International Rice Genome Sequencing Project(International Rice Genome Sequencing Project,2005).Thereafter,the reference genome was further updated in 2013 with improved genome assembly(IRGSP-1.0)and gene annotations(MSU7,RAP-DB)(Kawahara et al.,2013;Sakai et al.,2013).In the past 10 years,this reference has been serving as one of the most important genetic resources for subsequent rice functional genomics efforts.As several rice genomes had been assembled into gapless chromosomes with only 2–5 telomeres absent(Li et al.,2021;Song et al.,2021;Zhang et al.,2022),the IRGSP1.0 and its annotations still performed as the most widely used reference.However,limitations of sequencing technology and intricate genomic organization led to an under-representation of complex regions in this reference,leaving a total of 72 major gaps(including 19 telomeres),167 minor gaps,and 779 unknown bases(Kawahara et al.,2013),with an estimated length of3%of the genome unsolved. | Lianguang Shang Wenchuang He Tianyi Wang Yingxue Yang Qiang Xu Xianjia Zhao Longbo Yang Hong Zhang Xiaoxia Li Yang Lv Wu Chen Shuo Cao Xianmeng Wang Bin Zhang Xiangpei Liu Xiaoman Yu Huiying He Hua Wei Yue Leng Chuanlin Shi Mingliang Guo Zhipeng Zhang Bintao Zhang Qiaoling Yuan Hongge Qian Xinglan Cao Yan Cui Qianqian Zhang Xiaofan Dai Congcong Liu Longbiao Guo Yongfeng Zhou Xiaoming Zheng Jue Ruan Zhukuan Cheng Weihua Pan Qian Qian | 2023 | Molecular Plant2023，16，8： | 1 |
| 7 | Ultrasonic Generation by Exciting Electric Arc: a Tool for Grain Refinement in Welding Proeess显示文摘 | He Longbiao Li Luming Hao Hongwei | 2006 | Applied Physics Letters2006，89，13： | 1 |
| 8 | Chlorophyllide-a Oxygenase 1(OsCAO1) Over-Expression Affects Rice Photosynthetic Rate and Grain Yield显示文摘Leaf color and photosynthesis are important factors for rice growth and development.Hence,improving the photosynthetic rate is an effective approach for increasing rice yield.We isolated a gene,chlorophyllide-a oxygenase 1(OsCAO1),which characterized a rice near-isogenic line named fgl(faded green leaf). | HU Ping MA Jie KANG Shujing LI Sanfeng WU Xianmei ZENG Longjun LU Caolin HE Rui HE Huiying SHANG Lianguang RAO Yuchun ZHU Xudong XIONG Guosheng QIAN Qian GUO Longbiao WANG Yuexing | 2023 | Rice science2023，30，2： | 1 |
| 9 | Simultaneously Improved Tougheness and Dielectric Properties of Epoxy/Core-Shell Particle Blends 显示文摘 | Weitao Wan Demei Yu Jian He Yunchuan Xie Longbiao Huang Xiusheng Guo | 2008 | Journal of Applied Polymer Science2008，，107： | 1 |
| 10 | Ultrasonic generation by exciting electric arc : A tool for grain refinement in welding process 显示文摘 | He Longbiao Li Luming Hao Hongwei | 2006 | Applied Physics Letters2006，89，13： | 1 |
| 11 | Geomechanical and water vapor absorption characteristics of clay-bearing soft rocks at great depth显示文摘The geological and physico-mechanical properties characterization of deep soft rocks is one of the critical scientific issues for deep soft rock engineering. In the present study, X-ray diffraction(XRD) analysis,scanning electron microscope(SEM), and mercury intrusion porosimetry experiments were carried out to investigate the mineral compositions, microstructure and porosity characteristics of the 13 claybearing soft rock samples collected from a deep coal mine in China. Water vapor absorption and uniaxial compressive experiments were also performed to examine water absorption characteristics and waterinduced strength degradation effect of the investigated deep soft rock samples. The results show that the dominant mineral components in mudstone, coarse sandstone and fine sandstone samples were calcite, quartz and clay respectively. The contents of clay minerals in all samples were relatively high and ranged from 12.3%(N-4) to 56.5%(XS-1). Water vapor absorption processes of all the soft rock samples follow an exponential law which is very similar to the water vapor absorption behavior of conglomerate samples reported in our earlier study. Correlation analyses also suggested that there were good positive correlation relationships between water absorptivity and clay minerals for both mudstone and sandstone samples. Furthermore, it was found that vapor absorption was not correlated with the porosity for mudstone, however, positive correlation relationship was found between them for sandstone. Correlation analysis between UCS, modulus of elasticity and water content demonstrated that both of them tend to decrease with the increase of their water content due to water absorption. | Zhang Na Liu Longbiao Hou Dongwen He Manchao Liu Yilei | 2014 | International Journal of Mining Science and Technology2014，24，6： | 1 |
| 12 | Ultrasonic generation by exciting electric arc: a tool for grain refinement in welding process显示文摘 | He Longbiao Wu Minsheng Li Luming | 2006 | Applied Physics Letters2006，89，13： | 1 |
| 13 | A Non-Convex Optimization Approach to Dynamic Coverage Problem of Multi-agent Systems in an Environment with Obstacles显示文摘In this paper,a cooperative region reconnaissance problem is investigated where a group of agents are required to fly across and detect events occur in an environment with static obstacles until an effective coverage is achieved.First,the region reconnaissance is formulated as a non-convex optimization problem.A coverage performance index with additional collision and obstacle avoidance constraints is given.Since the optimization index is an implicit function of state variables and cannot be used to compute gradients on state variables directly,an approximate optimization index is selected.Then,a non-convex optimization-based coverage algorithm is proposed to find the optimal reconnaissance location for each agent and guarantee no collisions trajectories among agents and obstacles.Finally,simulation experiments are performed to verify the effectiveness of the proposed approach. | MA Longbiao HE Fenghua WANG Long LI Changxi YAO Yu | 2020 | Journal of Systems Science & Complexity2020，33，2： | 0 |
| 14 | Functional Analysis of Three Rice Chloroplast Transit Peptides显示文摘Chloroplast transit peptides(CTPs) can be used to transport non-chloroplastic proteins into the chloroplasts. Here, we studied the CTPs of three rice(Oryza sativa L.) chloroplast-localized proteins and found that their CTPs could be used to transport non-chloroplast-localized proteins into the chloroplasts. Fusion proteins lacking the CTP remained located in the cytoplasm. Furthermore, we constructed green fluorescent protein fusion vectors with the three CTPs and three non-chloroplast-localized proteins, Ghd10, MULTI-FLORET SPIKELET1(MFS1), and SHORTENED UPPERMOST INTERNODE 1(SUI1). After transforming these constructs into rice protoplasts, the fusion proteins all localized in the chloroplasts. Collectively, our results showed that these CTPs can transport non-chloroplast-localized proteins into the chloroplasts, and more importantly, these CTPs can be applied to engineer chloroplast metabolism. | HE Lei CHEN Guang ZHANG Sen QIU Zhennan HU Jiang ZENG Dali ZHANG Guangheng DONG Guojun GAO Zhenyu REN Deyong SHEN Lan GUO Longbiao QIAN Qian ZHU Li | 2019 | Rice science2019，26，1： | 0 |
| 15 | A centromere map based on super pan-genome highlights the structure and function of rice centromeres显示文摘Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary factors.Rice centromeres are crucial for chromosome segregation,and contain some unreported genes.Due to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is needed.We constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.We showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary patterns.We also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution.Furthermore,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging.We investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 methods.By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement. | Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen Longbo Yang Xiaofan Dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang Hongge Qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang Qiang Xu Yan Cui Qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou Qian Qian Longbiao Guo Lianguang Shang | 2024 | Journal of Integrative Plant Biology2024，66，2： | 0 |
| 16 | Coleoptile Purple Line Regulated by A-P Gene System Is a Valuable Marker Trait for Seed Purity Identification in Hybrid Rice显示文摘In plants,a large number of anthocyanin biosynthetic genes encoding enzymes and regulatory genes encoding transcription factors are required for anthocyanin synthesis.Coleoptile purple lines are two purple lines on both sides of coleoptiles after seed germination.However,the molecular mechanism of coleoptile purple line is not clear in rice so far.In this study,two major dominant genes,coleoptile purple line 1(OsCPL1,also known as OsC1)and coleoptile purple line 2(OsCPL2),were isolated via map-based cloning,and both of them were required for anthocyanin biosynthesis of coleoptile purple line in rice.The knockout and complementation experiments confirmed that OsC1 was required for purple color in most organs,such as coleoptile line,sheath,auricle,stigma and apiculus,whereas OsCPL2 was just required for coleoptile purple line.OsC1 was predominantly expressed in coleoptiles,flag leaves,and green panicles,and highly expressed in young leaves,whereas OsCPL2 was predominantly expressed in coleoptiles,and extremely lowly expressed in the other tested organs.Loss-of-function of either OsC1 or OsCPL2 resulted in significant reduction of transcript levels of multiple anthocyanin biosynthesis genes in coleoptiles.Coleoptile purple line was further used as a marker trait in hybrid rice.Purity identification in hybrid rice seeds via coleoptile purple line just needed a little water,soil and a small plate and could be completed within 5 d.Molecular marker and field identification analyses indicated that coleoptile purple line was reliable for the hybrid seed purity identification.Our findings disclosed that coleoptile purple line in rice was regulated by two major dominant genes,OsC1 and OsCPL2,and can be used as a simple,rapid,accurate and economic marker trait for seed purity identification in hybrid rice. | DU Shuanglin WANG Zhongwei CHEN Yun TAN Yao LI Xiang ZHU Wenping HE Guanghua LEI Kairong GUO Longbiao ZHANG Yi | 2022 | Rice science2022，29，5： | 0 |
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