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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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Yang M, Li H, Qiao H, Guo K, Xu R, Wei H, Wei J, Liu S, Xu C. Integrated Transcriptome and Metabolome Dynamic Analysis of Galls Induced by the Gall Mite Aceria pallida on Lycium barbarum Reveals the Molecular Mechanism Underlying Gall Formation and Development. Int J Mol Sci 2023; 24:9839. [PMID: 37372986 DOI: 10.3390/ijms24129839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Galls have become the best model for exploring plant-gall inducer relationships, with most studies focusing on gall-inducing insects but few on gall mites. The gall mite Aceria pallida is a major pest of wolfberry, usually inducing galls on its leaves. For a better understanding of gall mite growth and development, the dynamics of the morphological and molecular characteristics and phytohormones of galls induced by A. pallida were studied by histological observation, transcriptomics and metabolomics. The galls developed from cell elongation of the epidermis and cell hyperplasia of mesophylls. The galls grew quickly, within 9 days, and the mite population increased rapidly within 18 days. The genes involved in chlorophyll biosynthesis, photosynthesis and phytohormone synthesis were significantly downregulated in galled tissues, but the genes associated with mitochondrial energy metabolism, transmembrane transport, carbohydrates and amino acid synthesis were distinctly upregulated. The levels of carbohydrates, amino acids and their derivatives, and indole-3-acetic acid (IAA) and cytokinins (CKs), were markedly enhanced in galled tissues. Interestingly, much higher contents of IAA and CKs were detected in gall mites than in plant tissues. These results suggest that galls act as nutrient sinks and favor increased accumulation of nutrients for mites, and that gall mites may contribute IAA and CKs during gall formation.
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Affiliation(s)
- Mengke Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Huanle Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Haili Qiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Kun Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Rong Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Hongshuang Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Sai Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Changqing Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
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Zhao W, Liang J, Huang H, Yang J, Feng J, Sun L, Yang R, Zhao M, Wang J, Wang S. Tomato defence against Meloidogyne incognita by jasmonic acid-mediated fine-tuning of kaempferol homeostasis. THE NEW PHYTOLOGIST 2023; 238:1651-1670. [PMID: 36829301 DOI: 10.1111/nph.18837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Jasmonic acid (JA) is involved in the modulation of defence and growth activities in plants. The best-characterized growth-defence trade-offs stem from antagonistic crosstalk among hormones. In this study, we first confirmed that JA negatively regulates root-knot nematode (RKN) susceptibility via the root exudates (REs) of tomato plants. Omics and toxicological analyses implied that kaempferol, a type of flavonol, from REs has a negative effect on RKN infection. We demonstrated that SlMYB57 negatively regulated kaempferol contents in tomato roots, whereas SlMYB108/112 had the opposite effect. We revealed that JA fine-tuned the homeostasis of kaempferol via SlMYB-mediated transcriptional regulation and the interaction between SlJAZs and SlMYBs, thus ensuring a balance between lateral root (LR) development and RKN susceptibility. Overall, this work provides novel insights into JA-modulated LR development and RKN susceptibility mechanisms and elucidates a trade-off model mediated by JA in plants encountering stress.
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Affiliation(s)
- Wenchao Zhao
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Jingjing Liang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
| | - Huang Huang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Jinshan Yang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
| | - Jiaping Feng
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
| | - Lulu Sun
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Rui Yang
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Mengjia Zhao
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
| | - Jianli Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Shaohui Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
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Arraes FBM, Vasquez DDN, Tahir M, Pinheiro DH, Faheem M, Freitas-Alves NS, Moreira-Pinto CE, Moreira VJV, Paes-de-Melo B, Lisei-de-Sa ME, Morgante CV, Mota APZ, Lourenço-Tessutti IT, Togawa RC, Grynberg P, Fragoso RR, de Almeida-Engler J, Larsen MR, Grossi-de-Sa MF. Integrated Omic Approaches Reveal Molecular Mechanisms of Tolerance during Soybean and Meloidogyne incognita Interactions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202744. [PMID: 36297768 PMCID: PMC9612212 DOI: 10.3390/plants11202744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 05/08/2023]
Abstract
The root-knot nematode (RKN), Meloidogyne incognita, is a devastating soybean pathogen worldwide. The use of resistant cultivars is the most effective method to prevent economic losses caused by RKNs. To elucidate the mechanisms involved in resistance to RKN, we determined the proteome and transcriptome profiles from roots of susceptible (BRS133) and highly tolerant (PI 595099) Glycine max genotypes 4, 12, and 30 days after RKN infestation. After in silico analysis, we described major defense molecules and mechanisms considered constitutive responses to nematode infestation, such as mTOR, PI3K-Akt, relaxin, and thermogenesis. The integrated data allowed us to identify protein families and metabolic pathways exclusively regulated in tolerant soybean genotypes. Among them, we highlighted the phenylpropanoid pathway as an early, robust, and systemic defense process capable of controlling M. incognita reproduction. Associated with this metabolic pathway, 29 differentially expressed genes encoding 11 different enzymes were identified, mainly from the flavonoid and derivative pathways. Based on differential expression in transcriptomic and proteomic data, as well as in the expression profile by RT-qPCR, and previous studies, we selected and overexpressed the GmPR10 gene in transgenic tobacco to assess its protective effect against M. incognita. Transgenic plants of the T2 generation showed up to 58% reduction in the M. incognita reproduction factor. Finally, data suggest that GmPR10 overexpression can be effective against the plant parasitic nematode M. incognita, but its mechanism of action remains unclear. These findings will help develop new engineered soybean genotypes with higher performance in response to RKN infections.
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Affiliation(s)
- Fabricio B M Arraes
- Postgraduate Program in Cellular and Molecular Biology (PPGBCM), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, RS, Brazil
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Daniel D N Vasquez
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Postgraduate Program in Genomic Sciences and Biotechnology (PPGCGB), Catholic University of Brasilia (UCB), Brasilia 71966-700, DF, Brazil
| | - Muhammed Tahir
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Daniele H Pinheiro
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Muhammed Faheem
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi 46000, Punjab, Pakistan
| | - Nayara S Freitas-Alves
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- Postgraduate Program in Bioprocess Engineering and Biotechnology (PPGEBB), Federal University of Paraná (UFPR), Curitiba 80060-000, PR, Brazil
| | - Clídia E Moreira-Pinto
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
| | - Valdeir J V Moreira
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Postgraduate Program in Molecular Biology (PPGBiomol), University of Brasilia (UnB), Brasília 70910-900, DF, Brazil
| | - Bruno Paes-de-Melo
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
| | - Maria E Lisei-de-Sa
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Minas Gerais Agricultural Research Company (EPAMIG), Uberaba 31170-495, MG, Brazil
| | - Carolina V Morgante
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Embrapa Semiarid, Petrolina 56302-970, PE, Brazil
| | - Ana P Z Mota
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Isabela T Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Roberto C Togawa
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Priscila Grynberg
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Rodrigo R Fragoso
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Embrapa Agroenergy, Brasilia 70770-901, DF, Brazil
| | - Janice de Almeida-Engler
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Maria F Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Postgraduate Program in Genomic Sciences and Biotechnology (PPGCGB), Catholic University of Brasilia (UCB), Brasilia 71966-700, DF, Brazil
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Canella Vieira C, Zhou J, Usovsky M, Vuong T, Howland AD, Lee D, Li Z, Zhou J, Shannon G, Nguyen HT, Chen P. Exploring Machine Learning Algorithms to Unveil Genomic Regions Associated With Resistance to Southern Root-Knot Nematode in Soybeans. FRONTIERS IN PLANT SCIENCE 2022; 13:883280. [PMID: 35592556 PMCID: PMC9111516 DOI: 10.3389/fpls.2022.883280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Southern root-knot nematode [SRKN, Meloidogyne incognita (Kofold & White) Chitwood] is a plant-parasitic nematode challenging to control due to its short life cycle, a wide range of hosts, and limited management options, of which genetic resistance is the main option to efficiently control the damage caused by SRKN. To date, a major quantitative trait locus (QTL) mapped on chromosome (Chr.) 10 plays an essential role in resistance to SRKN in soybean varieties. The confidence of discovered trait-loci associations by traditional methods is often limited by the assumptions of individual single nucleotide polymorphisms (SNPs) always acting independently as well as the phenotype following a Gaussian distribution. Therefore, the objective of this study was to conduct machine learning (ML)-based genome-wide association studies (GWAS) utilizing Random Forest (RF) and Support Vector Machine (SVM) algorithms to unveil novel regions of the soybean genome associated with resistance to SRKN. A total of 717 breeding lines derived from 330 unique bi-parental populations were genotyped with the Illumina Infinium BARCSoySNP6K BeadChip and phenotyped for SRKN resistance in a greenhouse. A GWAS pipeline involving a supervised feature dimension reduction based on Variable Importance in Projection (VIP) and SNP detection based on classification accuracy was proposed. Minor effect SNPs were detected by the proposed ML-GWAS methodology but not identified using Bayesian-information and linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Enriched Compressed Mixed Linear Model (ECMLM) models. Besides the genomic region on Chr. 10 that can explain most of SRKN resistance variance, additional minor effects SNPs were also identified on Chrs. 10 and 11. The findings in this study demonstrated that overfitting in GWAS may lead to lower prediction accuracy, and the detection of significant SNPs based on classification accuracy limited false-positive associations. The expansion of the basis of the genetic resistance to SRKN can potentially reduce the selection pressure over the major QTL on Chr. 10 and achieve higher levels of resistance.
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Affiliation(s)
- Caio Canella Vieira
- Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States
| | - Jing Zhou
- Biological Systems Engineering, University of Wisconsin–Madison, Madison, WI, United States
| | - Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Tri Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Amanda D. Howland
- Department of Entomology, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Dongho Lee
- Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States
| | - Zenglu Li
- Institute of Plant Breeding, Genetics, and Genomics, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Jianfeng Zhou
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Grover Shannon
- Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States
| | - Henry T. Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Pengyin Chen
- Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States
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Gonçalves HV, Oki Y, Bordignon L, Ferreira MC, Dos Santos JE, Tameirão LBS, Santos FR, Kalapothakis E, Fernandes GW. Endophytic fungus diversity in soybean plants submitted to conditions of elevated atmospheric CO 2 and temperature. Can J Microbiol 2021; 67:290-300. [PMID: 33031708 DOI: 10.1139/cjm-2020-0261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Global climatic changes can have drastic impacts on plant species, including severe consequences for the agricultural species productivity. Many of these species present important mutualisms with endophytic fungi that positively influence their performance. The present study evaluated whether the increases in CO2 and temperature predicted for the year 2100 may cause changes in foliar carbon (C) and nitrogen (N) concentrations in soybean (Glycine max) and, consequently, the interactions with its endophytic fungi. The effects of elevated CO2 and temperature were evaluated in four treatments in open-top chambers: (i) control, (ii) increased temperature, (iii) increased CO2, and (iv) increased CO2 and temperature. Increased atmospheric CO2 resulted in decreased foliar N concentration, while increased temperature increased it. A total of 16 taxa of endophytic fungi were identified based on sequencing internal transcribed spacer regions of rRNA subunits. Increased atmospheric CO2 and temperature were observed to potentially modify the endophytic mycobiota of soybean plants. The results suggest that the fungi species substitution is a consequence of changes in foliar N concentration and C/N ratio. Predicted climatic changes shall affect the relationships between plant and endophytes, which in turn, will affect the performance and resistance of soybean, one of the most important crops in the world.
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Affiliation(s)
- Huberman Valadares Gonçalves
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Yumi Oki
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | | | - Mariana Costa Ferreira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - José Eustáquio Dos Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Lucas Barbosa Souza Tameirão
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Fabrício Rodrigues Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Evanguedes Kalapothakis
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Geraldo Wilson Fernandes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
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7
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Banakar P, Hada A, Papolu PK, Rao U. Simultaneous RNAi Knockdown of Three FMRFamide-Like Peptide Genes, Mi-flp1, Mi-flp12, and Mi-flp18 Provides Resistance to Root-Knot Nematode, Meloidogyne incognita. Front Microbiol 2020; 11:573916. [PMID: 33193182 PMCID: PMC7644837 DOI: 10.3389/fmicb.2020.573916] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/06/2020] [Indexed: 12/03/2022] Open
Abstract
Root-knot nematode, Meloidogyne incognita, is a devastating sedentary endoparasite that causes considerable damage to agricultural crops worldwide. Modern approaches targeting the physiological processes have confirmed the potential of FMRFamide like peptide (FLPs) family of neuromotor genes for nematode management. Here, we assessed the knock down effect of Mi-flp1, Mi-flp12, and Mi-flp18 of M. incognita and their combinatorial fusion cassette on infection and reproduction. Comparative developmental profiling revealed higher expression of all three FLPs in the infective 2nd stage juveniles (J2s). Further, Mi-flp1 expression in J2s could be localized in the ventral pharyngeal nerves near to metacarpal bulb of the central nervous system. In vitro RNAi silencing of three FLPs and their fusion cassette in M. incognita J2s showed that combinatorial silencing is the most effective and affected nematode host recognition followed by reduced penetration ability and subsequent infection into tomato and adzuki bean roots. Northern blot analysis of J2s soaked in fusion dsRNA revealed the presence of siRNA of all three target FLPs establishing successful processing of fusion gene dsRNA in the J2s. Further, evaluation of the fusion gene cassette is done through host-delivered RNAi in tobacco. Transgenic plants with fusion gene RNA-expressing vector were generated in which transgene integration was confirmed by PCR, qRT-PCR, and Southern blot analysis. Transcript accumulation of three FLPs constituting the fusion gene was reduced in the M. incognita females collected from the transgenic plants that provided additional evidence for successful gene silencing. Evaluation of positive T1 transgenic lines against M. incognita brought down the disease burden as indicated by various disease parameters that ultimately reduced the nematode multiplication factor (MF) by 85% compared to the wild-type plants. The study establishes the possibility of simultaneous silencing of more than one FLPs gene for effective management of M. incognita.
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Affiliation(s)
- Prakash Banakar
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India.,Department of Nematology and Centre for Bio-Nanotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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8
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Rodríguez-Alvarez CI, López-Vidriero I, Franco-Zorrilla JM, Nombela G. Basal differences in the transcriptional profiles of tomato leaves associated with the presence/absence of the resistance gene Mi-1 and changes in these differences after infestation by the whitefly Bemisia tabaci. BULLETIN OF ENTOMOLOGICAL RESEARCH 2020; 110:463-479. [PMID: 31813394 DOI: 10.1017/s0007485319000828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The tomato Mi-1 gene mediates plant resistance to whitefly Bemisia tabaci, nematodes, and aphids. Other genes are also required for this resistance, and a model of interaction between the proteins encoded by these genes was proposed. Microarray analyses were used previously to identify genes involved in plant resistance to pests or pathogens, but scarcely in resistance to insects. In the present work, the GeneChip™ Tomato Genome Array (Affymetrix®) was used to compare the transcriptional profiles of Motelle (bearing Mi-1) and Moneymaker (lacking Mi-1) cultivars, both before and after B. tabaci infestation. Ten transcripts were expressed at least twofold in uninfested Motelle than in Moneymaker, while other eight were expressed half or less. After whitefly infestation, differences between cultivars increased to 14 transcripts expressed more in Motelle than in Moneymaker and 14 transcripts less expressed. Half of these transcripts showed no differential expression before infestation. These results show the baseline differences in the tomato transcriptomic profile associated with the presence or absence of the Mi-1 gene and provide us with valuable information on candidate genes to intervene in either compatible or incompatible tomato-whitefly interactions.
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Affiliation(s)
- Clara I Rodríguez-Alvarez
- Department of Plant Protection Institute for Agricultural Sciences (ICA), Spanish National Research Council (CSIC), Serrano 115 Dpdo., Madrid28006, Spain
| | - Irene López-Vidriero
- Genomics Unit, Centro Nacional de Biotecnología (CNB), Spanish National Research Council (CSIC), Darwin 3, Madrid28049, Spain
| | - José M Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología (CNB), Spanish National Research Council (CSIC), Darwin 3, Madrid28049, Spain
| | - Gloria Nombela
- Department of Plant Protection Institute for Agricultural Sciences (ICA), Spanish National Research Council (CSIC), Serrano 115 Dpdo., Madrid28006, Spain
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9
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Molecular Changes Concomitant with Vascular System Development in Mature Galls Induced by Root-Knot Nematodes in the Model Tree Host Populus tremula × P. alba. Int J Mol Sci 2020; 21:ijms21020406. [PMID: 31936440 PMCID: PMC7013992 DOI: 10.3390/ijms21020406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
One of the most striking features occurring in the root-knot nematode Meloidogyne incognita induced galls is the reorganization of the vascular tissues. During the interaction of the model tree species Populus and M. incognita, a pronounced xylem proliferation was previously described in mature galls. To better characterise changes in expression of genes possibly involved in the induction and the formation of the de novo developed vascular tissues occurring in poplar galls, a comparative transcript profiling of 21-day-old galls versus uninfected root of poplar was performed. Genes coding for transcription factors associated with procambium maintenance and vascular differentiation were shown to be differentially regulated, together with genes partaking in phytohormones biosynthesis and signalling. Specific signatures of transcripts associated to primary cell wall biosynthesis and remodelling, as well as secondary cell wall formation (cellulose, xylan and lignin) were revealed in the galls. Ultimately, we show that molecules derived from the monolignol and salicylic acid pathways and related to secondary cell wall deposition accumulate in mature galls.
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10
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Cheng C, Wang X, Liu X, Yang S, Yu X, Qian C, Li J, Lou Q, Chen J. Candidate genes underlying the quantitative trait loci for root-knot nematode resistance in a Cucumis hystrix introgression line of cucumber based on population sequencing. JOURNAL OF PLANT RESEARCH 2019; 132:813-823. [PMID: 31654247 PMCID: PMC6831543 DOI: 10.1007/s10265-019-01147-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/03/2019] [Indexed: 05/17/2023]
Abstract
The southern root-knot nematode (RKN), Meloidogyne incognita (Kofoid & White) Chitwood, is one of most destructive species of plant parasitic nematodes, causing significant economic losses to numerous crops including cucumber (Cucumis sativus L. 2n = 14). No commercial cultivar is currently available with resistance to RKN, severely hindering the genetic improvement of RKN resistance in cucumber. An introgression line, IL10-1, derived from the interspecific hybridization between the wild species Cucumis hystrix Chakr. (2n = 24, HH) and cucumber, was identified with resistance to RKN. In this study, an ultrahigh-density genetic linkage bin-map, composed of high-quality single-nucleotide polymorphisms (SNPs), was constructed based on low-coverage sequences of the F2:6 recombinant inbred lines derived from the cross between inbred line IL10-1 and cultivar 'Beijingjietou' CC3 (hereinafter referred to as CC3). Three QTLs were identified accounting for 13.36% (qRKN1-1), 9.07% and 9.58% (qRKN5-1 and qRKN5-2) of the resistance variation, respectively. Finally, four genes with nonsynonymous SNPs from chromosome 5 were speculated to be the candidate RKN-resistant related genes, with annotation involved in disease resistance. Though several gaps still exist on the bin-map, our results could potentially be used in breeding programs and establish an understanding of the associated mechanisms underlying RKN resistance in cucumber.
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Affiliation(s)
- Chunyan Cheng
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China
| | - Xing Wang
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China
| | - Xuejiao Liu
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China
| | - Shuqiong Yang
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China
| | - Chuntao Qian
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China
| | - Ji Li
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China
| | - Qunfeng Lou
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China
| | - Jinfeng Chen
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Street, Nanjing, 210095, China.
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11
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Kankanala P, Nandety RS, Mysore KS. Genomics of Plant Disease Resistance in Legumes. FRONTIERS IN PLANT SCIENCE 2019; 10:1345. [PMID: 31749817 PMCID: PMC6842968 DOI: 10.3389/fpls.2019.01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/27/2019] [Indexed: 05/15/2023]
Abstract
The constant interactions between plants and pathogens in the environment and the resulting outcomes are of significant importance for agriculture and agricultural scientists. Disease resistance genes in plant cultivars can break down in the field due to the evolution of pathogens under high selection pressure. Thus, the protection of crop plants against pathogens is a continuous arms race. Like any other type of crop plant, legumes are susceptible to many pathogens. The dawn of the genomic era, in which high-throughput and cost-effective genomic tools have become available, has revolutionized our understanding of the complex interactions between legumes and pathogens. Genomic tools have enabled a global view of transcriptome changes during these interactions, from which several key players in both the resistant and susceptible interactions have been identified. This review summarizes some of the large-scale genomic studies that have clarified the host transcriptional changes during interactions between legumes and their plant pathogens while highlighting some of the molecular breeding tools that are available to introgress the traits into breeding programs. These studies provide valuable insights into the molecular basis of different levels of host defenses in resistant and susceptible interactions.
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12
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Zhao J, Li L, Liu Q, Liu P, Li S, Yang D, Chen Y, Pagnotta S, Favery B, Abad P, Jian H. A MIF-like effector suppresses plant immunity and facilitates nematode parasitism by interacting with plant annexins. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5943-5958. [PMID: 31365744 PMCID: PMC6812717 DOI: 10.1093/jxb/erz348] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/22/2019] [Indexed: 05/20/2023]
Abstract
Plant-parasitic nematodes secrete numerous effectors to facilitate parasitism, but detailed functions of nematode effectors and their plant targets remain largely unknown. Here, we characterized four macrophage migration inhibitory factors (MIFs) in Meloidogyne incognita resembling the MIFs secreted by human and animal parasites. Transcriptional data showed MiMIFs are up-regulated in parasitism. Immunolocalization provided evidence that MiMIF proteins are secreted from the nematode hypodermis to the parasite surface, detected in plant tissues and giant cells. In planta MiMIFs RNA interference in Arabidopsis decreased infection and nematode reproduction. Transient expression of MiMIF-2 could suppress Bax- and RBP1/Gpa2-induced cell death. MiMIF-2 ectopic expression led to higher levels of Arabidopsis susceptibility, suppressed immune responses triggered by flg22, and impaired [Ca2+]cyt influx induced by H2O2. The immunoprecipitation of MiMIF-2-interacting proteins, followed by co-immunoprecipitation and bimolecular fluorescence complementation validations, revealed specific interactions between MiMIF-2 and two Arabidopsis annexins, AnnAt1 and AnnAt4, involved in the transport of calcium ions, stress responses, and signal transduction. Suppression of expression or overexpression of these annexins modified nematode infection. Our results provide functional evidence that nematode effectors secreted from hypodermis to the parasite cuticle surface target host proteins and M. incognita uses MiMIFs to promote parasitism by interfering with the annexin-mediated plant immune responses.
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Affiliation(s)
- Jianlong Zhao
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Lijuan Li
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Qian Liu
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Pei Liu
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Shuang Li
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Dan Yang
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Yongpan Chen
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Sophie Pagnotta
- Centre Commun de Microscopie Appliquée (CCMA), Université de Nice Sophia Antipolis, Nice, France
| | | | - Pierre Abad
- Université Côte d’Azur, INRA, CNRS, ISA, France
| | - Heng Jian
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, China
- Correspondence:
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13
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Morozov SY, Solovyev AG, Kalinina NO, Taliansky ME. Double-Stranded RNAs in Plant Protection Against Pathogenic Organisms and Viruses in Agriculture. Acta Naturae 2019; 11:13-21. [PMID: 31993231 PMCID: PMC6977960 DOI: 10.32607/20758251-2019-11-4-13-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/29/2019] [Indexed: 11/24/2022] Open
Abstract
Recent studies have shown that plants are able to express the artificial genes responsible for the synthesis of double-stranded RNAs (dsRNAs) and hairpin double-stranded RNAs (hpRNAs), as well as uptake and process exogenous dsRNAs and hpRNAs to suppress the gene expression of plant pathogenic viruses, fungi, or insects. Both endogenous and exogenous dsRNAs are processed into small interfering RNAs (siRNAs) that can spread locally and systemically through the plant, enter pathogenic microorganisms, and induce RNA interference-mediated pathogen resistance in plants. There are numerous examples of the development of new biotechnological approaches to plant protection using transgenic plants and exogenous dsRNAs. This review summarizes new data on the use of transgenes and exogenous dsRNAs for the suppression of fungal and insect virulence genes, as well as viruses to increase the resistance of plants to these pathogens. We also analyzed the current ideas about the mechanisms of dsRNA processing and transport in plants.
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Affiliation(s)
- S. Y. Morozov
- International Laboratory «Resistom», The Skolkovo Innovation Center, Moscow, 143026 Russia**
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - A. G. Solovyev
- International Laboratory «Resistom», The Skolkovo Innovation Center, Moscow, 143026 Russia**
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - N. O. Kalinina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - M. E. Taliansky
- International Laboratory «Resistom», The Skolkovo Innovation Center, Moscow, 143026 Russia**
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, 117997 Russia
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14
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Ibrahim HMM, Ahmad EM, Martínez-Medina A, Aly MAM. Effective approaches to study the plant-root knot nematode interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:332-342. [PMID: 31207494 DOI: 10.1016/j.plaphy.2019.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/26/2019] [Accepted: 06/08/2019] [Indexed: 05/24/2023]
Abstract
Plant-parasitic nematodes cause major agricultural losses worldwide. Examining the molecular mechanisms underlying plant-nematode interactions and how plants respond to different invading pathogens is attracting major attention to reduce the expanding gap between agricultural production and the needs of the growing world population. This review summarizes the most recent developments in plant-nematode interactions and the diverse approaches used to improve plant resistance against root knot nematode (RKN). We will emphasize the recent rapid advances in genome sequencing technologies, small interfering RNA techniques (RNAi) and targeted genome editing which are contributing to the significant progress in understanding the plant-nematode interaction mechanisms. Also, molecular approaches to improve plant resistance against nematodes are considered.
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Affiliation(s)
- Heba M M Ibrahim
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt.
| | - Esraa M Ahmad
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Ainhoa Martínez-Medina
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research, Leipzig, Germany
| | - Mohammed A M Aly
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
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15
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Song W, Qi N, Liang C, Duan F, Zhao H. Soybean root transcriptome profiling reveals a nonhost resistant response during Heterodera glycines infection. PLoS One 2019; 14:e0217130. [PMID: 31125369 PMCID: PMC6534303 DOI: 10.1371/journal.pone.0217130] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 05/06/2019] [Indexed: 11/19/2022] Open
Abstract
Heterodera glycines (soybean cyst nematode, SCN) is one of the most devastating pathogens of soybean worldwide. The compatible and in compatible interactions between soybean and SCN have well documented. Nevertheless, the molecular mechanism of a nonhost resistant response in soybean against SCN infection remains obscure. Toward this end, a global transcriptional comparison was conducted between susceptible and resistant reactions of soybean roots infected by taking advantage of finding a new pathotype of SCN (SCNT). The soybean cultivar Lee, which exhibits resistant to SCNT and susceptible to HG 1.2.3.4.7 (SCNs) was utilized in the expriments. The results highlighted a nonhost resistant response of soybean. Transcriptome analysis indicated that the number of differentially expressed genes (DEGs) in the resistant interaction (3746) was much larger than that in the susceptible interaction (602). A great number of genes acting as intrinsic component of membrane, integral component of membrane, cell periphery and plasma membrance were remarkably enriched only in the resistant interaction, while the taurine and hypotaurine, phenylpropanoid pathway, plant-pathogen interaction and transcript factors were modulated in both interactions. This is the first study to examine genes expression patterns in a soybean genotype in response to invasion by a virulent and avirulent SCN population at the transcriptional level, which will provide insights into the complicate molecular mechanism of the nonhost resistant interaction.
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Affiliation(s)
- Wenwen Song
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Nawei Qi
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Chen Liang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fangmeng Duan
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Honghai Zhao
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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16
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Transcriptional profiling of wheat (Triticum aestivum L.) during a compatible interaction with the cereal cyst nematode Heterodera avenae. Sci Rep 2019; 9:2184. [PMID: 30778126 PMCID: PMC6379437 DOI: 10.1038/s41598-018-37824-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/26/2018] [Indexed: 12/27/2022] Open
Abstract
Cereal cyst nematode (CCN, Heterodera avenae) presents severe challenges to wheat (Triticum aestivum L.) production worldwide. An investigation of the interaction between wheat and CCN can greatly improve our understanding of how nematodes alter wheat root metabolic pathways for their development and could contribute to new control strategies against CCN. In this study, we conducted transcriptome analyses of wheat cv. Wen 19 (Wen19) by using RNA-Seq during the compatible interaction with CCN at 1, 3 and 8 days past inoculation (dpi). In total, 71,569 transcripts were identified, and 10,929 of them were examined as differentially expressed genes (DEGs) in response to CCN infection. Based on the functional annotation and orthologous findings, the protein phosphorylation, oxidation-reduction process, regulation of transcription, metabolic process, transport, and response process as well as many other pathways previously reported were enriched at the transcriptional level. Plant cell wall hydrolysis and modifying proteins, auxin biosynthesis, signalling and transporter genes were up-regulated by CCN infection to facilitate penetration, migration and syncytium establishment. Genes responding to wounding and jasmonic acid stimuli were enriched at 1 dpi. We found 16 NBS-LRR genes, 12 of which were down-regulated, indicating the repression of resistance. The expression of genes encoding antioxidant enzymes, glutathione S-transferases and UDP-glucosyltransferase was significantly up-regulated during CCN infection, indicating that they may play key roles in the compatible interaction of wheat with CCN. Taken together, the results obtained from the transcriptome analyses indicate that the genes involved in oxidation-reduction processes, induction and suppression of resistance, metabolism, transport and syncytium establishment may be involved in the compatible interaction of Wen 19 with CCN. This study provides new insights into the responses of wheat to CCN infection. These insights could facilitate the elucidation of the potential mechanisms of wheat responses to CCN.
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17
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Li X, Xing X, Tian P, Zhang M, Huo Z, Zhao K, Liu C, Duan D, He W, Yang T. Comparative Transcriptome Profiling Reveals Defense-Related Genes against Meloidogyne incognita Invasion in Tobacco. Molecules 2018; 23:E2081. [PMID: 30127271 PMCID: PMC6222693 DOI: 10.3390/molecules23082081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 08/15/2018] [Accepted: 08/17/2018] [Indexed: 01/20/2023] Open
Abstract
Root-knot nematodes Meloidogyne incognita are one of the most destructive pathogens, causing severe losses to tobacco productivity and quality. However, the underlying resistance mechanism of tobacco to M. incognita is not clear. In this study, two tobacco genotypes, K326 and Changbohuang, which are resistant and susceptible to M. incognita, respectively, were used for RNA-sequencing analysis. An average of 35 million clean reads were obtained. Compared with their expression levels in non-infected plants of the same genotype, 4354 and 545 differentially expressed genes (DEGs) were detected in the resistant and susceptible genotype, respectively, after M. incognita invasion. Overall, 291 DEGs, involved in diverse biological processes, were common between the two genotypes. Genes encoding toxic compound synthesis, cell wall modification, reactive oxygen species and the oxidative burst, salicylic acid signal transduction, and production of some other metabolites were putatively associated with tobacco resistance to M. incognita. In particular, the complex resistance response needed to overcome M. incognita invasion may be regulated by several transcription factors, such as the ethylene response factor, MYB, basic helix⁻loop⁻helix transcription factor, and indole acetic acid⁻leucine-resistant transcription factor. These results may aid in the identification of potential genes of resistance to M. incognita for tobacco cultivar improvement.
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Affiliation(s)
- Xiaohui Li
- Department of Tobacco, College of Tobacco, Henan Agricultural University, Zhengzhou 450002, Henan, China.
| | - Xuexia Xing
- Nanyang Branch of Henan Province Tobacco Company, Nanyang 473003, Henan, China.
| | - Pei Tian
- Department of Tobacco, College of Tobacco, Henan Agricultural University, Zhengzhou 450002, Henan, China.
| | - Mingzhen Zhang
- Xiaogan Agricultural Technical Extension Station, Xiaogan 432000, Hubei, China.
| | - Zhaoguang Huo
- Department of Tobacco, College of Tobacco, Henan Agricultural University, Zhengzhou 450002, Henan, China.
| | - Ke Zhao
- Department of Tobacco, College of Tobacco, Henan Agricultural University, Zhengzhou 450002, Henan, China.
| | - Chao Liu
- Department of Tobacco, College of Tobacco, Henan Agricultural University, Zhengzhou 450002, Henan, China.
| | - Duwei Duan
- Department of Tobacco, College of Tobacco, Henan Agricultural University, Zhengzhou 450002, Henan, China.
| | - Wenjun He
- Department of Tobacco, College of Tobacco, Henan Agricultural University, Zhengzhou 450002, Henan, China.
| | - Tiezhao Yang
- Department of Tobacco, College of Tobacco, Henan Agricultural University, Zhengzhou 450002, Henan, China.
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18
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Shukla N, Yadav R, Kaur P, Rasmussen S, Goel S, Agarwal M, Jagannath A, Gupta R, Kumar A. Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both host and nematode during susceptible and resistance responses. MOLECULAR PLANT PATHOLOGY 2018; 19:615-633. [PMID: 28220591 PMCID: PMC6638136 DOI: 10.1111/mpp.12547] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/19/2017] [Accepted: 02/17/2017] [Indexed: 05/10/2023]
Abstract
Root-knot nematodes (RKNs, Meloidogyne incognita) are economically important endoparasites with a wide host range. We used a comprehensive transcriptomic approach to investigate the expression of both tomato and RKN genes in tomato roots at five infection time intervals from susceptible plants and two infection time intervals from resistant plants, grown under soil conditions. Differentially expressed genes during susceptible (1827, tomato; 462, RKN) and resistance (25, tomato; 160, RKN) interactions were identified. In susceptible responses, tomato genes involved in cell wall structure, development, primary and secondary metabolite, and defence signalling pathways, together with RKN genes involved in host parasitism, development and defence, are discussed. In resistance responses, tomato genes involved in secondary metabolite and hormone-mediated defence responses, together with RKN genes involved in starvation stress-induced apoptosis, are discussed. In addition, 40 novel differentially expressed RKN genes encoding secretory proteins were identified. Our findings provide novel insights into the temporal regulation of genes involved in various biological processes from tomato and RKN simultaneously during susceptible and resistance responses, and reveal the involvement of a complex network of biosynthetic pathways during disease development.
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Affiliation(s)
- Neha Shukla
- Department of BotanyUniversity of DelhiDelhi110007India
| | - Rachita Yadav
- Department of Bio and Health InformaticsTechnical University of Denmark, Kemitorvet 208Lyngby2800Denmark
| | - Pritam Kaur
- Department of BotanyUniversity of DelhiDelhi110007India
| | - Simon Rasmussen
- Department of Bio and Health InformaticsTechnical University of Denmark, Kemitorvet 208Lyngby2800Denmark
| | | | - Manu Agarwal
- Department of BotanyUniversity of DelhiDelhi110007India
| | | | - Ramneek Gupta
- Department of Bio and Health InformaticsTechnical University of Denmark, Kemitorvet 208Lyngby2800Denmark
| | - Amar Kumar
- Department of BotanyUniversity of DelhiDelhi110007India
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19
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Salazar-Iribe A, Zúñiga-Sánchez E, Mejía EZ, Gamboa-deBuen A. Cell Wall Localization of Two DUF642 Proteins, BIIDXI and TEEBE, during Meloidogyne incognita Early Inoculation. THE PLANT PATHOLOGY JOURNAL 2017; 33:614-618. [PMID: 29238286 PMCID: PMC5720610 DOI: 10.5423/ppj.nt.05.2017.0101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/02/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
The root-knot nematode Meloidogyne incognita infects a variety of plants, including Arabidopsis thaliana. During migration, root-knot nematodes secrete different proteins to modify cell walls, which include pectolytic enzymes. However, the contribution of host cell wall proteins has not been described during this process. The function of two DUF642 cell wall proteins, BIIDXI (BDX, At4g32460) and TEEBE (TEB, At2g41800), in plant development could be related to the regulation of pectin methyl esterification status in the cell walls of different tissues. Accordingly, the expression of these two genes is up-regulated by auxin. BDX and TEB were highly induced during early M. incognita inoculation. Moreover, cell wall localization of the proteins was also induced. The cell wall localization of BDX and TEB DUF642 proteins during M. incognita early inoculation suggested that these two proteins could be involved in the regulation of the degree of pectin methylation during cell separation.
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Affiliation(s)
- Alexis Salazar-Iribe
- Instituto de Ecología, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C.P. 04510
| | - Esther Zúñiga-Sánchez
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C.P. 04510. Edificio E Laboratorio L-102
| | - Emma Zavaleta Mejía
- Colegio de Postgraduados (CP), Instituto de Fitosanidad, km 35.5 Carr. México-Texcoco, Montecillo, Edo. de México CP 56230
| | - Alicia Gamboa-deBuen
- Instituto de Ecología, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C.P. 04510
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Elucidation of the compatible interaction between banana and Meloidogyne incognita via high-throughput proteome profiling. PLoS One 2017; 12:e0178438. [PMID: 28575037 PMCID: PMC5456091 DOI: 10.1371/journal.pone.0178438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/12/2017] [Indexed: 12/16/2022] Open
Abstract
With a diverse host range, Meloidogyne incognita (root-knot nematode) is listed as one of the most economically important obligate parasites of agriculture. This nematode species establishes permanent feeding sites in plant root systems soon after infestation. A compatible host-nematode interaction triggers a cascade of morphological and physiological process disruptions of the host, leading to pathogenesis. Such disruption is reflected by altered gene expression in affected cells, detectable using molecular approaches. We employed a high-throughput proteomics approach to elucidate the events involved in a compatible banana- M. incognita interaction. This study serves as the first crucial step in developing natural banana resistance for the purpose of biological-based nematode management programme. We successfully profiled 114 Grand naine root proteins involved in the interaction with M. incognita at the 30th- and 60th- day after inoculation (dai). The abundance of proteins involved in fundamental biological processes, cellular component organisation and stress responses were significantly altered in inoculated root samples. In addition, the abundance of proteins in pathways associated with defence and giant cell maintenance in plants such as phenylpropanoid biosynthesis, glycolysis and citrate cycle were also implicated by the infestation.
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Ye DY, Qi YH, Cao SF, Wei BQ, Zhang HS. Histopathology combined with transcriptome analyses reveals the mechanism of resistance to Meloidogyne incognita in Cucumis metuliferus. JOURNAL OF PLANT PHYSIOLOGY 2017; 212:115-124. [PMID: 28314173 DOI: 10.1016/j.jplph.2017.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/05/2017] [Accepted: 02/07/2017] [Indexed: 05/08/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) cause serious threat to cucumber production. Cucumis metuliferus, a relative of cucumber, is reported to be resistant to Meloidogyne incognita, yet the underlying resistance mechanism remains unclear. In this study, the response of resistant C. metuliferus accession PI482443 following nematode infection was studied in comparison with susceptible C. sativus cv. Jinlv No.3. Roots of selected Cucumis seedings were analysed using histological and biochemical techniques. Transcriptome changes of the resistance reaction were investigated by RNA-seq. The results showed that penetration and development of the nematode in resistant plants were reduced when compared to susceptible plants. Infection of a resistant genotype with M. incognita resulted in a hypersensitive reaction. The induction of phenylalanine ammonia lyase and peroxidase activities after infection was greater in resistant than susceptible roots. Several of the most relevant genes for phenylpropanoid biosynthesis, plant hormone signal transduction, and the plant-pathogen interaction pathway that are involved in resistance to the nematode were significantly altered. The resistance in C. metuliferus PI482443 to M. incognita was associated with reduced nematode penetration, retardation of nematode development, and hypersensitive necrosis. The expression of genes resulting in the deposition of lignin, toxic compounds synthesis, cell wall reinforcement, suppression of nematode feeding and resistance protein accumulation, and activation of several transcription factors might all contribute to the resistance response to the pest. These results may lead to a better understanding of the resistance mechanism and aid in the identification of potential targets resistant to pests for cucumber improvement.
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Affiliation(s)
- De-You Ye
- Institute of Vegetables, Gansu Academy of Agricultural Sciences, Scientific Observations Experiment Station of Vegetables, Ministry of Agriculture in the Northwest of China, Lanzhou 730070, China.
| | - Yong-Hong Qi
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Su-Fang Cao
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Bing-Qiang Wei
- Institute of Vegetables, Gansu Academy of Agricultural Sciences, Scientific Observations Experiment Station of Vegetables, Ministry of Agriculture in the Northwest of China, Lanzhou 730070, China
| | - Hua-Sheng Zhang
- Institute of Vegetables, Gansu Academy of Agricultural Sciences, Scientific Observations Experiment Station of Vegetables, Ministry of Agriculture in the Northwest of China, Lanzhou 730070, China
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Sánchez Timm E, Hidalgo Pardo L, Pacheco Coello R, Chávez Navarrete T, Navarrete Villegas O, Santos Ordóñez E. Identification of Differentially-Expressed Genes in Response to Mycosphaerella fijiensis in the Resistant Musa Accession 'Calcutta-4' Using Suppression Subtractive Hybridization. PLoS One 2016; 11:e0160083. [PMID: 27487237 PMCID: PMC4972352 DOI: 10.1371/journal.pone.0160083] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/10/2016] [Indexed: 11/19/2022] Open
Abstract
Bananas and plantains are considered an important crop around the world. Banana production is affected by several constraints, of which Black Sigatoka Disease, caused by the fungus Mycosphaerella fijiensis, is considered one of the most important diseases in banana plantations. The banana accession ‘Calcutta-4’ has a natural resistance to Black Sigatoka; however, the fruit is not valuable for commercialization. Gene identification and expression studies in ‘Calcutta-4’ might reveal possible gene candidates for resistant to the disease and elucidate mechanisms for resistance. A subtracted cDNA library was generated from leaves after 6, 9 and 12 days inoculated with M. fijiensis conidia on greenhouse banana plants of the accession ‘Calcutta-4’. Bioinformatic analysis revealed 99 good quality sequences. Blast2go analysis revealed that 31% of the sequences could not be categorized and, according to the Biological Process Category, 32 and 28 ESTs are related to general metabolic and cellular processes, respectively; while 10 ESTs response to stimulus. Seven sequences were redundant and one was similar to genes that may be involved in pathogen resistance including the putative disease resistance protein RGA1. Genes encoding zinc finger domains were identified and may play an important role in pathogen resistance by inducing the expression of downstream genes. Expression analysis of four selected genes was performed using RT-qPCR during the early stage of the disease development at 6, 9, 12 and 15 days post inoculation showing a peak of up regulation at 9 or 12 days post inoculation. Three of the four genes showed an up-regulation of expression in ‘Calcutta-4’ when compared to ‘Williams’ after inoculation with M. fijiensis, suggesting a fine regulation of specific gene candidates that may lead to a resistance response. The genes identified in early responses in a plant-pathogen interaction may be relevant for the resistance response of ‘Calcutta-4’ to Black Sigatoka. Genes with different functions may play a role in plant response to the disease. The present study suggests a fine up regulation of these genes that might be needed to perform an incompatible interaction. Further gene functional studies need to be performed to validate their use as candidate resistance genes in susceptible banana cultivars.
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Affiliation(s)
- Eduardo Sánchez Timm
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Lisette Hidalgo Pardo
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Ricardo Pacheco Coello
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Tatiana Chávez Navarrete
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Oscar Navarrete Villegas
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Efrén Santos Ordóñez
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ciencias de la Vida, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- * E-mail:
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Jain S, Chittem K, Brueggeman R, Osorno JM, Richards J, Nelson BD. Comparative Transcriptome Analysis of Resistant and Susceptible Common Bean Genotypes in Response to Soybean Cyst Nematode Infection. PLoS One 2016; 11:e0159338. [PMID: 27441552 PMCID: PMC4956322 DOI: 10.1371/journal.pone.0159338] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/30/2016] [Indexed: 12/21/2022] Open
Abstract
Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) reproduces on the roots of common bean (Phaseolus vulgaris L.) and can cause reductions in plant growth and seed yield. The molecular changes in common bean roots caused by SCN infection are unknown. Identification of genetic factors associated with SCN resistance could help in development of improved bean varieties with high SCN resistance. Gene expression profiling was conducted on common bean roots infected by SCN HG type 0 using next generation RNA sequencing technology. Two pinto bean genotypes, PI533561 and GTS-900, resistant and susceptible to SCN infection, respectively, were used as RNA sources eight days post inoculation. Total reads generated ranged between ~ 3.2 and 5.7 million per library and were mapped to the common bean reference genome. Approximately 70-90% of filtered RNA-seq reads uniquely mapped to the reference genome. In the inoculated roots of resistant genotype PI533561, a total of 353 genes were differentially expressed with 154 up-regulated genes and 199 down-regulated genes when compared to the transcriptome of non- inoculated roots. On the other hand, 990 genes were differentially expressed in SCN-inoculated roots of susceptible genotype GTS-900 with 406 up-regulated and 584 down-regulated genes when compared to non-inoculated roots. Genes encoding nucleotide-binding site leucine-rich repeat resistance (NLR) proteins, WRKY transcription factors, pathogenesis-related (PR) proteins and heat shock proteins involved in diverse biological processes were differentially expressed in both resistant and susceptible genotypes. Overall, suppression of the photosystem was observed in both the responses. Furthermore, RNA-seq results were validated through quantitative real time PCR. This is the first report describing genes/transcripts involved in SCN-common bean interaction and the results will have important implications for further characterization of SCN resistance genes in common bean.
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Affiliation(s)
- Shalu Jain
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, 58108, United States of America
| | - Kishore Chittem
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, 58108, United States of America
| | - Robert Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, 58108, United States of America
| | - Juan M. Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58108, United States of America
| | - Jonathan Richards
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, 58108, United States of America
| | - Berlin D. Nelson
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, 58108, United States of America
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Baldacci-Cresp F, Sacré PY, Twyffels L, Mol A, Vermeersch M, Ziemons E, Hubert P, Pérez-Morga D, El Jaziri M, de Almeida Engler J, Baucher M. Poplar-Root Knot Nematode Interaction: A Model for Perennial Woody Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:560-572. [PMID: 27135257 DOI: 10.1094/mpmi-01-16-0015-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Plant root-knot nematode (RKN) interaction studies are performed on several host plant models. Though RKN interact with trees, no perennial woody model has been explored so far. Here, we show that poplar (Populus tremula × P. alba) grown in vitro is susceptible to Meloidogyne incognita, allowing this nematode to penetrate, to induce feeding sites, and to successfully complete its life cycle. Quantitative reverse transcription-polymerase chain reaction analysis was performed to study changes in poplar gene expression in galls compared with noninfected roots. Three genes (expansin A, histone 3.1, and asparagine synthase), selected as gall development marker genes, followed, during poplar-nematode interaction, a similar expression pattern to what was described for other plant hosts. Downregulation of four genes implicated in the monolignol biosynthesis pathway was evidenced in galls, suggesting a shift in the phenolic profile within galls developed on poplar roots. Raman microspectroscopy demonstrated that cell walls of giant cells were not lignified but mainly composed of pectin and cellulose. The data presented here suggest that RKN exercise conserved strategies to reproduce and to invade perennial plant species and that poplar is a suitable model host to study specific traits of tree-nematode interactions.
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Affiliation(s)
- Fabien Baldacci-Cresp
- 1 Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, B-6041 Gosselies, Belgium
| | - Pierre-Yves Sacré
- 2 University of Liege, CIRM, Department of Pharmacy, Laboratory of Analytical Chemistry, CHU, B36, B-4000 Liege, Belgium
| | - Laure Twyffels
- 3 Center for Microscopy and Molecular Imaging-CMMI, Université libre de Bruxelles
| | - Adeline Mol
- 1 Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, B-6041 Gosselies, Belgium
| | - Marjorie Vermeersch
- 3 Center for Microscopy and Molecular Imaging-CMMI, Université libre de Bruxelles
| | - Eric Ziemons
- 2 University of Liege, CIRM, Department of Pharmacy, Laboratory of Analytical Chemistry, CHU, B36, B-4000 Liege, Belgium
| | - Philippe Hubert
- 2 University of Liege, CIRM, Department of Pharmacy, Laboratory of Analytical Chemistry, CHU, B36, B-4000 Liege, Belgium
| | - David Pérez-Morga
- 3 Center for Microscopy and Molecular Imaging-CMMI, Université libre de Bruxelles
- 4 Laboratoire de Parasitologie Moléculaire, Université libre de Bruxelles; and
| | - Mondher El Jaziri
- 1 Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, B-6041 Gosselies, Belgium
| | - Janice de Almeida Engler
- 5 INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, F-06900 Sophia Antipolis, France
| | - Marie Baucher
- 1 Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, B-6041 Gosselies, Belgium
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Santini L, Munhoz CDF, Bonfim MF, Brandão MM, Inomoto MM, Vieira MLC. Host Transcriptional Profiling at Early and Later Stages of the Compatible Interaction Between Phaseolus vulgaris and Meloidogyne incognita. PHYTOPATHOLOGY 2016; 106:282-94. [PMID: 26551451 DOI: 10.1094/phyto-07-15-0160-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The root-knot nematode (Meloidogyne incognita) is one of most devastating pathogens that attack the common bean crop. Although there is evidence that some cultivars have race-specific resistance against M. incognita, these resistance sources have not proved effective, and nematodes are able to circumvent the host's defense system. We constructed RNA-seq based libraries and used a high-throughput sequencing platform to analyze the plant responses to M. incognita. Assessments were performed at 4 and 10 days after inoculation corresponding to the stages of nematode penetration and giant cell development, respectively. Large-scale transcript mapping to the common bean reference genome (G19833) resulted in the identification of 27,195 unigenes. Of these, 797 host genes were found to be differentially expressed. The functional annotation results confirm the complex interplay between abiotic and biotic stress signaling pathways. High expression levels of the wounding-responsive genes were observed over the interaction. At early response, an overexpression of the N gene, a TIR-NBS-LRR resistance gene, was understood as a host attempt to overcome the pathogen attack. However, the repression of heat shock proteins resulted in a lack of reactive oxygen species accumulation and absence of a hypersensitive response. Furthermore, the host basal response was broken by the repression of the ethylene/jasmonate pathway later in the response, resulting in a continuous compatible process with consequent plant susceptibility.
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Affiliation(s)
- Luciane Santini
- First, second, and sixth authors: Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; third author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil; fourth author: Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, Brazil; and fifth author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil
| | - Carla de Freitas Munhoz
- First, second, and sixth authors: Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; third author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil; fourth author: Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, Brazil; and fifth author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil
| | - Mauro Ferreira Bonfim
- First, second, and sixth authors: Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; third author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil; fourth author: Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, Brazil; and fifth author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil
| | - Marcelo Mendes Brandão
- First, second, and sixth authors: Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; third author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil; fourth author: Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, Brazil; and fifth author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil
| | - Mário Massayuki Inomoto
- First, second, and sixth authors: Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; third author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil; fourth author: Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, Brazil; and fifth author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- First, second, and sixth authors: Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; third author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil; Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil; fourth author: Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, Brazil; and fifth author: Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil
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Chi Y, Wang X, Le X, Ju Y, Guan T, Li H. Exposure to double-stranded RNA mediated by tobacco rattle virus leads to transcription up-regulation of effector gene Mi-vap-2 from Meloidogyne incognita and promotion of pathogenicity in progeny. Int J Parasitol 2016; 46:105-13. [PMID: 26545953 DOI: 10.1016/j.ijpara.2015.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/17/2015] [Indexed: 10/22/2022]
Abstract
Meloidogyne spp. are economically important plant parasites and cause enormous damage to agriculture world-wide. These nematodes use secreted effectors which modify host cells, allowing them to obtain the nutrients required for growth and development. A better understanding of the roles of effectors in nematode parasitism is critical for understanding the mechanisms of nematode-host interactions. In this study, Mi-vap-2 of Meloidogyne incognita, a gene encoding a venom allergen-like protein, was targeted by RNA interference mediated by the tobacco rattle virus. Unexpectedly, compared with a wild type line, a substantial up-regulation of Mi-vap-2 transcript was observed in juveniles collected at 7 days p.i. from Nicotiana benthamiana agroinfiltrated with TRV::vap-2. This up-regulation of the targeted transcript did not impact development of females or the production of galls, nor the number of females on the TRV::vap-2 line. In a positive control line, the transcript of Mi16D10 was knocked down in juveniles from the TRV::16D10 line at 7 days p.i., resulting in a significant inhibition of nematode development. The up-regulation of Mi-vap-2 triggered by TRV-RNAi was inherited by the progeny of the nematodes exposed to double-stranded RNA. Meanwhile, a substantial increase in Mi-VAP-2 expression in those juvenile progeny was revealed by ELISA. This caused an increase in the number of galls (71.2%) and females (84.6%) produced on seedlings of N. benthamiana compared with the numbers produced by control nematodes. Up-regulation of Mi-vap-2 and its encoded protein therefore enhanced pathogenicity of the nematodes, suggesting that Mi-vap-2 may be required for successful parasitism during the early parasitic stage of M. incognita.
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Affiliation(s)
- Yuankai Chi
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xuan Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiuhu Le
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yuliang Ju
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tinglong Guan
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hongmei Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, PR China.
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Favery B, Quentin M, Jaubert-Possamai S, Abad P. Gall-forming root-knot nematodes hijack key plant cellular functions to induce multinucleate and hypertrophied feeding cells. JOURNAL OF INSECT PHYSIOLOGY 2016. [PMID: 26211599 DOI: 10.1016/j.jinsphys.2015.07.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Among plant-parasitic nematodes, the root-knot nematodes (RKNs) of the Meloidogyne spp. are the most economically important genus. RKN are root parasitic worms able to infect nearly all crop species and have a wide geographic distribution. During infection, RKNs establish and maintain an intimate relationship with the host plant. This includes the creation of a specialized nutritional structure composed of multinucleate and hypertrophied giant cells, which result from the redifferentiation of vascular root cells. Giant cells constitute the sole source of nutrients for the nematode and are essential for growth and reproduction. Hyperplasia of surrounding root cells leads to the formation of the gall or root-knot, an easily recognized symptom of plant infection by RKNs. Secreted effectors produced in nematode salivary glands and injected into plant cells through a specialized feeding structure called the stylet play a critical role in the formation of giant cells. Here, we describe the complex interactions between RKNs and their host plants. We highlight progress in understanding host plant responses, focusing on how RKNs manipulate key plant processes and functions, including cell cycle, defence, hormones, cellular scaffold, metabolism and transport.
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Affiliation(s)
- Bruno Favery
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France; Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France; CNRS, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France
| | - Michaël Quentin
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France; Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France; CNRS, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France
| | - Stéphanie Jaubert-Possamai
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France; Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France; CNRS, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France
| | - Pierre Abad
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France; Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France; CNRS, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia-Antipolis, France.
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29
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Iberkleid I, Sela N, Brown Miyara S. Meloidogyne javanica fatty acid- and retinol-binding protein (Mj-FAR-1) regulates expression of lipid-, cell wall-, stress- and phenylpropanoid-related genes during nematode infection of tomato. BMC Genomics 2015; 16:272. [PMID: 25886179 PMCID: PMC4450471 DOI: 10.1186/s12864-015-1426-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 03/02/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The secreted Meloidogyne javanica fatty acid- and retinol-binding (FAR) protein Mj-FAR-1 is involved in nematode development and reproduction in host tomato roots. To gain further insight into the role of Mj-FAR-1 in regulating disease development, local transcriptional changes were monitored in tomato hairy root lines with constitutive mj-far-1 expression compared with control roots without inoculation, and 2, 5 and 15 days after inoculation (DAI), using mRNA sequencing analysis. RESULTS Gene-expression profiling revealed a total of 3970 differentially expressed genes (DEGs) between the two lines. Among the DEGs, 1093, 1039, 1959, and 1328 genes were up- or downregulated 2-fold with false discovery rate < 0.001 in noninoculated roots, and roots 2, 5, and 15 DAI compared with control roots, respectively. Four main groups of genes that might be associated with Mj-FAR-1-mediated susceptibility were identified: 1) genes involved in biotic stress responses such as pathogen-defense mechanisms and hormone metabolism; 2) genes involved in phenylalanine and phenylpropanoid metabolism; 3) genes associated with cell wall synthesis, modification or degradation; and 4) genes associated with lipid metabolism. All of these genes were overrepresented among the DEGs. Studying the distances between the treatments, samples from noninoculated roots and roots at 2 DAI clustered predominantly according to the temporal dynamics related to nematode infection. However, at the later time points (5 and 15 DAI), samples clustered predominantly according to mj-far-1 overexpression, indicating that at these time points Mj-FAR-1 is more important in defining a common transcriptome. CONCLUSIONS The presence of four groups of DEGs demonstrates a network of molecular events is mediated by Mj-FAR-1 that leads to highly complex manipulation of plant defense responses against nematode invasion. The results shed light on the in vivo role of secreted FAR proteins in parasitism, and add to the mounting evidence that secreted FAR proteins play a major role in nematode parasitism.
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Affiliation(s)
- Ionit Iberkleid
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, P.O. Box 6, Bet Dagan, 50250, Israel.
| | - Noa Sela
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 76100, Israel.
| | - Sigal Brown Miyara
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, P.O. Box 6, Bet Dagan, 50250, Israel.
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Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Xu D, Nguyen HT. Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe). BMC Genomics 2015; 16:148. [PMID: 25880563 PMCID: PMC4351908 DOI: 10.1186/s12864-015-1316-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/03/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most devastating pathogen of soybean. Many gene expression profiling studies have been conducted to investigate the responses of soybean to the infection by this pathogen using primarily the first-generation soybean genome array that covered approximately 37,500 soybean transcripts. However, no study has been reported yet using the second-generation Affymetrix soybean whole-genome transcript array (Soybean WT array) that represents approximately 66,000 predicted soybean transcripts. RESULTS In the present work, the gene expression profiles of two soybean plant introductions (PIs) PI 437654 and PI 567516C (both resistant to multiple SCN HG Types) and cultivar Magellan (susceptible to SCN) were compared in the presence or absence of the SCN inoculum at 3 and 8 days post-inoculation using the Soybean WT array. Data analysis revealed that the two resistant soybean lines showed distinctive gene expression profiles from each other and from Magellan not only in response to the SCN inoculation, but also in the absence of SCN. Overall, 1,413 genes and many pathways were revealed to be differentially regulated. Among them, 297 genes were constitutively regulated in the two resistant lines (compared with Magellan) and 1,146 genes were responsive to the SCN inoculation in the three lines, with 30 genes regulated both constitutively and by SCN. In addition to the findings similar to those in the published work, many genes involved in ethylene, protein degradation, and phenylpropanoid pathways were also revealed differentially regulated in the present study. GC-rich elements (e.g., GCATGC) were found over-represented in the promoter regions of certain groups of genes. These have not been observed before, and could be new defense-responsive regulatory elements. CONCLUSIONS Different soybean lines showed different gene expression profiles in the presence and absence of the SCN inoculum. Both inducible and constitutive gene expression may contribute to resistance to multiple SCN HG Types in the resistant soybean PI lines. Ethylene, protein degradation, and phenylpropanoid pathways, as well as many other pathways reported previously, may play important roles in mediating the soybean-SCN interactions. The revealed genes, pathways, and promoter elements can be further explored to regulate or engineer soybean for resistance to SCN.
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Affiliation(s)
- Jinrong Wan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Tri Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Yongqing Jiao
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
- Current address: Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, 430062, China.
| | - Trupti Joshi
- Department of Computer Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Hongxin Zhang
- Department of Computer Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Dong Xu
- Department of Computer Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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Hosseini P, Matthews BF. Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction. BMC PLANT BIOLOGY 2014; 14:300. [PMID: 25421055 PMCID: PMC4262236 DOI: 10.1186/s12870-014-0300-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/22/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant-parasitic nematodes (PPNs) are obligate parasites that feed on the roots of living host plants. Often, these nematodes can lay hundreds of eggs, each capable of surviving without a host for as long as 12 years. When it comes to wreaking havoc on agricultural yield, few nematodes can compare to the soybean cyst nematode (SCN). Quantifying soybean (Glycine max) transcription factor binding sites (TFBSs) during a late-stage SCN resistant and susceptible reaction can shed light onto the systematic interplay between host and pathogen, thereby elucidating underlying cis-regulatory mechanisms. RESULTS We sequenced the soybean root transcriptome at 6 and 8 days upon independent inoculation with a virulent and avirulent SCN population. Genes such as β-1,4 glucanase, chalcone synthase, superoxide dismutase and various heat shock proteins (HSPs) exhibited reaction-specific expression profiles. Several likely defense-response genes candidates were also identified which are believed to confer SCN resistance. To explore magnitude of TFBS representation during SCN pathogenesis, a multivariate statistical software identified 46 over-represented TFBSs which capture soybean regulatory dynamics across both reactions. CONCLUSIONS Our results reveal a set of soybean TFBSs which are over-represented solely throughout a resistant and susceptible SCN reaction. This set furthers our understanding of soybean cis-regulatory dynamics by providing reaction-specific levels of over-representation at 6 and 8 days after inoculation (dai) with SCN.
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Affiliation(s)
- Parsa Hosseini
- />School of Systems Biology, George Mason University, Manassas, VA USA
- />Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD USA
- />Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD USA
| | - Benjamin F Matthews
- />Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD USA
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Saraiva KDC, Fernandes de Melo D, Morais VD, Vasconcelos IM, Costa JH. Selection of suitable soybean EF1α genes as internal controls for real-time PCR analyses of tissues during plant development and under stress conditions. PLANT CELL REPORTS 2014; 33:1453-65. [PMID: 24820128 DOI: 10.1007/s00299-014-1628-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE The EF1α genes were stable in the large majority of soybean tissues during development and in specific tissues/conditions under stress. Quantitative real-time PCR (qPCR) analysis strongly depends on transcript normalization using stable reference genes. Reference genes are generally encoded by multigene families and are used in qPCR normalization; however, little effort has been made to verify the stability of different gene members within a family. Here, the expression stability of members of the soybean EF1α gene family (named EF1α 1a1, 1a2, 1b, 2a, 2b and 3) was evaluated in different tissues during plant development and stress exposure (SA and PEG). Four genes (UKN1, SKIP 16, EF1β and MTP) already established as stably expressed were also used in the comparative analysis. GeNorm analyses revealed different combinations of reference genes as stable in soybean tissues during development. The EF1α genes were the most stable in cotyledons (EF1α 3 and EF1α 1b), epicotyls (EF1α 1a2, EF1α 2b and EF1α 1a1), hypocotyls (EF1α 1a1 and EF1β), pods (EF1α 2a and EF1α 2b) and roots (EF1α 2a and UKN1) and less stable in tissues such as trifoliate and unifoliate leaves and germinating seeds. Under stress conditions, no suitable combination including only EF1α genes was found; however, some genes were relatively stable in leaves (EF1α 1a2) and roots (EF1α 1a1) treated with SA as well as in roots treated with PEG (EF1α 2b). EF1α 2a was the most stably expressed EF1α gene in all soybean tissues under stress. Taken together, our data provide guidelines for the selection of EF1α genes for use as reference genes in qPCR expression analyses during plant development and under stress conditions.
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Affiliation(s)
- Kátia D C Saraiva
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Campus do Pici, Cx., Postal 6033, Fortaleza, Ceará, 60451-970, Brazil
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Maldonado A, Youssef R, McDonald M, Brewer E, Beard H, Matthews B. Modification of the expression of two NPR1 suppressors, SNC1 and SNI1, in soybean confers partial resistance to the soybean cyst nematode, Heterodera glycines. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:714-726. [PMID: 32481026 DOI: 10.1071/fp13323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 01/23/2014] [Indexed: 06/11/2023]
Abstract
Systemic acquired resistance (SAR) is an enhanced defence response triggered when plants detect a pathogen. The response is extended to uninfected organs to protect against future attack. NPR1 is a nuclear leucine-rich repeat protein with a key role in SAR. It binds specifically to salicylic acid, and acts as a transcriptional coregulator of SAR activators and an inhibitor of transcriptional repressors. The proteins encoded by Suppressor of NPR1, Constitutive (SNC1) and Suppressor of NPR1, Inducible (SNI1) interact with NPR1 to regulate the expression of pathogenesis-related genes. The Arabidopsis thaliana (L.) Heynh. snc1 mutant exhibits a constitutive resistance response, but in the sni1 mutant, the SNI1 protein is rendered incapable of suppressing pathogen resistance genes. To study the influence of SNC1 and SNI1 on resistance to the soybean cyst nematode (Heterodera glycines), soybean (Glycine max (L.) Merr.) roots were separately transformed with four constructs designed to: (i) overexpress GmSNC1, the soybean orthologue of AtSNC1; (ii) overexpress AtSNI1; (iii) silence GmSNC1 and (iv) silence GmSNI1. A significant reduction of the female nematode population was observed in Treatments (i) and (iv). The expression of SAR marker genes was analysed in these treatments. The unusual pattern of expression of pathogen resistance genes shows there are differences in the effect resistance genes have on soybean and A. thaliana. Although NPR1 is involved in the cross-talk between the salicylic acid, jasmonic acid and ethylene pathways, understanding the nematode resistance mechanism in plants is still imprecise. These results provide further insights into the soybean defence response.
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Affiliation(s)
- Andrea Maldonado
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Reham Youssef
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Margaret McDonald
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Eric Brewer
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Hunter Beard
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Benjamin Matthews
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
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Ozalvo R, Cabrera J, Escobar C, Christensen SA, Borrego EJ, Kolomiets MV, Castresana C, Iberkleid I, Brown Horowitz S. Two closely related members of Arabidopsis 13-lipoxygenases (13-LOXs), LOX3 and LOX4, reveal distinct functions in response to plant-parasitic nematode infection. MOLECULAR PLANT PATHOLOGY 2014; 15:319-32. [PMID: 24286169 PMCID: PMC6638665 DOI: 10.1111/mpp.12094] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The responses of two closely related members of Arabidopsis 13-lipoxygenases (13-LOXs), LOX3 and LOX4, to infection by the sedentary nematodes root-knot nematode (Meloidogyne javanica) and cyst nematode (Heterodera schachtii) were analysed in transgenic Arabidopsis seedlings. The tissue localization of LOX3 and LOX4 gene expression using β-glucuronidase (GUS) reporter gene constructs showed local induction of LOX3 expression when second-stage juveniles reached the vascular bundle and during the early stages of plant-nematode interaction through gall and syncytia formation. Thin sections of nematode-infested knots indicated LOX3 expression in mature giant cells, and high expression in neighbouring cells and those surrounding the female body. LOX4 promoter was also activated by nematode infection, although the GUS signal weakened as infection and disease progressed. Homozygous insertion mutants lacking LOX3 were less susceptible than wild-type plants to root-knot nematode infection, as reflected by a decrease in female counts. Conversely, deficiency in LOX4 function led to a marked increase in females and egg mass number and in the female to male ratio of M. javanica and H. schachtii, respectively. The susceptibility of lox4 mutants was accompanied by increased expression of allene oxide synthase, allene oxide cyclase and ethylene-responsive transcription factor 4, and the accumulation of jasmonic acid, measured in the roots of lox4 mutants. This response was not found in lox3 mutants. Taken together, our results reveal that LOX4 and LOX3 interfere differentially with distinct metabolic and signalling pathways, and that LOX4 plays a major role in controlling plant defence against nematode infection.
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Affiliation(s)
- Rachel Ozalvo
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, 50250, Israel
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Koringa PG, Jakhesara SJ, Bhatt VD, Meshram CP, Patel AK, Fefar DT, Joshi CG. Comprehensive transcriptome profiling of squamous cell carcinoma of horn in Bos indicus. Vet Comp Oncol 2013; 14:122-36. [PMID: 24314272 DOI: 10.1111/vco.12079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/25/2013] [Accepted: 10/31/2013] [Indexed: 01/05/2023]
Abstract
Squamous cell carcinoma (SCC) of horn is frequently observed in Bos indicus affecting 1% of cattle population and accounting 83.34% of total tumours found. The transcriptome profile of horn cancer (HC) tissue and the matched normal (HN) tissue were analysed by RNA-seq using Roche 454 sequencing. A total of 1 504 900 reads comprising of 612 MB data were used to identify differentially expressed genes using CLC Genomic Workbench. These include up-regulation of KRT6A, KRT6B, KRT6C, KRT14, SFN, KRT84, PI3, COL17A1, ANLN, SERPINB5 and down-regulation of BOLA, SCGB1A1, CXCL17, KRT19, BPIFB1, NR4A1 and TFF3 in HC, which are involved in regulation of gene transcription, cell proliferation, apoptosis, cell survival and metabolic pathways. The qPCR analysis of several targets suggested concordance of gene expression profile with RNA-seq analysis. The present findings would provide basis for further screening of genes and identification of markers for early diagnosis and therapeutic intervention of HC.
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Affiliation(s)
- P G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - S J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - V D Bhatt
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - C P Meshram
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - A K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - D T Fefar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - C G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
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Morgante CV, Brasileiro ACM, Roberts PA, Guimaraes LA, Araujo ACG, Fonseca LN, Leal-Bertioli SCM, Bertioli DJ, Guimaraes PM. A survey of genes involved in Arachis stenosperma resistance to Meloidogyne arenaria race 1. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1298-1309. [PMID: 32481196 DOI: 10.1071/fp13096] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/11/2013] [Indexed: 06/11/2023]
Abstract
Root-knot nematodes constitute a constraint for important crops, including peanut (Arachis hypogaea L.). Resistance to Meloidogyne arenaria has been identified in the peanut wild relative Arachis stenosperma Krapov. & W. C. Greg., in which the induction of feeding sites by the nematode was inhibited by an early hypersensitive response (HR). Here, the transcription expression profiles of 19 genes selected from Arachis species were analysed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), during the early phases of an A. stenosperma-M. arenaria interaction. Sixteen genes were significantly differentially expressed in infected and non-infected roots, in at least one of the time points analysed: 3, 6, and 9 days after inoculation. These genes are involved in the HR and production of secondary metabolites related to pathogen defence. Seven genes encoding a resistance protein MG13, a helix-loop helix protein, an ubiquitin protein ligase, a patatin-like protein, a catalase, a DUF538 protein, and a resveratrol synthase, were differentially expressed in all time points analysed. Transcripts of two genes had their spatial and temporal distributions analysed by in situ hybridisation that validated qRT-PCR data. The identification of candidate resistance genes involved in wild peanut resistance to Meloidogyne can provide additional resources for peanut breeding and transgenic approaches.
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Affiliation(s)
| | - Ana C M Brasileiro
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - Philip A Roberts
- University of California, Nematology Department, 2251 Spieth Hall Riverside, CA 92521, USA
| | - Larissa A Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - Ana C G Araujo
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - Leonardo N Fonseca
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - Soraya C M Leal-Bertioli
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
| | - David J Bertioli
- Universidade de Brasília, Departamento de Genética e Morfologia, Campus Universitario Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Patricia M Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, PqEB - Av W5 Norte, CP 02372, 70770-917, Brasília, DF, Brazil
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Goto DB, Miyazawa H, Mar JC, Sato M. Not to be suppressed? Rethinking the host response at a root-parasite interface. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 213:9-17. [PMID: 24157203 DOI: 10.1016/j.plantsci.2013.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 05/11/2023]
Abstract
Root-knot nematodes are highly efficient plant parasites that establish permanent feeding sites within host roots. The initiation of this feeding site is critical for parasitic success and requires an interaction with multiple signaling pathways involved in plant development and environmental response. Resistance against root-knot nematodes is relatively rare amongst their broad host range and they remain a major threat to agriculture. The development of effective and sustainable control strategies depends on understanding how host signaling pathways are manipulated during invasion of susceptible hosts. It is generally understood that root-knot nematodes either suppress host defense signaling during infestation or are able to avoid detection altogether, explaining their profound success as parasites. However, when compared to the depth of knowledge from other well-studied pathogen interactions, the published data on host responses to root-knot nematode infestation do not yet provide convincing support for this hypothesis and alternative explanations also exist. It is equally possible that defense-like signaling responses are actually induced and required during the early stages of root-knot nematode infestation. We describe how defense-signaling is highly context-dependent and that caution is necessary when interpreting transcriptional responses in the absence of appropriate control data or stringent validation of gene annotation. Further hypothesis-driven studies on host defense-like responses are required to account for these limitations and advance our understanding of root-knot nematode parasitism of plants.
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Affiliation(s)
- Derek B Goto
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia.
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Kyndt T, Vieira P, Gheysen G, de Almeida-Engler J. Nematode feeding sites: unique organs in plant roots. PLANTA 2013; 238:807-18. [PMID: 23824525 DOI: 10.1007/s00425-013-1923-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/13/2013] [Indexed: 05/19/2023]
Abstract
Although generally unnoticed, nearly all crop plants have one or more species of nematodes that feed on their roots, frequently causing tremendous yield losses. The group of sedentary nematodes, which are among the most damaging plant-parasitic nematodes, cause the formation of special organs called nematode feeding sites (NFS) in the root tissue. In this review we discuss key metabolic and cellular changes correlated with NFS development, and similarities and discrepancies between different types of NFS are highlighted.
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Affiliation(s)
- Tina Kyndt
- Department Molecular Biotechnology, Ghent University (UGent), Coupure Links 653, 9000, Ghent, Belgium,
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Ji H, Gheysen G, Denil S, Lindsey K, Topping JF, Nahar K, Haegeman A, De Vos WH, Trooskens G, Van Criekinge W, De Meyer T, Kyndt T. Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3885-98. [PMID: 23881398 PMCID: PMC3745741 DOI: 10.1093/jxb/ert219] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
One of the reasons for the progressive yield decline observed in aerobic rice production is the rapid build-up of populations of the rice root knot nematode Meloidogyne graminicola. These nematodes induce specialized feeding cells inside root tissue, called giant cells. By injecting effectors in and sipping metabolites out of these cells, they reprogramme normal cell development and deprive the plant of its nutrients. In this research we have studied the transcriptome of giant cells in rice, after isolation of these cells by laser-capture microdissection. The expression profiles revealed a general induction of primary metabolism inside the giant cells. Although the roots were shielded from light induction, we detected a remarkable induction of genes involved in chloroplast biogenesis and tetrapyrrole synthesis. The presence of chloroplast-like structures inside these dark-grown cells was confirmed by confocal microscopy. On the other hand, genes involved in secondary metabolism and more specifically, the majority of defence-related genes were strongly suppressed in the giant cells. In addition, significant induction of transcripts involved in epigenetic processes was detected inside these cells 7 days after infection.
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Affiliation(s)
- Hongli Ji
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- * To whom correspondence should be addressed. E-mail:
| | - Simon Denil
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Keith Lindsey
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Jennifer F. Topping
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Kamrun Nahar
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Winnok H. De Vos
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- NXTGNT, Ghent University, Medical Research Building, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
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Bagnaresi P, Sala T, Irdani T, Scotto C, Lamontanara A, Beretta M, Rotino GL, Sestili S, Cattivelli L, Sabatini E. Solanum torvum responses to the root-knot nematode Meloidogyne incognita. BMC Genomics 2013; 14:540. [PMID: 23937585 PMCID: PMC3750854 DOI: 10.1186/1471-2164-14-540] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 08/05/2013] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Solanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseases as bacterial, fungal wilts and root-knot nematodes. The little information on Solanum torvum (hereafter Torvum) resistance mechanisms, is mostly attributable to the lack of genomic tools (e.g. dedicated microarray) as well as to the paucity of database information limiting high-throughput expression studies in Torvum. RESULTS As a first step towards transcriptome profiling of Torvum inoculated with the nematode M. incognita, we built a Torvum 3' transcript catalogue. One-quarter of a 454 full run resulted in 205,591 quality-filtered reads. De novo assembly yielded 24,922 contigs and 11,875 singletons. Similarity searches of the S. torvum transcript tags catalogue produced 12,344 annotations. A 30,0000 features custom combimatrix chip was then designed and microarray hybridizations were conducted for both control and 14 dpi (day post inoculation) with Meloidogyne incognita-infected roots samples resulting in 390 differentially expressed genes (DEG). We also tested the chip with samples from the phylogenetically-related nematode-susceptible eggplant species Solanum melongena. An in-silico validation strategy was developed based on assessment of sequence similarity among Torvum probes and eggplant expressed sequences available in public repositories. GO term enrichment analyses with the 390 Torvum DEG revealed enhancement of several processes as chitin catabolism and sesquiterpenoids biosynthesis, while no GO term enrichment was found with eggplant DEG.The genes identified from S. torvum catalogue, bearing high similarity to known nematode resistance genes, were further investigated in view of their potential role in the nematode resistance mechanism. CONCLUSIONS By combining 454 pyrosequencing and microarray technology we were able to conduct a cost-effective global transcriptome profiling in a non-model species. In addition, the development of an in silico validation strategy allowed to further extend the use of the custom chip to a related species and to assess by comparison the expression of selected genes without major concerns of artifacts. The expression profiling of S. torvum responses to nematode infection points to sesquiterpenoids and chitinases as major effectors of nematode resistance. The availability of the long sequence tags in S. torvum catalogue will allow precise identification of active nematocide/nematostatic compounds and associated enzymes posing the basis for exploitation of these resistance mechanisms in other species.
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Affiliation(s)
- Paolo Bagnaresi
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Genomics Research Centre, via S Protaso 302, I-29107, Fiorenzuola d’Arda (PC), Italy
| | - Tea Sala
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Unità di Ricerca per l’Orticoltura, Montanaso Lombardo (LO), Italy
| | - Tiziana Irdani
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di ricerca per l’agrobiologia e la pedologia, Cascine del Riccio, 50125, Firenze, Italy
| | - Cristina Scotto
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di ricerca per l’agrobiologia e la pedologia, Cascine del Riccio, 50125, Firenze, Italy
| | - Antonella Lamontanara
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Genomics Research Centre, via S Protaso 302, I-29107, Fiorenzuola d’Arda (PC), Italy
| | - Massimiliano Beretta
- UNIMORE, Scienze Agrarie e degli Alimenti, Università degli Studi di Modena e Reggio Emilia, via Giovanni Amendola 2, Padiglione Besta, Reggio Emilia 42122, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Unità di Ricerca per l’Orticoltura, Montanaso Lombardo (LO), Italy
| | - Sara Sestili
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Unità di Ricerca per l’Orticoltura, Monsampolo del Tronto, AP, Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Genomics Research Centre, via S Protaso 302, I-29107, Fiorenzuola d’Arda (PC), Italy
| | - Emidio Sabatini
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Unità di Ricerca per l’Orticoltura, Monsampolo del Tronto, AP, Italy
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Pham AT, McNally K, Abdel-Haleem H, Roger Boerma H, Li Z. Fine mapping and identification of candidate genes controlling the resistance to southern root-knot nematode in PI 96354. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1825-38. [PMID: 23568221 DOI: 10.1007/s00122-013-2095-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 03/26/2013] [Indexed: 05/24/2023]
Abstract
Meloidogyne incognita (Kofoid and White) Chitwood (Mi) is the most economically damaging species of the root-knot nematode to soybean and other crops in the southern USA. PI 96354 was identified to carry a high level of resistance to galling and Mi egg production. Two Quantitative Trait Locus (QTLs) were found to condition the resistance in PI 96354 including a major QTL and a minor QTL on chromosome 10 and chromosome 18, respectively. To fine map the major QTL on chromosome 10, F5:6 recombinant inbred lines from the cross between PI 96354 and susceptible genotype Bossier were genotyped with Simple Sequence Repeats (SSR) markers to identify recombinational events. Analysis of lines carrying key recombination events placed the Mi-resistant allele on chromosome 10 to a 235-kb region of the 'Williams 82' genome sequence with 30 annotated genes. Candidate gene analysis identified four genes with cell wall modification function that have several mutations in promoter, exon, 5', and 3'UTR regions. qPCR analysis showed significant difference in expression levels of these four genes in Bossier compared to PI 96354 in the presence of Mi. Thirty Mi-resistant soybean lines were found to have same SNPs in these 4 candidate genes as PI 96354 while 12 Mi-susceptible lines possess the 'Bossier' genotype. The mutant SNPs were used to develop KASP assays to detect the resistant allele on chromosome 10. The four candidate genes identified in this study can be used in further studies to investigate the role of cell wall modification genes in conferring Mi resistance in PI 96354.
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Affiliation(s)
- Anh-Tung Pham
- Center for Applied Genetic Technologies and Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA.
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Vieira P, Kyndt T, Gheysen G, Engler JDA. An insight into critical endocycle genes for plant-parasitic nematode feeding sites establishment. PLANT SIGNALING & BEHAVIOR 2013; 8:e24223. [PMID: 23518580 PMCID: PMC3907419 DOI: 10.4161/psb.24223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 05/19/2023]
Abstract
Root-knot and cyst nematodes are biotrophic parasites that invade the root apex of host plants and migrate toward the vascular cylinder where they cause the differentiation of root cells into galls (or root-knots) containing hypertrophied multinucleated giant-feeding cells, or syncytia, respectively. The precise molecular mechanisms that drive the formation of such unique nematode feeding sites are still far-off from being completely understood. The diverse gene expression changes occurring within the host cells suggest that both types of plant-parasitic nematodes modulate a variety of plant processes. Induction and repression of genes belonging to the host cell cycle control machinery have shown to be essential to drive the formation of such specialized nematode feeding cells. We demonstrate that nematodes usurp key components regulating the endocycle in their favor. This is illustrated by the involvement of anaphase-promoting complex (APC) genes (CCS52A and CCS52B), the endocycle repressor DP-E2F-like (E2F/DEL1) gene and the ROOT HAIRLESS 1 PROTEIN (RHL1), which is part of a multiprotein complex of the toposiomerase VI, in the proper formation of nematode feeding sites. Altering the expression of these genes in Arabidopsis plants by down- or overexpressing strategies strongly influences the extent of endoreduplication in both types of nematode feeding site leading to a disturbance of the nematode's life cycle and reproduction.
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Affiliation(s)
- Paulo Vieira
- Institut National de la Recherche Agronomique; Centre National de la Recherche Scientifique; Université de Nice-Sophia Antipolis; Sophia-Antipolis, France
| | - Tina Kyndt
- Department of Molecular Biotechnology; Ghent University; Ghent, Belgium
| | - Godelieve Gheysen
- Department of Molecular Biotechnology; Ghent University; Ghent, Belgium
| | - Janice de Almeida Engler
- Institut National de la Recherche Agronomique; Centre National de la Recherche Scientifique; Université de Nice-Sophia Antipolis; Sophia-Antipolis, France
- Correspondence to: Janice de Almeida Engler,
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Miranda VDJ, Coelho RR, Viana AAB, de Oliveira Neto OB, Carneiro RMDG, Rocha TL, Grossi de Sa MF, Fragoso RR. Validation of reference genes aiming accurate normalization of qPCR data in soybean upon nematode parasitism and insect attack. BMC Res Notes 2013; 6:196. [PMID: 23668315 PMCID: PMC3660166 DOI: 10.1186/1756-0500-6-196] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 05/04/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Soybean pathogens and pests reduce grain production worldwide. Biotic interaction cause extensive changes in plant gene expression profile and the data produced by functional genomics studies need validation, usually done by quantitative PCR. Nevertheless, this technique relies on accurate normalization which, in turn, depends upon the proper selection of stable reference genes for each experimental condition. To date, only a few studies were performed to validate reference genes in soybean subjected to biotic stress. Here, we report reference genes validation in soybean during root-knot nematode (Meloidogyne incognita) parasitism and velvetbean caterpillar (Anticarsia gemmatalis) attack. FINDINGS The expression stability of nine classical reference genes (GmCYP2, GmELF1A, GmELF1B, GmACT11, GmTUB, GmTUA5, GmG6PD, GmUBC2 and GmUBC4) was evaluated using twenty-four experimental samples including different organs, developmental stages, roots infected with M. incognita and leaves attacked by A. gemmatalis. Two different algorithms (geNorm and NormFinder) were used to determine expression stability. GmCYP2 and GmUBC4 are the most stable in different organs. Considering the developmental stages, GmELF1A and GmELF1B genes are the most stable. For spatial and temporal gene expression studies, normalization may be performed using GmUBC4, GmUBC2, GmCYP2 and GmACT11 as reference genes. Our data indicate that both GmELF1A and GmTUA5 are the most stable reference genes for data normalization obtained from soybean roots infected with M. incognita, and GmCYP2 and GmELF1A are the most stable in soybean leaves infested with A. gemmatalis. CONCLUSIONS Future expression studies using nematode infection and caterpilar infestation in soybean plant may utilize the reference gene sets reported here.
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Affiliation(s)
- Vívian de Jesus Miranda
- Department of Cell Biology Graduate Program in Molecular Biology, University of Brasília, Brasília, DF, Brazil
| | - Roberta Ramos Coelho
- Department of Cell Biology Graduate Program in Molecular Biology, University of Brasília, Brasília, DF, Brazil
- Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, PqEB Final Av. W/5 Norte, Brasília, DF, Brazil
| | - Antônio Américo Barbosa Viana
- Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, PqEB Final Av. W/5 Norte, Brasília, DF, Brazil
- Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Osmundo Brilhante de Oliveira Neto
- Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, PqEB Final Av. W/5 Norte, Brasília, DF, Brazil
- Faculdades Integradas do Planalto Central – Faciplac, Brasília, DF, Brazil
| | | | - Thales Lima Rocha
- Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, PqEB Final Av. W/5 Norte, Brasília, DF, Brazil
| | - Maria Fatima Grossi de Sa
- Department of Cell Biology Graduate Program in Molecular Biology, University of Brasília, Brasília, DF, Brazil
- Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, PqEB Final Av. W/5 Norte, Brasília, DF, Brazil
- Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Rodrigo Rocha Fragoso
- Department of Cell Biology Graduate Program in Molecular Biology, University of Brasília, Brasília, DF, Brazil
- Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil
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Beneventi MA, da Silva OB, de Sá MEL, Firmino AAP, de Amorim RMS, Albuquerque ÉVS, da Silva MCM, da Silva JP, Campos MDA, Lopes MJC, Togawa RC, Pappas GJ, Grossi–de–Sa MF. Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction. BMC Genomics 2013; 14:322. [PMID: 23663436 PMCID: PMC3701510 DOI: 10.1186/1471-2164-14-322] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/01/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Root-knot nematodes (RKN- Meloidogyne genus) present extensive challenges to soybean crop. The soybean line (PI 595099) is known to be resistant against specific strains and races of nematode species, thus its differential gene expression analysis can lead to a comprehensive gene expression profiling in the incompatible soybean-RKN interaction. Even though many disease resistance genes have been studied, little has been reported about phytohormone crosstalk on modulation of ROS signaling during soybean-RKN interaction. RESULTS Using 454 technology to explore the common aspects of resistance reaction during both parasitism and resistance phases it was verified that hormone, carbohydrate metabolism and stress related genes were consistently expressed at high levels in infected roots as compared to mock control. Most noteworthy genes include those encoding glycosyltransferases, peroxidases, auxin-responsive proteins and gibberellin-regulated genes. Our data analysis suggests the key role of glycosyltransferases, auxins and components of gibberellin signal transduction, biosynthesis and deactivation pathways in the resistance reaction and their participation in jasmonate signaling and redox homeostasis in mediating aspects of plant growth and responses to biotic stress. CONCLUSIONS Based on this study we suggest a reasonable model regarding to the complex mechanisms of crosstalk between plant hormones, mainly gibberellins and auxins, which can be crucial to modulate the levels of ROS in the resistance reaction to nematode invasion. The model also includes recent findings concerning to the participation of DELLA-like proteins and ROS signaling controlling plant immune or stress responses. Furthermore, this study provides a dataset of potential candidate genes involved in both nematode parasitism and resistance, which can be tested further for their role in this biological process using functional genomics approaches.
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Affiliation(s)
- Magda Aparecida Beneventi
- Federal University of Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF 70770-917, Brazil
| | | | - Maria Eugênia Lisei de Sá
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF 70770-917, Brazil
- Agricultural Research Company of Minas Gerais State, Uberaba, MG 38001-970, Brazil
| | - Alexandre Augusto Pereira Firmino
- Federal University of Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF 70770-917, Brazil
| | | | | | | | | | | | | | | | | | - Maria Fatima Grossi–de–Sa
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF 70770-917, Brazil
- Catholic University of Brasília, Brasília, DF 70790-160, Brazil
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Matthews BF, Beard H, MacDonald MH, Kabir S, Youssef RM, Hosseini P, Brewer E. Engineered resistance and hypersusceptibility through functional metabolic studies of 100 genes in soybean to its major pathogen, the soybean cyst nematode. PLANTA 2013; 237:1337-57. [PMID: 23389673 PMCID: PMC3634990 DOI: 10.1007/s00425-013-1840-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/06/2013] [Indexed: 05/11/2023]
Abstract
During pathogen attack, the host plant induces genes to ward off the pathogen while the pathogen often produces effector proteins to increase susceptibility of the host. Gene expression studies of syncytia formed in soybean root by soybean cyst nematode (Heterodera glycines) identified many genes altered in expression in resistant and susceptible roots. However, it is difficult to assess the role and impact of these genes on resistance using gene expression patterns alone. We selected 100 soybean genes from published microarray studies and individually overexpressed them in soybean roots to determine their impact on cyst nematode development. Nine genes reduced the number of mature females by more than 50 % when overexpressed, including genes encoding ascorbate peroxidase, β-1,4-endoglucanase, short chain dehydrogenase, lipase, DREPP membrane protein, calmodulin, and three proteins of unknown function. One gene encoding a serine hydroxymethyltransferase decreased the number of mature cyst nematode females by 45 % and is located at the Rhg4 locus. Four genes increased the number of mature cyst nematode females by more than 200 %, while thirteen others increased the number of mature cyst nematode females by more than 150 %. Our data support a role for auxin and ethylene in susceptibility of soybean to cyst nematodes. These studies highlight the contrasting gene sets induced by host and nematode during infection and provide new insights into the interactions between host and pathogen at the molecular level. Overexpression of some of these genes result in a greater decrease in the number of cysts formed than recognized soybean cyst nematode resistance loci.
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Affiliation(s)
- Benjamin F Matthews
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Ave, Bldg 006, Beltsville, MD 20705, USA.
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Lawo NC, Griesser M, Forneck A. Expression of putative expansin genes in phylloxera ( Daktulosphaira vitifoliae Fitch) induced root galls of Vitis spp. EUROPEAN JOURNAL OF PLANT PATHOLOGY 2013; 136:383-391. [PMID: 26074670 PMCID: PMC4461154 DOI: 10.1007/s10658-013-0173-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/14/2013] [Indexed: 05/29/2023]
Abstract
Grape phylloxera (Daktulosphaira vitifoliae Fitch) is a serious global pest in viticulture. The insects are sedentary feeders and require a gall to feed and reproduce. The insects induce their feeding site within the meristematic zone of the root tip, where they stay attached, feeding both intra- and intercellularly, and causing damage by reducing plant vigour. Several changes in cell structure and composition, including increased cell division and tissue swelling close to the feeding site, cause an organoid gall called a nodosity to develop. Because alpha expansin genes are involved in cell enlargement and cell wall loosening in many plant tissues it may be anticipated that they are also involved in nodosity formation. To identify expansin genes in Vitis vinifera cv. Pinot noir, we mined for orthologues genes in a comparative analysis. Eleven putative expansin genes were identified and shown to be present in the rootstock Teleki 5C (V. berlandieri Planch. x V. riparia Michx.) using specific PCR followed by DNA sequencing. Expression analysis of young and mature nodosities and uninfested root tips were conducted via quantitative real time PCR (qRT-PCR). Up-regulation was measured for three putative expansin genes (VvEXPA15, -A17 and partly -A20) or down-regulation for three other putative genes (VvEXPA7, -A12, -A20) in nodosities. The present study clearly shows the involvement of putative expansin genes in the phylloxera-root interaction.
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Affiliation(s)
- N. C. Lawo
- Division of Viticulture and Pomology, Department of Crop Sciences, University of Natural Resources and Life Sciences, Konrad-Lorenz Str. 24, 3430 Tulln, Austria
- Present Address: Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - M. Griesser
- Division of Viticulture and Pomology, Department of Crop Sciences, University of Natural Resources and Life Sciences, Konrad-Lorenz Str. 24, 3430 Tulln, Austria
| | - A. Forneck
- Division of Viticulture and Pomology, Department of Crop Sciences, University of Natural Resources and Life Sciences, Konrad-Lorenz Str. 24, 3430 Tulln, Austria
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de Sá MEL, Conceição Lopes MJ, de Araújo Campos M, Paiva LV, dos Santos RMA, Beneventi MA, Firmino AAP, de Sá MFG. Transcriptome analysis of resistant soybean roots infected by Meloidogyne javanica. Genet Mol Biol 2012; 35:272-82. [PMID: 22802712 PMCID: PMC3392879 DOI: 10.1590/s1415-47572012000200008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Soybean is an important crop for Brazilian agribusiness. However, many factors can limit its production, especially root-knot nematode infection. Studies on the mechanisms employed by the resistant soybean genotypes to prevent infection by these nematodes are of great interest for breeders. For these reasons, the aim of this work is to characterize the transcriptome of soybean line PI 595099-Meloidogyne javanica interaction through expression analysis. Two cDNA libraries were obtained using a pool of RNA from PI 595099 uninfected and M. javanica (J(2)) infected roots, collected at 6, 12, 24, 48, 96, 144 and 192 h after inoculation. Around 800 ESTs (Expressed Sequence Tags) were sequenced and clustered into 195 clusters. In silico subtraction analysis identified eleven differentially expressed genes encoding putative proteins sharing amino acid sequence similarities by using BlastX: metallothionein, SLAH4 (SLAC1 Homologue 4), SLAH1 (SLAC1 Homologue 1), zinc-finger proteins, AN1-type proteins, auxin-repressed proteins, thioredoxin and nuclear transport factor 2 (NTF-2). Other genes were also found exclusively in nematode stressed soybean roots, such as NAC domain-containing proteins, MADS-box proteins, SOC1 (suppressor of overexpression of constans 1) proteins, thioredoxin-like protein 4-Coumarate-CoA ligase and the transcription factor (TF) MYBZ2. Among the genes identified in non-stressed roots only were Ser/Thr protein kinases, wound-induced basic protein, ethylene-responsive family protein, metallothionein-like protein cysteine proteinase inhibitor (cystatin) and Putative Kunitz trypsin protease inhibitor. An understanding of the roles of these differentially expressed genes will provide insights into the resistance mechanisms and candidate genes involved in soybean-M. javanica interaction and contribute to more effective control of this pathogen.
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Affiliation(s)
- Maria Eugênia Lisei de Sá
- Empresa de Pesquisa Agropecuária de Minas Gerais, Uberaba, MG, Brazil
- Laboratório Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Marcus José Conceição Lopes
- Universidade Federal de Campina Grande, Centro de Educação e Saúde, Cuité, PB, Brazil
- Universidade Federal de Lavras, Lavras, MG, Brazil
| | - Magnólia de Araújo Campos
- Universidade Federal de Campina Grande, Centro de Educação e Saúde, Cuité, PB, Brazil
- Universidade Federal de Lavras, Lavras, MG, Brazil
| | | | | | - Magda Aparecida Beneventi
- Laboratório Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Alexandre Augusto Pereira Firmino
- Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Maria Fátima Grossi de Sá
- Laboratório Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
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Damiani I, Baldacci-Cresp F, Hopkins J, Andrio E, Balzergue S, Lecomte P, Puppo A, Abad P, Favery B, Hérouart D. Plant genes involved in harbouring symbiotic rhizobia or pathogenic nematodes. THE NEW PHYTOLOGIST 2012; 194:511-522. [PMID: 22360638 DOI: 10.1111/j.1469-8137.2011.04046.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The establishment and development of plant-microorganism interactions involve impressive transcriptomic reprogramming of target plant genes. The symbiont (Sinorhizobium meliloti) and the root knot-nematode pathogen (Meloidogyne incognita) induce the formation of new root organs, the nodule and the gall, respectively. Using laser-assisted microdissection, we specifically monitored, at the cell level, Medicago gene expression in nodule zone II cells, which are preparing to receive rhizobia, and in gall giant and surrounding cells, which play an essential role in nematode feeding and constitute the typical root swollen structure, respectively. We revealed an important reprogramming of hormone pathways and C1 metabolism in both interactions, which may play key roles in nodule and gall neoformation, rhizobia endocytosis and nematode feeding. Common functions targeted by rhizobia and nematodes were mainly down-regulated, whereas the specificity of the interaction appeared to involve up-regulated genes. Our transcriptomic results provide powerful datasets to unravel the mechanisms involved in the accommodation of rhizobia and root-knot nematodes. Moreover, they raise the question of host specificity and the evolution of plant infection mechanisms by a symbiont and a pathogen.
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Affiliation(s)
- Isabelle Damiani
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
| | - Fabien Baldacci-Cresp
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
| | - Julie Hopkins
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
| | - Emilie Andrio
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
| | - Sandrine Balzergue
- URGV UMR INRA 1165 - CNRS 8114 - UEVE, 2 rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Philippe Lecomte
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
| | - Alain Puppo
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
| | - Pierre Abad
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
| | - Bruno Favery
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
| | - Didier Hérouart
- INRA, UMR 1301, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
- Université de Nice Sophia-Antipolis, Interactions Biotiques et Santé Végétale, 400 route des Chappes, F-06903 Sophia Antipolis, France
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