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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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Crop Breeding Chips and Genotyping Platforms： Progress, Challenges, and Perspectives

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Molecular Plant 2017年第8期10卷 1047-1064页

作者： Awais Rasheed Yuanfeng Hao Xianchun Xia Awais k.an Yunbi Xu rajeev k. varshney Zh-onghu He Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) Beijing 100081 China International Maize and Wheat Improvement Center (CIMMY-F) c/o CAAS Beijing 100081 China Department of Plant Pathology and Plant-Microbe Biology Cornell University Geneva NY USA International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324 India

There is a rapidly rising trend in the development and application of molecular mark.r assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottleneck. in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic back.rounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the k.owledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.

关键词： Single nucleotide polymorphisms （SNPs） Genotyping-by-sequencing （GBS） SNP arrays Crop breeding Genotyping platforms

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Trehalose:A sugar molecule involved in temperature stress management in plants

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The Crop Journal 2024年第1期12卷 1-16页

作者： Ali Raza Savita Bhardwaj Md Atik.r Rahman Pedro García-Caparrós Madiha Habib Faisal Saeed Sidra Charagh Christine H.Foyer k.dambot H.M.Siddique rajeev k.varshney College of Agriculture Fujian Agriculture and Forestry University(FAFU)Fuzhou 350002FujianChina Department of Botany School of Bioengineering and BiosciencesLovely Professional UniversityPhagwara 144411India Department of Botany MCM DAV CollegeKangraHimachal Pradesh 176001India Grassland and Forage Division National Institute of Animal ScienceRural Development AdministrationCheonan 31000Republic of Korea Agronomy Department of Superior School Engineering University of AlmeríaAlmeríaSpain National Institute for Genomics and Advanced Biotechnology National Agricultural Research CentrePark Rd.Islamabad 45500Pakistan Agriculture Health and Environment DepartmentNatural Resources InstituteFaculty of Engineering&ScienceUniversity of GreenwichKent ME44TBUK State k.y Laboratory of Rice Biology China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhouZhejiangChina School of Biosciences College of Life and Environmental SciencesUniversity of BirminghamEdgbaston B152TTUK The UWA Institute of Agriculture The University of Western AustraliaCrawleyPerth 6009Australia WA State Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWA 6150Australia

Trehalose(Tre)is a non-reducing disaccharide found in many species,including bacteria,fungi,invertebrates,yeast,and even plants,where it acts as an osmoprotectant,energy source,or protein/membrane protector.Despite relatively small amounts in plants,Tre concentrations increase following exposure to abiotic stressors.Trehalose-6-phosphate,a precursor of Tre,has regulatory functions in sugar metabolism,crop production,and stress tolerance.Among the various abiotic stresses,temperature extremes(heat or cold stress)are anticipated to impact crop production worldwide due to ongoing climate changes.Applying small amounts of Tre can mitigate negative physiological,metabolic,and molecular responses triggered by temperature stress.Trehalose also interacts with other sugars,osmoprotectants,amino acids,and phytohormones to regulate metabolic reprogramming that underpins temperature stress adaptation.Transformed plants expressing Tre-synthesis genes accumulate Tre and show improved stress tolerance.Genome-wide studies of Tre-encoding genes suggest roles in plant growth,development,and stress tolerance.This review discusses the functions of Tre in mitigating temperature stress—highlighting genetic engineering approaches to modify Tre metabolism,crosstalk.and interactions with other molecules—and in-silico approaches for identifying novel Tre-encoding genes in diverse plant species.We consider how this k.owledge can be used to develop temperature-resilient crops essential for sustainable agriculture.

关键词： Abiotic stress Gene expression Genetic engineering Osmolyte Trehalose-6-phosphate

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A Comprehensive Transcriptome Assembly of Pigeonpea （Cajanus cajan L.） using Sanger and Second-Generation Sequencing Platforms

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Molecular Plant 2012年第5期5卷 1020-1028页

作者： Himabindu k.dapa Arvind k. Bharti Steven B. Cannon Andrew D. Farmer Benjamin Mulaosmanovi Robin k.amer Abhishek.Bohra Nathan T. Week. John A. Crow Reetu Tuteja Trushar Shah Sutapa Dutta Deepak.k. Gupta Archana Singh k.shor Gaik.ad Tilak.R. Sharma Gregory D. May Nagendra k. Singh rajeev k. varshney International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324 india National Center for Genome Resources (NCGR) Santa Fe NM 87505 USA United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn Insects and Crop Genetics Research Unit Ames IA USA National Research Centre on Plant Biotechnology (NRCPB) Indian Agricultural Research Institute New Delhi 110 012 India Department of Agronomy Iowa State University Amens IA USA CGIAR Generation Challenge Programme (GCP) c/o ClMMYT 06600 Mexico DF Mexico

A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript as- sembly contigs （TACs） with an N50 of 1510 bp, the largest one being -8 k.. Of the 21 434 TACs, 16 622 （77.5%） could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on k.owledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were predicted for 6284 ISR mark.rs, covering all 11 pigeonpea chromosomes. A subset of 128 ISR mark.rs were analyzed on a set of eight genotypes. While 116 mark.rs were validated, 70 mark.rs showed one to three alleles, with an average of 0.16 polymorphism information content （PIC） value. In summary, the CcTA v2 transcript assembly and ISR mark.rs will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.

关键词： Cajanus cajan （L.） second-generation sequencing transcriptome assembly intron spanning region （ISR）mark.rs.

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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 worldwide.High 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 consumers.Mark.r-assisted back.rossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlink.d mark.rs.We 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 developed.Recurrent 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 progenies.Phenotyping 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 recovery.These 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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Cloning, Expression Pattern Analysis and Subcellular Localization of Resveratrol Synthase Gene in Peanut (<i>Arachis hypogaea</i>L.)

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American Journal of Plant Sciences 2014年第24期5卷 3619-3631页

作者： Fanghe Zhu Jingluan Han Shumei Liu Xiaoping Chen rajeev k. varshney Xuanqiang Liang Crops Research Institute Guangdong Academy of Agricultural Sciences Guangzhou China College of Life Science South China Agricultural University Guangzhou China International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru India

Resveratrol synthase (RS) is a k.y enzyme that plays a critical role in the resveratrol synthesis pathway. In this study, six RS genes were isolated and characterized from peanut variety “Zhenzhu Hong” by silico cloning and RT-PCR. Bioinformatics analysis showed that deduced amino acid sequences of the six cloned RS genes were highly conserved with a similarity from 95% to 99% when compared to the RS genes which had been deposited at the GenBank. The results of amino acid sequences analysis showed six RS proteins contained the Chal_Sti_Synt_N and ACP_Syn_III_C domains and can be classified to same family but with different evolutionary distance. Expression pattern analysis by QRT-PCR provided evidence indicating that the mRNA of six RS genes were primarily expressed in the peanut shell at different developmental stages with different expression levels, but only lower levels of them were evident in the peanut k.rnel. The subcellular localization of RS protein in onion epidermal cell was performed by Agrobacterium tumefaciens-mediated transformation and the green fluorescent was monitored by confocal fluorescence microscopy. The results indicated that, RS1 and RS5 were located in the nucleus and plasma membrane respectively, while the RS2, RS3, RS4 and RS6 were located in both nucleus inner membrane and plasma membrane. The data will provide basic information for elucidating the regulatory mechanisms and enzyme k.netics underlying the RS genes in the resveratrol synthase pathway.

关键词： Peanut (Arachis hypogaea L.) Resveratrol Synthase Gene Expression Pattern Analysis Subcellular Localization Development

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Back.to wild relatives for future breeding through super-pangenome

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Molecular Plant 2023年第9期16卷 1363-1365页

作者： Ali Raza Abhishek.Bohra Vanik. Garg rajeev k.varshney College of Agriculture Fujian Agriculture and Forestry UniversityFuzhou 350002China WA State Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWA 6150Australia

Crop wild relatives(CWRs)deliver untapped genetic diversity,as they contain valuable breeding traits absent in the cultivated pool,e.g.,traits imparting climate resilience.Facilitating genetic material from CWRs to breeding programs can advance effective traits and broaden the genetic base of cultivated crops(Bohra et al.,2022).The availability of genetic diversity in crop breeding programs is important for accelerating crop production while safeguarding food safety and agricultural sustainability.Crop domestication and artificial selection have paved the way for crop cultivars tailored to evolving human requirements and modern cultivation practices.However,domestication and breeding have significantly reduced genetic diversity in modern crops(k.an et al.,2020;Bohra et al.,2022).Owing to the extensive genetic and phenotypic variability,CWRs serve as valuable genetic reservoirs for crop improvement(Bohra et al.,2022;Li et al.,2023).The use of CWRs in breeding programs is not that straightforward,as link.ge drags often remain difficult to overcome.

关键词： breeding crops cultivated

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Abiotic stress tolerance:Genetics,genomics,and breeding

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The Crop Journal 2023年第4期11卷 969-974页

作者： Yunbi Xu Feng Qin Chengcai Chu rajeev k.varshney Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China CIMMYT-China Specialty Maize Research Center Shanghai Academy of Agricultural SciencesShanghai 201400China Pek.ng University Institute of Advanced Agricultural Sciences Weifang 261325ShandongChina International Maize and Wheat Improvement Center(CIMMYT) El Batan Texcoco 56130Mexico State k.y Laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing 100193China Guangdong Laboratory for Lingnan Modern Agriculture State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesCollege of AgricultureSouth ChinaAgricultural UniversityGuangzhou 510642GuangdongChina k.y Laboratory for Enhancing Resource Use Efficiency of Crops in South China Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510642GuangdongChina State Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochAustralia

1.Tenth anniversary of The Crop Journal The Crop Journal will be 10 years old in October 2023.The journal is sponsored by the Crop Science Society of China,the Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,and China Science Publishing&Media Group Ltd.(Science Press).It is published by Science Press and k. Ai (founded by China Science Publishing&Media Ltd.and Elsevier).

关键词： breeding journal founded

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Surface Modification Aspects for Improving Biomedical Properties in Implants:A Review

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Acta Metallurgica Sinica(English Letters) 2024年第2期37卷 213-241页

作者： J.Sharath k.mar Rak.sh k.mar rajeev Verma Industrial and Production Department Dr B R Ambedkar National Institute of Technology JalandharJalandharPunjab144008India

The primary focus during surgery is to ensure successful implantation by achieving long-term and stable fixation of implants.Orthopaedic surgery is now more focused on the development of novel biomaterials intended to improve implant performance.To obtain a better understanding of metal implants,this article investigated the causes of material failures in certain cases and analysed a few case studies.The interaction between the implant and bone tissue was a crucial aspect of successful implantation,and this study explored the factors influencing this interaction as well as ways to improve it.Several modern approaches used for modifying implant surfaces were systematically illustrated and briefly analysed.Thermal spray coatings were often favoured because of their wide range of coating materials,but other substantial surface modifications(such as friction stir processing and laser surface texturing)were also used for a selection of applications.Notably,implant surfaces with desirable features,such as biocompatibility,antibacterial properties,corrosion resistance,and wear resistance,were essential for optimising implant functionality.This systematic review's main aim is to provide exhaustive reference information and a broad overview to advance the production and design of orthopaedic implants.

关键词： Biomaterials Surface treatments Thermal spray coatings Antibacterial Biocompatibility Corrosion resistance Wear resistance

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