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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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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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Construction and Identification of Bacterial Artificial Chromosome Library for 0-613-2R in Upland Cotton

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Journal of Integrative Plant Biology 2006年第2期48卷 219-222页

作者： Jian-Mei Yin Wang-zhen Guo tian-zhen zhang State Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural University Nanjing 210095 China

A bacterial artificial chromosome （BAC） library containing a large genomlc DNA insert is an important tool for genome physical mapping, map-based cloning, and genome sequencing. To Isolate genes via a map-based cloning strategy and to perform physical mapping of the cotton genome, a high-quality BAC library containing large cotton DNA Inserts Is needed. We have developed a BAC library of the restoring line 0-613-2R for Isolating the fertility restorer （Rf1） gene and genomic research in cotton （Gossypium hirsutum L.）. The BAC library contains 97 825 clones stored In 255 pieces of a 384-well mlcrotiter plate. Random samples of BACs digested with the Notl enzyme Indicated that the average Insert size Is approximately 130 kb, with a range of 80-275 kb, and 95.7% of the BAC clones in the library have an average insert size larger than 100 kb. Based on a cotton genome size of 2 250 Mb, library coverage is 5.7 × haploid genome equivalents. Four clones were selected randomly from the library to determine the stability of the BAC clones. There were no different fingerprints for 0 and 100 generations of each clone digested with Notl and Hlndiii enzymes. Thus, the atabiiity of a single BAC clone can be sustained at iesat for 100 generations. Eight simple sequence repeat （SSR） markers flanking the Rf; gene were chosen to screen the BAC library by pool using PCR method and 25 positive clones were identified with 3.1 positive clones per SSR marker.

关键词： bacterial artificial chromosome library cotton map-based cloning Rf gene.

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Sequence Divergence of Microsatellites and Phylogeny Analysis in Tetraploid Cotton Species and Their Putative Diploid Ancestors

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Journal of Integrative Plant Biology 2005年第12期47卷 1418-1430页

作者： Wang-zhen GUO Dong FANG Wen-Duo YU tian-zhen zhang State Key Laboratory of Crop Genetics and Germplasm Enhancement Cotton Research Institute Nanjing Agricultural University Nanjing 210095 China

To determine the level of microsatellite sequence differences and to use the information to construct a phylogenetic relationship for cultivated tetraploid cotton （Gossypium spp.） species and their putative diploid ancestors, 10 genome-derived microsatellite primer pairs were used to amplify eight species, including two tetraploid and six diploid species, in Gossypium. A total of 92 unique amplicons were resolved using polyacrylamide gel electrophoresis. Each amplicon was cloned, sequenced, and analyzed using standard phylogenetic software. Allelic diversities were caused mostly by changes in the number of simple sequence repeat （SSR） motif repeats and only a small proportion resulted from interruption of the SSR motif within the locus for the same genome. The frequency of base substitutions was 0.5%-1.0% in different genomes, with only few indels found. Based on the combined 10 SSR flanking sequence data, the homology of A-genome diploid species averaged 98.9%, even though most of the amplicons were of the same size, and the sequence homology between G. gossypioides （Ulbr.） Standl. and three other D-genome species （G. raimondii Ulbr., G. davidsonii Kell., and G. thurberi Tod.） was 98.5%, 98.6%, and 98.5%, respectively. Phylogenetic trees of the two allotetraploid species and their putative diploid progenitors showed that homoelogous sequences from the A- and D-subgenome were still present in the polyploid subgenomes and they evolved independently. Meanwhile, homoelogous sequence interaction that duplicated loci in the polyploid subgenomes became phylogenetic sisters was also found in the evolutionary history of tetraploid cotton species. The results of the present study suggest that evaluation of SSR variation at the sequence level can be effective in exploring the evolutionary relationships among Gossypuim species.

关键词： diploid Gossypium microsatellite phylogenetic tree simple sequence repeat (SSR) tetraploid.

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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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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 *** 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 *** show that the promising HER catalysts include Pt atoms in C_(4) and Sc atoms in C_(1)N_(3) coordination ***,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 *** 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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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 ***,explicit formulas for the first passage density have only been obtained for a few *** paper derives an explicit formula for the first passage density of Brownian motion with twosided piecewise continuous boundaries which may have some points of *** are used to obtain a simplified formula for estimating the first passage ***,the results are also generalized to the case of two-sided general nonlinear *** 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 ***,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 ***,these distortions are particularly significant in compact neutron radiography systems with low neutron ***,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 *** neutron radiographic image datasets with various types and levels of distortion were built for the first time as multi-distortion suppression ***,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 *** 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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Multiresponsive,easy-reversible,and dual-visual Pt(Ⅱ)salt nanostructures for advanced anti-counterfeiting application

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Nano Research 2024年第1期17卷 372-381页

作者： zhen Su§ Depeng Li§ Lixin zhang Si tian Yuhong Su Xiaoyun Hu Duan Xiong Qingqing Guan Key Laboratory of Oil and Gas Fine Chemicals Ministry of Education College of Chemical EngineeringXinjiang UniversityUrumqi 830017China

Smart materials that integrate multi-stimuli response,full reversibility,and dual-visual read-out channel are highly desired for anticounterfeiting and information encryption ***,we developed a multiresponsive perchlorate terpyridyl Pt(Ⅱ)nano complex which could undergo fully reversible conversion between three forms stimulated by water or formaldehyde molecule due to the extent of Pt–Pt ***,a dual-visual channel,i.e.,the colorimetric channel changed from yellow to orange or red and the corresponding luminescent channel from orange to orange-red or red,has also been *** weak and equivalent strength of ion-dipole interaction and hydrogen bond that generated between formaldehyde/water and Pt(II)salt result in the easy-control reversibility between the three ***,by introducing different polymer matrices,1Cl·ClO_(4)@PMMA(1Cl·ClO_(4):[Pt(tpy)Cl]·ClO4,tpy:2,2':6',2''-terpyridine),PMMA:poly(methyl methacrylate))and 1Cl·ClO4@PVA(PVA:polyvinyl alcohol)are successfully constructed,which exhibit different reversible behaviors since the PMMA and PVA matrix exert different influences on the strength of *** smart Pt(II)salt nanostructures present great potential for high-security-level anticounterfeiting application.

关键词： Pt(II)complex multiresponse reversibility anticounterfeiting information encryption

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