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A zinc finger protein, interacted with cyclophilin,affects root development via IAA pathway in rice

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Journal of Integrative Plant Biology 2017年第7期59卷 496-505页

作者： Peng Cui Hongbo Liu Songlin Ruan Basharat ali rafaqat ali Gill Huasheng Ma Zhifu Zheng Weijun Zhou Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm Zhejiang University College of Agriculture and Food Science Zhejiang A & F University Plant Molecular Biology and Proteomics Lab Institute of Biotechnology Hangzhou Academy of Agricultural Sciences

The plant hormone auxin plays a crucial role in lateral root development. To better understand the rnolecular mechanisms underlying lateral root formation, an auxin-responsive gene OsCYP2 （Oso2g0121300） was characterized from rice. Compared to the wild type, OsCYP2-RNAi （RNA interference） lines exhibited distinctive defects in lateral root development. Yeast two-hybrid and glutathione S-transferase puIl-down results confirmed that OsCYP2 interacted with a C2HC-type zinc finger protein （OsZFP, O501g0252900） which is located in the rice nucleus. T2OsZFP-RNAi lines had significantly fewer lateral roots than did wild-type plants, which suggests a role for OsCYP2 and OsZFP in regulating lateral root *** real-time polymerase chain reaction showed that the expression of certain Aux/IAA （auxin/indole-3- acetic acid） genes was altered in OsCYP2- and OsZFP-RNAi lines in response to IAA. These findings imply that OsCYP2 and OsZFP participate in IAA signal pathways controlling lateral root development. More importantly, OslAA11 showed functional redundancy not only in OsCYP2-RNAi lines but also in OsZFP-RNAi lines, which provides important clues for the elucidation of mechanisms controlling lateral root development in response to auxin.

关键词： IAA of gene root A zinc finger protein ZFP RNAi with

Microwave-assisted pre-ionization experiments on GLAST-Ⅲ

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Plasma Science and Technology 2021年第8期23卷 53-61页

作者： Riaz KHAN Sehrish SHAKIR Ahmad ali Muhammad Khawar AYUB Moazzam NAZIR Zia UR-REHMAN Abdul QAYYUM Muhammad Athar NAVEED Sarfraz AHMAD Zahoor AHMAD rafaqat ali Shahid HUSSAIN Pakistan Tokamak Plasma Research Institute P.O.NiloreIslamabad 44000Pakistan Theoretical Physics Division PINSTECHP.O.NiloreIslamabad 44000Pakistan

GLAss Spherical Tokamak(GLAST-Ⅲ)is a spherical tokamak with an insulating vacuum vessel that has a unique single-passage capability for incident *** this work,electron cyclotron resonance heating(ECRH)-assisted plasma pre-ionization in GLAST-Ⅲis explored for three radio-frequency(RF)polarizations(the O-,X-,and M-modes)at different toroidal-field(TF)strengths and filled gas *** optimum hydrogen pressure is identified for efficient plasma pre-ionization.A comparison of the plasma pre-ionizations initiated by the O-,X-,and M-modes shows prominent differences in the breakdown time,location,and wave *** the case of O-mode polarization,microwave absorption occurs for a relatively shorter duration,resulting in a bell-shaped electron-temperature(Te)temporal *** absorption is dominant in the case of the X-mode,leading to a broader Te temporal *** M-mode discharge contains features of both the X-and *** plasma pre-ionization is achieved in the X-mode polarization for the intermediate TF strengths(with a central toroidal magnetic field B0=0.075 T).Traces of the electron-number density show a similar tendency,as revealed by *** results suggest that the X-mode is the best candidate for efficient plasma pre-ionization at low filled gas pressures(10-2 Pa)in small tokamaks.

关键词： GLAST-Ⅲ microwave ECRH pre-ionization polarization

Computational Tools and Resources for CRISPR/Cas Genome Editing

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 108-126页

作者： Chao Li Wen Chu rafaqat ali Gill Shifei Sang Yuqin Shi Xuezhi Hu Yuting Yang Qamar U.Zaman Baohong Zhang Oil Crops Research Institute Chinese Academy of Agricultural SciencesKey Laboratory for Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062China Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081China Department of Biology East Carolina UniversityGreenvilleNC 27858USA

The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)nucleases and their functional variants,as well as in developing precise CRISPR/Cas-derived genome *** programmable and robust features of the genome editors provide an effective RNAguided platform for fundamental life science research and subsequent applications in diverse scenarios,including biomedical innovation and targeted crop *** of the most essential principles is to guide alterations in genomic sequences or genes in the intended manner without undesired off-target impacts,which strongly depends on the efficiency and specificity of single guide RNA(sgRNA)-directed recognition of targeted DNA *** advances in empirical scoring algorithms and machine learning models have facilitated sgRNA design and off-target *** this review,we first briefly introduce the different features of CRISPR/Cas tools that should be taken into consideration to achieve specific ***,we focus on the computer-assisted tools and resources that are widely used in designing sgRNAs and analyzing CRISPR/Cas-induced on-and off-target ***,we provide insights into the limitations of available computational tools that would help researchers of this field for further ***,we suggest a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.

关键词： Genome editing Efficiency and specificity CRISPR/Cas9 sgRNA Computational tool Algorithm

Effects of ZJ0273 on barley and growth recovery of herbicide-stressed seedlings through application of branched-chain amino acids

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2019年第1期20卷 71-83页

作者： Ling XU Jian-yao SHOU rafaqat ali GILL Xiang GUO Ullah NAJEEB Wei-jun ZHOU Zhejiang Key Lab of Plant Secondary Metabolism and Regulation and College of Life Sciences Zhejiang Sci-Tech University Zhuji Municipal Agro-Tech Extension Center Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm Zhejiang University Queensland Alliance for Agriculture and Food Innovation Centre for Plant Science the University of Queensland

In this study, we evaluated the effect of the herbicide propyl 4-(2-(4,6-dimethoxypyrimidin-2-yloxy)benzylamino) benzoate(ZJ0273) on barley growth and explored the potential to trigger growth recovery through the application of branched-chain amino acids(BCAAs). Barley plants were foliar-sprayed with various concentrations of ZJ0273(100, 500, or 1000 mg/L) at the four-leaf stage. Increasing either the herbicide concentration or measurement time after herbicide treatment significantly impaired plant morphological parameters such as plant height and biomass, and affected physiological indexes, i.e. maximal photochemical efficiency(Fv/Fm), quantum yield of photosystem II(ФPSII), net photosynthetic rate(Pn), and chlorophyll meter value(soil and plant analyzer development(SPAD)). Cellular injury of herbicide-treated plants was also evidenced by increased levels of reactive oxygen species(ROS) and antioxidative enzyme activity. Elevated levels of herbicide significantly reduced the activity of acetolactate synthase(ALS)-a keyD, enzyme in the biosynthesis of BCAAs. In a separate experiment, growth recovery in herbicide-stressed barley plants ? was studied using various concentrations of BCAAs(10, 50, 100, and 200 mg/L). Increasing BCAA concentration in growth media significantly increased the biomass of herbicide-stressed barley seedlings, but had no significant effect on non-stressed plants. Further, BCAAs(100 mg/L) significantly down-regulated ROS and consequently antioxidant enzyme levels in herbicide-stressed plants. Our results showed that exogenous application of BCAAs could reverse the inhibitory effects of ZJ0273 by restoring protein biosynthesis in barley seedlings.

关键词： Antioxidant enzyme activity Barley Branched-chain amino acid Photosynthetic system Reactive oxygen species ZJ0273

Salicylic acid mediates oxidative injury and antioxidant enzymes in Oryza sativa japonica cultivars against quinclorac toxicity

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Salicylic acid mediates oxidative injury and antioxidant enz...

Dissection of the genetic control of plant architecture by associative transcriptomics in Brassica napus

第十二届全国杂草科学大会

作者： Jian Wang Quyu Kong Chong Yang rafaqat ali Gill Jinwen Zhu Weijun Zhou College of Agriculture and Biotechnology Zhejiang University

The quinolinecarboxylic acid quinclorac is a new class of highly selective auxin herbicide and used by both,pre and post transplanting and direct-seeded *** the present study,different concentrations(0,0.1,0.25,1 g/L)of quinclorac were used in order to investigate the physio-chemical changes in two Oryza sativa japonica cultivars Zhejing 88 and Xiushui *** applied salicylic acid(SA)was pre-treated to regulate the oxidative damage caused by auxin *** showed that quinclorac induced a significant inhibition in growth parameters of two rice *** antioxidant enzymes activities in both cultivars were closely associated with quinclorac *** activities of POD,APX,SOD and GSTs were significantly increased,while CAT activity was reduced after quinclorac ***,GSH content was reduced and GSSG was increased in Zhejing 88but no significant change in Xiushui *** accumulation of MDA and ROS contents was elevated with the increasing concentrations of quinclorac as compared with untreated *** of SA significantly increased the plant biomass and the activity of antioxidant enzymes while reduced the MDA and ROS as compared to the quinclorac toxicity *** staining(NBT and DAB)and ultrastrucrural observations solidify our results that higher level of quinclorac(1g/L)significantly reduced the plant physio-chemical attributes as compared to control *** analyses verify that SA statistically alleviated the negative effects of quinclorac and also further improve the plant defense ***,according to these findings cultivar Xiushui 134 showed the higher tolerance to quinclorac than Zhejing 88 with respect to physio-histo-chemical parameters.

关键词： quinclorac salicylic acid rice antioxidant histochemical staining microscopic study

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Dissection of the genetic control of plant architecture by a...

Hydrothermal synthesis and characterization of carbon-doped TiO2 nanoparticles

2018全国植物生物学大会

作者： Meili Xie Md Mostofa Uddin Helal rafaqat ali Gill Lingli Yang Yuanyuan Zhang Chaobo Tong Minqiang Tang Xiaohui Cheng Yueying Liu Shengyi Liu The Key Laboratory of Biology and Genetic Improvement of Oil Crops The Ministry of Agriculture of PRCOil Crops Research InstituteChinese Academy of Agriculture Sciences

Plant architecture refers to the morphological characteristics and spatial arrangement of the plant crops and has shown significant impacts on crop adaptation and yield *** few genes related to plant architecture have been identified,little is known about the genetic control of the important traits in Brassica *** Transcriptomics(AT) is an advanced method to identify molecular markers associated with trait variation across a diversity panel,exploiting both gene sequence variation and gene expression *** a genetic diversity panel of more than 300 accessions are chose to dissect the genetic control of plant *** associative transcriptomics,we identify molecular markers for a suite of important ***,based on conserved synteny with Arabidopsis thalinan we are able to provide a biological context to the candidate genes detected and verify the function of these genes in *** study not only furthers our understanding of the gene network for plant architecture but also provieds a set of markers for the breeding programmes.

关键词： plant architecture associative transcriptomics Brassica napus

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Chinese Physics B 2020年第11期29卷 516-521页

作者： Zafar ali Javaid Ismail rafaqat Hussain AShah Arshad Mahmood Arbab Mohammad Toufiq Shams ur Rahman Department of Physics COMSATS University IslamabadPark RoadIslamabad 45550Pakistan Department of Chemistry COMSATS University IslamabadPark RoadIslamabad 45550Pakistan National Institute of Lasers and Optronics College Pakistan Institute of Engineering and Applied Sciences(NILOP-CPIEAS)Nilore 45650IslamabadPakistan Department of Physics Hazara University MansehraMansehra 21300Pakistan

We report the hydrothermal growth of pure and doped TiO2 nanoparticles with different concentrations of *** microstructure of the as-synthesized samples is characterized by x-ray diffraction(XRD),field emission scanning electron microscopy(FESEM),energy dispersive x-ray spectroscopy(EDX),and Raman spectroscopy to understand the structure and *** XRD patterns confirm the formation of anatase phase of TiO2 with the average crystallite size is calculated to be in the range of 13 nm to 14.7 *** functional groups of these nanostructures are characterized by Fourier transformed infrared(FT-IR)spectroscopy,which further confirms the single anatase phase of the synthesized ***-visible absorption spectroscopy is used to understand the absorption behavior,which shows modification in the optical bandgap from 3.13 eV(pure TiO2)to 3.74 eV(1.2 mol%C-doped TiO2).Furthermore,the Ti^3+centers associated with oxygen vacancies are identified using electron paramagnetic resonance spectroscopy(EPR).

关键词： titanium dioxide hydrothermal synthesis defect states bandgap

Estimation of Genetic Divergence and Character Association Studies in Local and Exotic Diversity Panels of Soybean(Glycine max L.)Genotypes

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Phyton-International Journal of Experimental Botany 2023年第6期92卷 1887-1906页

作者： Syed ali Zafar Muhammad Aslam Haroon Zaman Khan Sehrish Sarwar Rao Saad Rehman Mariam Hassan Ramala Masood Ahmad rafaqat AGill Basharat ali Ibrahim Al-Ashkar Abdullah Ibrahim Md Atikur Rahman Ayman El Sabagh Oilseeds Research Institute Ayub Agricultural Research InstituteFaisalabadPakistan Department of Plant Breeding and Genetics University of AgricultureFaisalabadPakistan Department of Agronomy University of AgricultureFaisalabadPakistan College of Plant Science and Technology Huazhong Agricultural UniversityWuhanChina Key Laboratory of Biology and Genetic Improvement of Oil Crops The Ministry of Agriculture and Rural AffairsOil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan430062China Department of Agricultural Engineering Khwaja Fareed University of Engineering and Information TechnologyRahim Yar KhanPakistan Department of Plant Production College of Food and Agriculture SciencesKing Saud UniversityRiyadhSaudi Arabia Grassland and Forage Division National Institute of Animal ScienceRural Development AdministrationCheonanKorea Department of Agronomy Faculty of AgricultureUniversity of KafrelsheikhKafr ElsheikhEgypt

The availability of favorable genetic diversity is a thriving vitality for the success of a breeding *** provides a firm basis of selecting superior breeding lines for the development of high yielding crop *** this context,present investigation aimed to generate information on genetic divergence and character association in a diversity panel of 123 local and exotic soybean *** of variance revealed significant response of the evaluated genotypes based on studied *** depicted the probability of selecting desirable soybean genotypes by focusing on character association studies and genetic diversity *** analysis revealed that seed yield per plant showed high positive correlation with 100-seed weight followed by pods per plant and plant ***,path coefficient analysis exposed that pods per plant had maximum direct contribution in seed yield per plant followed by 100-seed weight,days to flowering and SPAD *** named“G-10”showed maximum yield per plant followed by 24607,G-52,24593,Arisoy,24566,17426,A-3127,24570 and *** diversity analysis grouped the evaluated germplasm into 17 *** clusters showed zero intra-cluster variability;while inter-cluster divergence ranged from 9.00 to *** V showed maximum inter-cluster distance with cluster XII followed by that of between V and ***,cluster IV with superior genotypes(G-10,24607,24593 and 24566),VI(17426 and 24567),XIII(24570)and X(Arisoy and G-52)showed above mean values for most of the studied ***,the results of hybridization between the superior genotypes of these cluster pairs might be useful for soybean breeding with improving agronomic traits and adaptability.

关键词： Genetic variability correlation path analysis genetic diversity analysis soybean selective breeding