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Bairwa A, Sood S, Bhardwaj V, Rawat S, Tamanna T, Siddappa S, Venkatasalam EP, Dipta B, Sharma AK, Kumar A, Singh B, Mhatre PH, Sharma S, Kumar V. Identification of genes governing resistance to PCN (Globodera rostochiensis) through transcriptome analysis in Solanum tuberosum. Funct Integr Genomics 2023; 23:242. [PMID: 37453957 DOI: 10.1007/s10142-023-01164-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Potato cyst nematodes (PCNs) are major pests worldwide that affect potato production. The molecular changes happening in the roots upon PCN infection are still unknown. Identification of transcripts and genes governing PCN resistance will help in the development of resistant varieties. Hence, differential gene expression of compatible (Kufri Jyoti) and incompatible (JEX/A-267) potato genotypes was studied before (0 DAI) and after (10 DAI) inoculation of Globodera rostochiensis J2s through RNA sequencing (RNA-Seq). Total sequencing reads generated ranged between 33 and 37 million per sample, with a read mapping of 48-84% to the potato reference genome. In the infected roots of the resistant genotype JEX/A-267, 516 genes were downregulated, and 566 were upregulated. In comparison, in the susceptible genotype Kufri Jyoti, 316 and 554 genes were downregulated and upregulated, respectively. Genes encoding cell wall proteins, zinc finger protein, WRKY transcription factors, MYB transcription factors, disease resistance proteins, and pathogenesis-related proteins were found to be majorly involved in the incompatible reaction after PCN infection in the resistant genotype, JEX/A-267. Furthermore, RNA-Seq results were validated through quantitative real-time PCR (qRT-PCR), and it was observed that ATP, FLAVO, CYTO, and GP genes were upregulated at 5 DAI, which was subsequently downregulated at 10 DAI. The genes encoding ATP, FLAVO, LBR, and GP were present in > 1.5 fold before infection in JEX-A/267 and upregulated 7.9- to 27.6-fold after 5 DAI; subsequently, most of these genes were downregulated to 0.9- to 2.8-fold, except LBR, which was again upregulated to 44.4-fold at 10 DAI.
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Affiliation(s)
- Aarti Bairwa
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India.
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India.
| | - Shashi Rawat
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Tamanna Tamanna
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Sundaresha Siddappa
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - E P Venkatasalam
- ICAR-Central Potato Research Station, Muthorai, 643004, The Nilgiris, Udhagamandalam, Tamil Nadu, India
| | - Bhawna Dipta
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Ashwani K Sharma
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Ashwani Kumar
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Baljeet Singh
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Priyank H Mhatre
- ICAR-Central Potato Research Station, Muthorai, 643004, The Nilgiris, Udhagamandalam, Tamil Nadu, India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
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Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S, Masson H, Inagaki S, Federici F, Sinha N, Deal RB, Bailey-Serres J, Brady SM. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. PLANT PHYSIOLOGY 2014; 166:455-69. [PMID: 24868032 PMCID: PMC4213079 DOI: 10.1104/pp.114.239392] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/26/2014] [Indexed: 05/18/2023]
Abstract
Agrobacterium rhizogenes (or Rhizobium rhizogenes) is able to transform plant genomes and induce the production of hairy roots. We describe the use of A. rhizogenes in tomato (Solanum spp.) to rapidly assess gene expression and function. Gene expression of reporters is indistinguishable in plants transformed by Agrobacterium tumefaciens as compared with A. rhizogenes. A root cell type- and tissue-specific promoter resource has been generated for domesticated and wild tomato (Solanum lycopersicum and Solanum pennellii, respectively) using these approaches. Imaging of tomato roots using A. rhizogenes coupled with laser scanning confocal microscopy is facilitated by the use of a membrane-tagged protein fused to a red fluorescent protein marker present in binary vectors. Tomato-optimized isolation of nuclei tagged in specific cell types and translating ribosome affinity purification binary vectors were generated and used to monitor associated messenger RNA abundance or chromatin modification. Finally, transcriptional reporters, translational reporters, and clustered regularly interspaced short palindromic repeats-associated nuclease9 genome editing demonstrate that SHORT-ROOT and SCARECROW gene function is conserved between Arabidopsis (Arabidopsis thaliana) and tomato.
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Affiliation(s)
- Mily Ron
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Kaisa Kajala
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Germain Pauluzzi
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Dongxue Wang
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Mauricio A Reynoso
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Kristina Zumstein
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Jasmine Garcha
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Sonja Winte
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Helen Masson
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Soichi Inagaki
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Fernán Federici
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Neelima Sinha
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Roger B Deal
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Julia Bailey-Serres
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
| | - Siobhan M Brady
- Department of Plant Biology (M.R., K.K., K.Z., J.G., S.W., H.M., S.I., N.S., S.M.B.) and Genome Center (M.R., K.K., J.G., S.W., H.M., S.I., S.M.B.), University of California, Davis, California 95616;Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521 (G.P., M.A.R., J.B.-S.);Department of Biology, Emory University, Atlanta, Georgia 30322 (D.W., R.B.D.);Department of Integrated Genetics, National Institute of Genetics, Mishima 411-8540, Japan (S.I.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (F.F.)
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