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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 makes 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 markers. The protein sequences of 54 known 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 known 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 kinases, 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 marker （RGA121） was identified. Two polymerase chain reaction-based markers （Ahsw-1 and Ahsw-2） developed from RGA013 were homologous to the Tomato Spotted Wilt Virus （TSWV） resistance gene. All three markers were mapped on the same linkage group AhIV. These expressed RGAs are the source for RGA-tagged marker 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 markers and SNP array in marker-assisted backcrossing

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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.Vishwakarma Surendra S.Manohar Sunil S.Gangurde Manda Sriswathi Hari kishan Sudini keshavji L.Dobariya Sandip k.Bera Thankappan Radhakrishnan 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 key market trait in groundnut,as it increases the shelf life of the produce/products in addition to providing health benefits to ***-assisted backcrossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlinked *** 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 backcross *** 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 backgrounds 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 Marker-assisted backcrossing SNP array Background genome recovery

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Diversification of primary gene pool through introgression of resistance to foliar diseases from synthetic amphidiploids to cultivated groundnut(Arachis hypogaea L.)

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The Crop Journal 2014年第Z1期2卷 110-119页

作者： Varsha kumari M.V.C.Gowda Vinod Tasiwal manish k.pandey Ramesh S.Bhat Nalini Mallikarjuna Hari D.Upadhyaya Rajeev k.Varshney Department of Genetics and Plant Breeding University of Agricultural Sciences Dharwad International Crops Research Institute for the Semi-Arid Tropics Department of Plant Pathology University of Agricultural Sciences Dharwad Department of Biotechnology University of Agricultural Sciences Dharwad CGIAR Generation Challenge Programme c/o CIMMYT

Groundnut(Arachis hypogaea L.)is widely grown and consumed around the world and is considered to have originated from a single hybridization event between two wild *** utilization of wild germplasm in breeding programs has been restricted by reproductive barriers between wild and cultivated species and technical difficulties in making large numbers of *** to overcome these hurdles have resulted in the development of synthetic amphidiploids,namely ISATGR 278-18(Arachis duranesis×Arachis batizocoi)and ISATGR 5B(Arachis magna×***),which possess several desirable traits,including resistance to foliar diseases that generally cause huge yield losses annually in groundnut growing areas of Asia,America,and *** an objective to improve foliar disease resistance,the primary gene pool was diversified by introgressing foliar disease resistance in five cultivated genotypes(ICGV 91114,ICGS 76,ICGV 91278,JL 24,and DH 86)from synthetic amphidiploids using a backcross breeding *** introgression lines with resistance to two foliar diseases(rust and late leaf spot)were identified with levels of resistance equal to the *** backcross derived lines have shown a wide range of variation for several morphological and agronomic *** lines,after further evaluation and selection,can serve as donors in future breeding programs aimed atdeveloping improved cultivars with desirable agronomic traits,high resilience to biotic/abiotic stresses and a broadened genetic base.

关键词： Groundnut Peanut Wild species Wide crosses Interspecific hybridization

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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. Barkley Ran Hovav Mark Burow Spurthi N. Nayak Annapurna Chitikineni Thomas G. Isleib C. Corley Holbrook Scott A. Jackson Rajeev k. Varshney Peggy Ozias-Akins 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 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic re- gions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone pos- itive selection. These observations provide key 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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Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

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Molecular Plant 2019年第7期12卷 920-934页

作者： Xiaoping Chen Qing Lu Hao Liu Jianan Zhang Yanbin Hong Haofa Lan Haifen Li Jinpeng Wang Haiyan Liu Shaoxiong Li manish k.pandey Zhikang Zhang Guiyuan Zhou Jigao Yu Guoqiang Zhang Jiaqing Yuan Xingyu Li Shijie Wen Fanbo Meng Shanlin Yu Xiyin Wang kadambot H.M.Siddique Zhong-Jian Liu Andrew H.Paterson Rajeev k.Varshney Xuanqiang Liang South China Peanut Sub-center of National Center of Oilseed Crops Improvement Guangdong Key Laboratory for Crops Genetic Improvement Crops Research Institute Guangdong Academy of Agricultural Sciences (GAAS) Guangzhou China Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources College of Forestry Fujian Agriculture and Forestry University Fuzhou 350002 China Plant Genome Mapping Laboratory University of Georgia Athens USA National Foxtail Millet Improvement Center Minor Cereal Crops Laboratory of Hebei Province Institute of Millet Crops Hebei Academy of Agriculture and Forestry Sciences Shijiazhuang China MolBreeding Biotechnology Co. Ltd. Shijiazhuang China School of Life Sciences and Center for Genomics and Computational Biology North China University of Science and Technology Tangshan China Center of Excellence in Genomics & Systems Biology International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad India Shenzhen key Laboratory for Orchid Conservation and Utilization National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen Shenzhen China Shandong Peanut Research Institute Shandong Academy of Agricultural Sciences Qingdao China UWA Institute of Agriculture The University of Western Australia Crawley Australia key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture Fujian Agriculture and Forestry University Fuzhou 350002 China

Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

关键词： cultivated peanut denovo sequencing comparative genomics genome evolution oil metabolism

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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 Prakash 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 Uttarakhand,India,using advanced ensemble models that combined Radial Basis Function Networks(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-making.

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

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Genetic map construction and widely distributed meiotic recombination hot spots detected by SLAF in peanut(Arachis hypogaea L.)

Genetic map construction and widely distributed meiotic reco...

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中国作物学会油料作物专业委员会第八次会员代表大会暨学术年会

作者： WANG Xiao-hua XU Ping YIN Liang REN Yan LI Shuang-ling SHI Yan-mao CHI Xiao-yuan YU Tian-yi SHAN Shi-hua HE Guo-hao manish k pandey Rajeev k Varshney YUAN Mei key Laboratory of Peanut Biology and Genetic Improvement Ministry of AgricultureShandong Peanut Research Institute Tuskegee University International Crops Research Institute for Semi-Arid Tropics(ICRISAT) Greater Hyderabad

Recombination hot spots,caused by meiosis,are considered playing crucial roles in crop domestication and *** peanut is one of the most staple,rich-source of oil and protein ***,no direct scale of recombination events and hot spots have been estimated for peanut *** examine the scale of recombination events and hot spots in peanut,we constructed a genetic map using a recombinant inbred line(RIL) population including 200 lines with 605 631 markers detected using the specific-locus amplified fragment sequencing(SLAF-seq) approach and 49 natural cultivars with 61 942 insertion-deletion(InDels) markers detected using the transcriptome sequencing,*** precise integrated map comprised 4 837 SLAF markers with a total genetic length of 2 915.46 cM,a density of 1.66 markers per *** average of 30.0 crossover(c.2.06 cM/Mb) events was detected per F peanut plant,which is similar to the values in Arabidopsis and *** crossover events showed uneven distribution among B sub-genome(with average of 2.32) and A sub-genome(with average of 1.85).There were 4.34%and 7.86%of the genome contained large numbers of crossovers(>50 cM/Mb) along chromosomes in F population and natural population,*** density of crossover events region called recombination hot spots,showed negative relationship to marker haplotypes conservative region but positive to heatmap of *** genes located within the recombination hot spot regions by gene ontology(GO) categories showed responses to environmental stimuli,suggesting that recombination plays a crucial role in peanut adaptation to changing environments.

关键词： Arachis hypogaea L. genetic map meiotic recombination hot spots SLAF-seq(specific-locus amplified fragment sequencing)

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Integrated eQTL and pQTL analysis identified candidate genes controlling deep purple testa color in peanut(Arachis hypogaea)

Integrated eQTL and pQTL analysis identified candidate genes...

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中国作物学会油料作物专业委员会第八次会员代表大会暨学术年会

作者： HUANG Li REN Xiao-ping manish k pandey LIU Xia CHEN Hai-wen XUE Xiao-meng HUAI Dong-xin LIU Nian CHEN Yu-ning ZHOU Xiao-jing CHEN Wei-gang LUO Huai-yong LIU ke-de LEI Yong XIAO Ying-jie Rajeev k Varshney LIAO Bo-shou JIANG Hui-fang key Laboratory of Biology and Genetic Improvement of Oil Crops Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences National key Laboratory of Crop Genetic Improvement Huazhong Agricultural University International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)

Peanuts with dark testa color are preferred in domestic and international markets leading to higher acceptance of such varieties among farmers for *** good understanding of anthocyanin biosynthesis in model plants,regulatory network of anthocyanin biosynthesis remains plausible in *** this context,we performed RNA-based sequencing(RNA-seq) of unmatured seed in a recombinant inbred line(RIL) population of peanut and analyzed transcript abundance for 49 691 genes.A small percentage of genes(0.4%)had non-Mendelian inheritance and 92 of these expressed genes across RILs followed Paramutation-like pattern.A global expression quantitative trait loci(eQTL) mapping identified 17 044 eQTLs including 1 207 local eQTLs and 15 837 distant *** addition,135 eQTL hot spots were identified possessing genes related to cellular process,metabolic process,and bindingand catalytic *** eQTL and phenotypic quantitative trait loci(pQTL) analyses identified 3 potential candidate genes,Aradu.10006110,Araip.10005867 and Araip.10013322 encoding flavonoid 3 ’-hydroxylase(F3 ’ H),transparent testa 8(TT8) transcription factor and anthocyanidin 3-0-glucosyltransferase(3-GT),*** andidate genes identified for controlling purple testa play key role in regulating anthocyanidin *** gene Araip.10013322 was specifically high expressed in early seed development stage in peanut lines with purple *** is the first eQTL mapping study in peanut and results showed that this approach can be successfully used for candidate gene discovery in non-model plants,such as peanut.

关键词： expression quantitative trait locus(eQTL) peanut RNA-based sequencing(RNA-seq) candidate gene anthocyanidin biosynthesis purple testa

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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 key genes belonging to the family of selective ion transporters(NHX, HkT) 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 markers 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 ketan 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 unsoaked 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 unsoaked 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 unsoaked 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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