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Functional diversifications of Gh ERF1 duplicate genes after the formation of allotetraploid cotton

Journal of Integrative Plant Biology 2019年第1期61卷 60-74页

作者： Chunxiao Liu tian zhen zhang National Key Laboratory of Crop Genetics & Germplasm Enhancement Cotton Research InstituteNanjing Agricultural University Crop Science Institute Agronomy DepartmentCollege of Agriculture and BiotechnologyZhejiang University

Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors(GhERF1 s), anchored on Chr-A07 and Chr-D07 were isolated from a high-yielding cotton hybrid(XZM2)and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress Nucleotide sequence analysis of 524 diverse accessions together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7 A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7 A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7 A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7 A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de-and neofunctionalization occurred in one of the duplicate genes,thus providing new genomic insight into the evolution of allotetraploid cotton species.

关键词： Functional diversifications of Gh ERF1 duplicate genes after the formation of allotetraploid cotton

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Quantitative Trait Loci Mapping of Leaf Morphological Traits and Chlorophyll Content in Cultivated Tetraploid Cotton

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Journal of Integrative Plant Biology 2005年第11期47卷 1382-1390页

作者： Xian-Liang SONG Wang-zhen GUO Zhi-Guo HAN tian-zhen zhang State Key Laboratory of Crop Genetics and Germplasm Enhancement Cotton Research Institute Nanjing Agricultural University Nanjing 210095 China Shandong Agricultural University College of Agronomy Taian 271018 China

Genetic mapping provides a powerful tool for quantitative trait loci （QTL） analysis at the molecular level. A simple sequence repeat （SSR） genetic map containing 590 markers and a BCI population from two cultivated tetraploid cotton （Gossypium hirsutum L.） cultivars, namely TM-1 and Hai 7124 （G. barbadense L.）, were used to map and analyze QTL using the composite interval mapping （CIM） method. Thirty one QTLs, 10 for lobe length, 13 for lobe width, six for lobe angle, and two for leaf chlorophyll content, were detected on 15 chromosomes or linkage groups at logarithm of odds （LOD）≥2.0, of which 15 were found for leaf morphology at LOD≥3.0. The genetic effects of the QTL were estimated. These results are fundamental for marker-assisted selection （MAS） of these traits in tetraploid cotton breeding.

关键词： chlorophyll cotton leaf morphology quantitative trait locus mapping simple sequencerepeat.

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Insights into the Bamboo Genome:Syntenic Relationships to Rice and Sorghum

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Journal of Integrative Plant Biology 2010年第11期52卷 1008-1015页

作者： Yi-Jie Gui Yan Zhou Yu Wang Sheng Wang Sheng-Yue Wang Yan Hu Shi-Ping Bo Huan Chen Chang-Ping Zhou Nai-Xun Ma tian-zhen zhang Long-Jiang Fan Institute of Crop Science & Institute of Bioinformatics Zhejiang UniversityHangzhou 310029China State Key Laboratory of Genetic Engineering Department of MicrobiologySchool of Life SciencesFudan UniversityShanghai 200032China Hangzhou Dianzi University XiashaHangzhou 310018China MOST Key Laboratory of Health and Disease Genomics Chinese National Human Genome Center at ShanghaiShanghai 201203China National Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agriculture UniversityNanjing 210095China Anji Bamboo Exposition Garden Anji 313300China The Research Institute of Subtropical Forestry Chinese Academy of ForestryFuyang 311400China

Bamboo occupies an important phylogenetic node in the grass family and plays a significant role in the forest industry.We produced 1.2 Mb of tetraploid moso bamboo （Phyllostachys pubescens E.Mazel ex H.de Leh.） sequences from 13 bacterial artificial chromosome （BAC） clones,and these are the largest genomic sequences available so far from the subfamily Bambusoideae.The content of repetitive elements （36.2%） in bamboo is similar to that in rice.Both rice and sorghum exhibit high genomic synteny with bamboo,which suggests that rice and sorghum may be useful as models for decoding Bambusoideae genomes.

关键词： Bamboos Sorghum Rice Genomes

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The miR319-Targeted GhTCP4 Promotes the Transition from Cell Elongation to Wall Thickening in Cotton Fiber

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Molecular Plant 2020年第7期13卷 1063-1077页

作者： Jun-Feng Cao Bo Zhao Chao-Chen Huang Zhi-Wen Chen Ting Zhao Hong-Ru Liu Guan-Jing Hu Xiao-Xia Shangguan Chun-Min Shan- Ling-Jian Wang tian-zhen zhang Jonathan F.Wendel Xue-Ying Guan Xiao-Ya Chen National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China Plant Stress Biology Center Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Shanghai 200032China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China Agronomy Department College of Agriculture and BiotechnologyZhejiang UniversityHangzhouZhejiang 310058China Department of Ecology Evolution and Organismal BiologyIowa State UniversityAmesIA 50011.USA Plant Science Research Center Shanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghai 201602China

Plant cell growth involves a complex interplay among cell-wall expansion, biosynthesis, and, in specific tissues, secondary cell wall (SCW) deposition, yet the coordination of these processes remains elusive. Cotton fiber cells are developmentally synchronous, highly elongated, and contain nearly pure cellulose when mature. Here, we report that the transcription factor GhTCP4 plays an important role in balancing cotton fiber cell elongation and wall synthesis. During fiber development the expression of miR319 declines while GhTCP4 transcript levels increase, with high levels of the latter promoting SCW deposition. GhTCP4 interacts with a homeobox-containing factor, GhHOX3, and repressing its transcriptional activity. GhTCP4 and GhHOX3 function antagonistically to regulate cell elongation, thereby establishing temporal control of fiber cell transition to the SCW stage. We found that overexpression of GhTCP4A upregulated and accelerated activation of the SCW biosynthetic pathway in fiber cells, as revealed by transcriptome and promoter activity analyses, resulting in shorter fibers with varied lengths and thicker walls. In contrast, GhTCP4 downregulation led to slightly longer fibers and thinner cell walls. The GhHOX3–GhTCP4 complex may represent a general mechanism of cellular development in plants since both are conserved factors in many species, thus providing us a potential molecular tool for the design of fiber traits.

关键词： cell elongation secondary cell wall cotton fiber Gossypium hirsutum TCP microRNA

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Data-driven rational design of single-atom materials for hydrogen evolution and sensing

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Nano Research 2024年第4期17卷 3352-3358页

作者： Lei Zhou Pengfei tian Bowei zhang Fu-zhen Xuan Shanghai Key Laboratory of Intelligent Sensing and Detection Technology East China University of Science and TechnologyShanghai 200237China School of Mechanical and Power Engineering East China University of Science and TechnologyShanghai 200237China Key Laboratory of Pressure Systems and Safety of Ministry of Education East China University of Science and TechnologyShanghai 200237China

Herein we proposed a data-driven high-throughput principle to screen high-performance single-atom materials for hydrogen evolution reaction(HER)and hydrogen sensing by combing the theoretical computations and a topology-based multi-scale convolution kernel machine learning algorithm.After the rational training by 25 groups of data and prediction of all 168 groups of single-atom materials for HER and sensing,respectively,a high prediction accuracy(>0.931 R^(2) score)was achieved by our model.Results show that the promising HER catalysts include Pt atoms in C_(4) and Sc atoms in C_(1)N_(3) coordination environment.Moreover,Y atoms in C_(4) coordination environment and Cd atoms in C_(2)N_(2)-ortho coordination environment were predicted with great potential as hydrogen sensing materials.This method provides a way to accelerate the discovery of innovative materials by avoiding the time-consuming empirical principles in experiments.

关键词： machine learning single-atom materials sensing hydrogen evolution

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Ni-catalyzed highly regio- and stereo-selective diborylative cyclization of 1,6-enynes with diboron reagent

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Science China Chemistry 2024年第3期67卷 981-989页

作者： Qitao Guan zhen Shen Yiqiang tian Genping Huang Chun zhang Institute of Molecular Plus Tianjin Key Laboratory of Molecular Optoelectronic ScienceDepartment of ChemistrySchool of SciencesTianjin UniversityTianjin 300072China State Key Laboratory of Elemento-Organic Chemistry Nankai UniversityTianjin 300071China

The Ni-catalyzed highly selective diborylative cyclization of 1,6-enynes with diboron reagent has been developed. When pinB-Bdan was used, multiple types of boron-containing functional groups could be installed into organic molecule with great chemoselectivity and regioselectivity though this reaction. Meanwhile, if B_2pai_2 was employed, the asymmetric diborylative cyclization could be well induced by using strategy of dynamic kinetic resolution. Importantly, the above reactions could afford desired product with 100% atomic economy, and could be compatible with different series of substituents. The studies of further transformation well illustrated that different type products could serve diverse synthetic strategy. Notably, the reaction mechanism was intensively studied by density functional theory(DFT) calculations, which could reveal the mechanism of regio- and enantio-selective control.

关键词： nickel-catalyzed organoboron cyclization regioselectivity enantioselectivity

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Construction of a Bacterial Artificial Chromosome Library of TM-1,a Standard Line for Genetics and Genomics in Upland Cotton

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Journal of Integrative Plant Biology 2009年第1期51卷 107-112页

作者： Yan Hu Wang-zhen Guo tian-zhen zhang National Key Laboratory of Crop Genetics & Germplasm Enhancement Cotton Research Institute Nanjing Agricultural University Nanjing 210095 China

A bacterial artificial chromosome （BAC） library was constructed for Gossypium hirsutum acc. TM-1, a genetic and genomic standard line for Upland cotton. The library consists of 147 456 clones with an average insert size of 122.8 kb ranging from 97 to 240 kb. About 96.0% of the clones have inserts over 100 kb. Therefore, this library represents theoretically 7.4 haploid genome equivalents based on an AD genome size of 2 425 Mb. Clones were stored in 384 384- well plates and arrayed into multiplex pools for rapid and reliable library screening. BAC screening was carried out by four-round poiymerase chain reactions using 23 simple sequence repeats （SSR） markers, three sequence-related amplified polymorphism markers and one pair of primers for a gene associated with fiber development to test the quality of the library. Correspondingly, in total 92 positive BAC clones were identified with an average four positive clones per SSR marker, ranging from one to eight hits. Additionally, since these SSR markers have been localized to chromosome 12 （A12） and 26 （D12） according to the genetic map, these BAC clones are expected to serve as seeds for the physical mapping of these two homologous chromosomes, sequentially map-based cloning of quantitative trait loci or genes associated with important agronomic traits.

关键词： bacterial artificial chromosome library polymerase chain reaction screening simple sequence repeats markers TM-1 upland cotton.

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Epileptic brain network mechanisms and neuroimaging techniques for the brain network

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Neural Regeneration Research 2024年第12期19卷 2637-2648页

作者： Yi Guo Zhonghua Lin zhen Fan Xin tian Department of Neurology Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuan ProvinceChina Sichuan Provincial Center for Mental Health Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuan ProvinceChina Department of Geriatrics Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuan ProvinceChina Department of Neurology Chongqing Key Laboratory of NeurologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina

Epilepsy can be defined as a dysfunction of the brain network,and each type of epilepsy involves different brain-network changes that are implicated diffe rently in the control and propagation of interictal or ictal discharges.Gaining more detailed information on brain network alterations can help us to further understand the mechanisms of epilepsy and pave the way for brain network-based precise therapeutic approaches in clinical practice.An increasing number of advanced neuroimaging techniques and electrophysiological techniques such as diffusion tensor imaging-based fiber tra ctography,diffusion kurtosis imaging-based fiber tractography,fiber ball imagingbased tra ctography,electroencephalography,functional magnetic resonance imaging,magnetoencephalography,positron emission tomography,molecular imaging,and functional ultrasound imaging have been extensively used to delineate epileptic networks.In this review,we summarize the relevant neuroimaging and neuroelectrophysiological techniques for assessing structural and functional brain networks in patients with epilepsy,and extensively analyze the imaging mechanisms,advantages,limitations,and clinical application ranges of each technique.A greater focus on emerging advanced technologies,new data analysis software,a combination of multiple techniques,and the construction of personalized virtual epilepsy models can provide a theoretical basis to better understand the brain network mechanisms of epilepsy and make surgical decisions.

关键词： electrophysiological techniques epilepsy functional brain network functional magnetic resonance imaging functional near-infrared spectroscopy machine leaning molecular imaging neuroimaging techniques structural brain network virtual epileptic models

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First Passage Density of Brownian Motion with Two-sided Piecewise Linear Boundaries

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Acta Mathematica Sinica,English Series 2024年第6期40卷 1505-1520页

作者： zhen YU Mao Zai tian Center for Applied Statistics School of StatisticsRenmin University of ChinaBeijing 100872P.R.China School of Mathematics and Data Science Changji UniversityChangji 831100P.R.China

The first passage time has many applications in fields like finance,econometrics,statistics,and biology.However,explicit formulas for the first passage density have only been obtained for a few cases.This paper derives an explicit formula for the first passage density of Brownian motion with twosided piecewise continuous boundaries which may have some points of discontinuity.Approximations are used to obtain a simplified formula for estimating the first passage density.Moreover,the results are also generalized to the case of two-sided general nonlinear boundaries.Simulations can be easily carried out with Monte Carlo method and it is demonstrated for several typical two-sided boundaries that the proposed approximation method offers a highly accurate approximation of first passage density.

关键词： Boundary non-crossing probability first density passage density two-sided piecewise continuous boundaries Brownian motion

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Multi-distortion suppression for neutron radiographic images based on generative adversarial network

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Nuclear Science and Techniques 2024年第4期35卷 176-188页

作者： Cheng-Bo Meng Wang-Wei Zhu zhen zhang Zi-Tong Wang Chen-Yi Zhao Shuang Qiao tian zhang School of Physics Northeast Normal UniversityChangchun 130024China

Neutron radiography is a crucial nondestructive testing technology widely used in the aerospace,military,and nuclear industries.However,because of the physical limitations of neutron sources and collimators,the resulting neutron radiographic images inevitably exhibit multiple distortions,including noise,geometric unsharpness,and white spots.Furthermore,these distortions are particularly significant in compact neutron radiography systems with low neutron fluxes.Therefore,in this study,we devised a multi-distortion suppression network that employs a modified generative adversarial network to improve the quality of degraded neutron radiographic images.Real neutron radiographic image datasets with various types and levels of distortion were built for the first time as multi-distortion suppression datasets.Thereafter,the coordinate attention mechanism was incorporated into the backbone network to augment the capability of the proposed network to learn the abstract relationship between ideally clear and degraded images.Extensive experiments were performed;the results show that the proposed method can effectively suppress multiple distortions in real neutron radiographic images and achieve state-of-theart perceptual visual quality,thus demonstrating its application potential in neutron radiography.

关键词： Neutron radiography Multi-distortion suppression Generative adversarial network Coordinate attention mechanism

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