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Identification of ExpIdentification of Expressed Resistance Gene Analogs from Peanut (Arachis hypogaea L.) Expressed Sequence Tags

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Journal of Integrative Plant Biology 2013年第5期55卷 453-461页

作者： Zhanji Liu Suping Feng manish k. pandey Xiaoping Chen Albert k. Culbreath Rajeev k. Varshney Baozhu Guo University of Georgia Department of Plant Pathology Shandong Academy of Agricultural Sciences High-Tech Research Center Qiongzhou University College of Bioscience and Biotechnology International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Guangdong Academy of Agricultural Sciences Crops Research Institute US Department of Agriculture Agricultural Research ServiceCrop Protection and Management Research Unit

Low genetic diversity mak.s peanut （Arachis hypogaea L.） very vulnerable to plant pathogens, causing severe yield loss and reduced seed quality. Several hundred partial genomic DNA sequences as nucleotide-binding-site leucine-rich repeat （NBS-LRR） resistance genes （R） have been identified, but a small portion with expressed transcripts has been found. We aimed to identify resistance gene analogs （RGAs） from peanut expressed sequence tags （ESTs） and to develop polymorphic mark.rs. The protein sequences of 54 k.own R genes were used to identify homologs from peanut ESTs from public databases. A total of 1,053 ESTs corresponding to six different classes of k.own R genes were recovered, and assembled 156 contigs and 229 singletons as peanut-expressed RGAs. There were 69 that encoded for NBS-LRR proteins, 191 that encoded for protein k.nases, 82 that encoded for LRR-Pk.transmembrane proteins, 28 that encoded for Toxin reductases, 11 that encoded for LRR-domain containing proteins and four that encoded for TM-domain containing proteins. Twenty-eight simple sequence repeats （SSRs） were identified from 25 peanut expressed RGAs. One SSR polymorphic mark.r （RGA121） was identified. Two polymerase chain reaction-based mark.rs （Ahsw-1 and Ahsw-2） developed from RGA013 were homologous to the Tomato Spotted Wilt Virus （TSWV） resistance gene. All three mark.rs were mapped on the same link.ge group AhIV. These expressed RGAs are the source for RGA-tagged mark.r development and identification of peanut resistance genes.

关键词： Arachis hypogaea expressed sequence tags resistance gene analogs Tomato Spotted Wilt Virus.

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Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR mark.rs and SNP array in mark.r-assisted back.rossing

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The Crop Journal 2020年第1期8卷 1-15页

作者： Yaduru Shasidhar Murali T.Variath manish k.Vishwak.rma Surendra S.Manohar Sunil S.Gangurde Manda Sriswathi Hari k.shan Sudini k.shavji L.Dobariya Sandip k.Bera Thank.ppan Radhak.ishnan manish k.pandey Pasupuleti Janila Rajeev k.Varshney International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) HyderabadIndia Department of Genetics Osmania UniversityHyderabadIndia Junagadh Agricultural University JunagadhIndia ICAR-Directorate of Groundnut Research JunagadhIndia

Foliar fungal diseases(rust and late leaf spot)incur large yield losses,in addition to the deterioration of fodder quality in groundnut *** oleic acid has emerged as a k.y mark.t trait in groundnut,as it increases the shelf life of the produce/products in addition to providing health benefits to ***-assisted back.rossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlink.d *** used MABC to improve three popular Indian cultivars(GJG 9,GG 20,and GJGHPS 1)for foliar disease resistance(FDR)and high oleic acid content.A total of 22 BC3F4 and 30 BC2F4 introgression lines(ILs)for FDR and 46 BC3F4 and 41 BC2F4 ILs for high oleic acid were *** parent genome analysis using the 58 k.Axiom_Arachis array identified several lines showing upto 94%of genome recovery among second and third back.ross *** of these ILs revealed FDR scores comparable to the resistant parent,GPBD 4,and ILs with high(~80%)oleic acid in addition to high genome *** ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic back.rounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India.

关键词： Foliar disease resistance High oleic acid Late leaf spot Mark.r-assisted back.rossing SNP array Back.round genome recovery

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Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut

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Molecular Plant 2017年第2期10卷 309-322页

作者： Josh Clevenger Ye Chu Carolina Chavarro Gaurav Agarwal David J. Bertioli Soraya C.M. LeaI-Bertioli manish k. pandey Justin Vaughn Brian Abernathy Noelle A. Bark.ey Ran Hovav Mark.Burow Spurthi N. Nayak.Annapurna Chitik.neni Thomas G. Isleib C. Corley Holbrook.Scott A. Jack.on Rajeev k. Varshney Peggy Ozias-Ak.ns Department of Horticulture and Institute of Plant Breeding Genetics & Genomics The University of Georgia 2356 Rainwater Road Tifton GA 31793 USA Center for Applied Genetic Technologies and Institute of Plant Breeding Genetics & Genomics The University of Georgia Athens GA 30602 USA International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad 502324 India University of Brasilia Institute of Biological Sciences Campus Darcy Ribeiro 70910-900 Brasilia DF Brazil Embrapa Genetic Resources and Biotechnology 70770-917 Brasflia DF Brazil eUSDA-ARS PGRCU Griffin GA 30223 USA Agricultural Research Organization Plant Sciences Institute 7528809 Rishon LeZion Israel Department of Plant and Soil Science Texas Tech University Lubbock TX 79409-2122 USA Department of Crop and Soil Sciences North Carolina State University Box 7629 Raleigh NC 28695-7629 USA USDA-ARS Tifton GA 31793. USA

Peanut （Arachis hypogaea; 2n = 4x = 40） is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facil- itate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide poiymorphisms （SNPs） were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 mark.rs that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic mark.rs between cultivated and interspecific hybrids, and 15 897 polymorphic mark.rs within A. hypogaea germplasm. An additional 1193 mark.rs were identified that illuminated genomic re- gions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that mak. up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone pos- itive selection. These observations provide k.y insights on the inclusion of new genetic diversity in culti- vated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.

关键词： single nucleotide polymorphism groundnut Arachis hypogaea

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Landslide Susceptibility Mapping Using RBFN-Based Ensemble Machine Learning Models

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Computer Modeling in Engineering & Sciences 2025年第1期142卷 467-500页

作者： Landslide Susceptibility Mapping Using RBFN-Based Ensemble Machine Learning Models Duc-Dam Nguyen Nguyen Viet Tiep Quynh-Anh Thi Bui Hiep Van Le Indra Prak.sh Romulus Costache manish pandey Binh Thai Pham Faculty of Civil Engineering University of Transport TechnologyThanh XuanHa Noi100000Vietnam Faculty of Hydraulic Engineering Hanoi University of Civil EngineeringHa Noi100000Vietnam DDG(R)Geological Survey of India Gandhinagar382010India Research Institute of the University of Bucharest Bucharest050663Romania National Institute of Hydrology and Water Management Bucharest013686Romania Department of Civil Engineering Transilvania University of BrasovBrasov500152Romania Danube Delta National Institute for Research and Development Tulcea820112Romania Marwadi University Research Center(MURC) Marwadi UniversityRajkotGujaratBharat360003India Department of Civil Engineering Faculty of Engineering&TechnologyMarwadi UniversityRajkotGujaratBharat360003India

This study was aimed to prepare landslide susceptibility maps for the Pithoragarh district in Uttarak.and,India,using advanced ensemble models that combined Radial Basis Function Network.(RBFN)with three ensemble learning techniques:DAGGING(DG),MULTIBOOST(MB),and ADABOOST(AB).This combination resulted in three distinct ensemble models:DG-RBFN,MB-RBFN,and ***,a traditional weighted method,Information Value(IV),and a benchmark.machine learning(ML)model,Multilayer Perceptron Neural Network.MLP),were employed for comparison and *** models were developed using ten landslide conditioning factors,which included slope,aspect,elevation,curvature,land cover,geomorphology,overburden depth,lithology,distance to rivers and distance to *** factors were instrumental in predicting the output variable,which was the probability of landslide *** analysis of the models’performance indicated that the DG-RBFN model,with an Area Under ROC Curve(AUC)of 0.931,outperformed the other *** AB-RBFN model achieved an AUC of 0.929,the MB-RBFN model had an AUC of 0.913,and the MLP model recorded an AUC of *** results suggest that the advanced ensemble ML model DG-RBFN was more accurate than traditional statistical model,single MLP model,and other ensemble models in preparing trustworthy landslide susceptibility maps,thereby enhancing land use planning and decision-mak.ng.

关键词： Landslide susceptibility map spatial analysis ensemble modelling information values(IV)

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Time course of physiological,biochemical,and gene expression changes under short-term salt stress in Brassica juncea L.

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The Crop Journal 2017年第3期5卷 219-230页

作者： manish pandey Suprasanna Penna Plant Stress Physiology and Biotechnology Section Nuclear Agriculture and Biotechnology DivisionBhabha Atomic Research CentreTrombayMumbai 400085India

Salinity-imposed limitations on plant growth are manifested through osmotic and ionic imbalances. However, because salinity-induced responses vary considerably among crop plants, monitoring of such responses at an early stage has relevance. In this study,physiological(seed germination, seed vigor index, root length, shoot length, fresh weight,dry weight) and biochemical attributes(osmoprotectants, k.+/Na^+ ratio) were analyzed for a time-course assessment of salt responses in Indian mustard(Brassica juncea L.) with an emphasis on early monitoring. The results showed strong correlations for total soluble sugars at germination phase(24 h), proline content in the seedling establishment phase(48 h) and various physiological parameters including seed vigor index(R^2= 0.901), shoot length(R^2= 0.982), and fresh weight(R^2= 0.980) at 72 h(adaptation under stress). In addition, transcriptional changes were observed under NaCl treatment for k.y genes belonging to the family of selective ion transporters(NHX, Hk.) and abscisic acid synthesis(AAO-3). The status of mitochondrial respiration was also examined as a probe for salinity tolerance at an early stage. The results suggested that although all the analyzed parameters showed correlations(negative or positive) with salt stress magnitude, their critical response times differed, with most of the studied biochemical, physiological, or molecular mark.rs providing valuable information only after radicle emergence, whereas mitochondrial respiration via alternative oxidase was useful for the early detection of salt responses.

关键词： Alternative oxidase Brassica Osmolytes Salinity Seed germination

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Influence of cohesion on California bearing ratio of clay-gravel mixtures

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International Journal of Sediment Research 2023年第3期38卷 374-386页

作者： Rajesh Jain k.tan Timani manish pandey Civil Engineering Department L.D.College of Engineering 2. Vishwakarma Government Engineering College Department of Civil Engineering National Institute of Technology

An understanding of the behavior of cohesive sediment is required to solve various engineering problems such as scour around bridge elements, mitigation of soil erosion, pavement design, river bed degradation,stable channel design. Pavement foundation designers principally use the California bearing ratio(CBR)to describe the subgrade and subbase materials and their strength. Several laboratory experiments were done to study the variation in the CBR of cohesive mixtures comprised of clay-gravel mixtures. Nine different clay-gravel mixtures were used in which the clay content varies from 10% to 50% by *** variation of the CBR with clay percentage, moisture content, and undrained shear strength parameters was studied. The CBR value reduces with the increase in the moisture content and clay fraction in the mixtures and increases with an increase in the dry density of the mixture under unsoak.d conditions. The CBR also increases with the increase of the angle of internal friction of clay-gravel mixtures.A functional relation has been identified to estimate the CBR of clay-gravel mixtures. Using multiple linear regression analysis(MLRA), a relation is proposed to estimate the CBR of clay-gravel mixtures under unsoak.d conditions. A statistical analysis was done to judge the behavior of the pertinent variables on the CBR. The proposed relation predicts the CBR of clay-gravel mixtures very well. Artificial neural network.ANN) analysis using R programming was also done to determine the effects of the pertinent variables on the CBR. ANN methodology was applied to predict the contribution of each variable. Three different methods: Garson algorithm, Olden algorithm, and Lek.s profile model are used to assess the influence of variable parameters. The Olden algorithm and Lek.s profile both show positive association of cohesion with CBR in an unsoak.d condition. The role of moisture content was found to be marginally negative in the Olden algorithm and Lek.s profile results

关键词： Clay–gravel mixture Cohesive sediment California bearing ratio Clay percentage Sediment properties

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A Novel Approach for Enhancement of Geometric and Contrast Resolution Properties of Low Contrast Images

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IEEE/CAA Journal of Automatica Sinica 2018年第2期5卷 628-638页

作者： k.ushlendra k.mar Singh manish k.mar Bajpai Rajesh k.mar pandey Department of Computer Science and Engineering National Institute of Technology Jamshedpur 831014 India Indian Institute of Information Technology Design & Manufacturing Jabalpur MP 482005 India Department of Mathematical Sciences In- dian Institute of Technology Varanasi U.P. 221005 India

The present work.encompasses a new image enhancement algorithm using newly constructed Chebyshev fractional order differentiator. We have used Chebyshev polynomials to design Chebyshev fractional order differentiator. We have generated the high pass filter corresponding to it. The designed filters are applied for decomposing the input image into four bands and low-low(L-L) sub-band is updated using correction coefficients. Reconstructed image with updated L-L sub-band provides the enhanced image. The visual results obtained are encouraging for image enhancement. The applicability of the developed algorithm is illustrated on three different test *** effects of order of differentiation on the edges of images have also been presented and discussed.

关键词： Index Terms-Chebyshev polynomial based approximation contrast enhancement fractional order differentiator.

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Molecular subtypes of colorectal cancer: An emerging therapeutic opportunity for personalized medicine

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Genes & Diseases 2021年第2期8卷 133-145页

作者： manish Pratap Singh Sandhya Rai Ashutosh pandey Nand k.Singh Sameer Srivastava Department of Biotechnology Motilal Nehru National Institute of TechnologyAllahabadUP211004India

Molecular subtypes-based therapies offer new potential framework.for desired and precise outcome in clinical *** treatment strategies in colorectal cancer are largely‘one drug fit all’model for patients that display same pathological ***,CRC is a very heterogenous set ofmalignancy that does not support for above *** subtype displays different pathological and genetic *** on these features,therapeutic stratification for individual patients may be designed,which may ultimately lead to improved therapeutic *** this comprehensive review,we have attempted to briefly outline major CRC pathways.A detailed overview of molecular subtypes and their clinical significance has been *** and futuremethods,governing CRC subtyping in the era of personalized therapywith a special emphasis on CMS subtypes of CRC has been ***,discovery and validation of new CRC patient stratification methods,screening for novel therapeutic targets,and enhanced diagnosis of CRC may improve the treatment outcome.

关键词： Biomark.rs CMS subtypes Immunotherapy Molecular screening Personalized medicine

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Flow turbulence presented by different vegetation spacing sizes within a submerged vegetation patch

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Journal of Hydrodynamics 2023年第6期35卷 1131-1145页

作者： Chuk.uemek. k.ngsley John Jaan H.Pu Yak.n Guo Prashanth R.Hanmaiahgari manish pandey Faculty of Engineering and Informatics University of BradfordBradfordUK Department of Civil Engineering Indian Institute of TechnologyKharagpurIndia National Institute of Technology(NIT) WarangalIndia

This study presents results from a vegetation-induced flow experimental study which investigates 3-D turbulence structure profiles,including Reynolds stress,turbulence intensity and bursting analysis of open channel *** vegetation densities have been built between the adjacent vegetations,and the flow measurements are tak.n using acoustic Doppler velocimeter(ADV)at the locations within and downstream of the vegetation *** different tests are conducted,where the first test has compact vegetations,while the second and the third tests have open spaces created by one and two empty vegetation slots within the vegetated *** reveals that over 10%of eddies size is generated within the vegetated zone of compact vegetations as compared with the fewer *** turbulence structures variation is also observed at the points in the non-vegetated *** findings from burst-cycle analysis show that the sweep and outward interaction events are dominant,where they further increase away from the *** effect of vegetation on the turbulent burst cycle is mostly obvious up to approximately two-third of vegetation height where this phenomenon is also observed for most other turbulent structure.

关键词： Velocity profiles acoustic Doppler velocimeter(ADV) turbulent intensities Reynolds stress turbulent bursting vegetated flow vegetation spacing sizes

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Experimental assessment and prediction of temporal scour depth around a spur dik.

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International Journal of Sediment Research 2021年第1期36卷 17-28页

作者： manish pandey Manousos Valyrak.s Meilan Qi Anurag Sharma Ajay Singh Lodhi Department of Civil Engineering National Institute of Technology School of Engineering University of Glasgow School of Civil Engineering Beijing Jiaotong University Department of Civil Engineering Institute of Infrastructure Technology Research and Management 5. College of Agriculture Waraseoni District

Spur dik.s are river training structures that have been extensively used worldwide for towards enhancing flood control and the stability of embank.ents and ***,scour around spur dik.s can be a major problem affecting their stability and hydraulic *** precise computation of temporal scour depth at spur dik.s is very important for the design of economical and safe spur *** study focuses on experimentally assessing the temporal variation of scour depth around a vertical wall spur dik. and identifying the parameters,which mostly influence spur dik. performance for a channel bed surface comprised of sand-gravel *** the current study,the authors did physical experiments in a flume based study to obtain new data,aimed at deriving a new predictive model for spur dik. scour and comparing its performance to others found in the *** was found that the dimensionless temporal scour depth variation increases with an increase in(i) the threshold velocity ratio,(ii) the densimetric Froude number of the bed surface sediment mixture,(iii) the flow shallowness(defined as the ratio of the approach flow depth,y,to the spur dik.’s transverse length,l),and(iv) the flow depth-particle size *** is also concluded that the temporal scour depth variation in the sediment mixture is influenced by the non-uniformity of sediment and decreases with an increase in the non-uniformity of the sediment mixture.A new mathematical model is derived for the estimation of temporal scour depths in sand-gravel sediment *** proposed equation has been calibrated and validated with the experimental data,demonstrating a good predictive capacity for the estimation of temporal scour depth evolution.

关键词： Spur dik. Sand-gravel sediment mixture Clear-water scour Time-dependent scour depth

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