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Khan A, Chen S, Fatima S, Ahamad L, Siddiqui MA. Biotechnological Tools to Elucidate the Mechanism of Plant and Nematode Interactions. PLANTS (BASEL, SWITZERLAND) 2023; 12:2387. [PMID: 37376010 DOI: 10.3390/plants12122387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
Plant-parasitic nematodes (PPNs) pose a threat to global food security in both the developed and developing worlds. PPNs cause crop losses worth a total of more than USD 150 billion worldwide. The sedentary root-knot nematodes (RKNs) also cause severe damage to various agricultural crops and establish compatible relationships with a broad range of host plants. This review aims to provide a broad overview of the strategies used to identify the morpho-physiological and molecular events that occur during RKN parasitism. It describes the most current developments in the transcriptomic, proteomic, and metabolomic strategies of nematodes, which are important for understanding compatible interactions of plants and nematodes, and several strategies for enhancing plant resistance against RKNs. We will highlight recent rapid advances in molecular strategies, such as gene-silencing technologies, RNA interference (RNAi), and small interfering RNA (siRNA) effector proteins, that are leading to considerable progress in understanding the mechanism of plant-nematode interactions. We also take into account genetic engineering strategies, such as targeted genome editing techniques, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system, and quantitative trait loci (QTL), to enhance the resistance of plants against nematodes.
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Affiliation(s)
- Arshad Khan
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Shaohua Chen
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Saba Fatima
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Lukman Ahamad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
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2
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Sahu PK, Jayalakshmi K, Tilgam J, Gupta A, Nagaraju Y, Kumar A, Hamid S, Singh HV, Minkina T, Rajput VD, Rajawat MVS. ROS generated from biotic stress: Effects on plants and alleviation by endophytic microbes. FRONTIERS IN PLANT SCIENCE 2022; 13:1042936. [PMID: 36352882 PMCID: PMC9638130 DOI: 10.3389/fpls.2022.1042936] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/03/2022] [Indexed: 05/26/2023]
Abstract
Aerobic living is thought to generate reactive oxygen species (ROS), which are an inevitable chemical component. They are produced exclusively in cellular compartments in aerobic metabolism involving significant energy transfer and are regarded as by-products. ROS have a significant role in plant response to pathogenic stress, but the pattern varies between necrotrophs and biotrophs. A fine-tuned systemic induction system is involved in ROS-mediated disease development in plants. In regulated concentrations, ROS act as a signaling molecule and activate different pathways to suppress the pathogens. However, an excess of these ROS is deleterious to the plant system. Along with altering cell structure, ROS cause a variety of physiological reactions in plants that lower plant yield. ROS also degrade proteins, enzymes, nucleic acids, and other substances. Plants have their own mechanisms to overcome excess ROS and maintain homeostasis. Microbes, especially endophytes, have been reported to maintain ROS homeostasis in both biotic and abiotic stresses by multiple mechanisms. Endophytes themselves produce antioxidant compounds and also induce host plant machinery to supplement ROS scavenging. The structured reviews on how endophytes play a role in ROS homeostasis under biotic stress were very meager, so an attempt was made to compile the recent developments in ROS homeostasis using endophytes. This review deals with ROS production, mechanisms involved in ROS signaling, host plant mechanisms in alleviating oxidative stress, and the roles of endophytes in maintaining ROS homeostasis under biotic stress.
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Affiliation(s)
- Pramod Kumar Sahu
- Indian Council of Agricultural Research (ICAR)-National Bureau of Agriculturally Important Microorganisms, Uttar Pradesh, India
| | - K. Jayalakshmi
- Plant Pathology, Indian Council of Agricultural Research (ICAR)-Directorate of Onion Garlic Research, Maharashtra, India
| | - Jyotsana Tilgam
- Indian Council of Agricultural Research (ICAR)-National Bureau of Agriculturally Important Microorganisms, Uttar Pradesh, India
| | - Amrita Gupta
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Yalavarthi Nagaraju
- Indian Council of Agricultural Research (ICAR)-National Bureau of Agriculturally Important Microorganisms, Uttar Pradesh, India
| | - Adarsh Kumar
- Indian Council of Agricultural Research (ICAR)-National Bureau of Agriculturally Important Microorganisms, Uttar Pradesh, India
| | | | - Harsh Vardhan Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Agriculturally Important Microorganisms, Uttar Pradesh, India
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Mahendra Vikram Singh Rajawat
- Indian Council of Agricultural Research (ICAR)-National Bureau of Agriculturally Important Microorganisms, Uttar Pradesh, India
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3
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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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5
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Berrios L, Rentsch JD. Linking Reactive Oxygen Species (ROS) to Abiotic and Biotic Feedbacks in Plant Microbiomes: The Dose Makes the Poison. Int J Mol Sci 2022; 23:ijms23084402. [PMID: 35457220 PMCID: PMC9030523 DOI: 10.3390/ijms23084402] [Citation(s) in RCA: 6] [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: 03/17/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
In nature, plants develop in complex, adaptive environments. Plants must therefore respond efficiently to environmental stressors to maintain homeostasis and enhance their fitness. Although many coordinated processes remain integral for achieving homeostasis and driving plant development, reactive oxygen species (ROS) function as critical, fast-acting orchestrators that link abiotic and biotic responses to plant homeostasis and development. In addition to the suite of enzymatic and non-enzymatic ROS processing pathways that plants possess, they also rely on their microbiota to buffer and maintain the oxidative window needed to balance anabolic and catabolic processes. Strong evidence has been communicated recently that links ROS regulation to the aggregated function(s) of commensal microbiota and plant-growth-promoting microbes. To date, many reports have put forth insightful syntheses that either detail ROS regulation across plant development (independent of plant microbiota) or examine abiotic–biotic feedbacks in plant microbiomes (independent of clear emphases on ROS regulation). Here we provide a novel synthesis that incorporates recent findings regarding ROS and plant development in the context of both microbiota regulation and plant-associated microbes. Specifically, we discuss various roles of ROS across plant development to strengthen the links between plant microbiome functioning and ROS regulation for both basic and applied research aims.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence:
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC 29502, USA;
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RNA-Seq of Cyst Nematode Infestation of Potato (Solanum tuberosum L.): A Comparative Transcriptome Analysis of Resistant and Susceptible Cultivars. PLANTS 2022; 11:plants11081008. [PMID: 35448735 PMCID: PMC9025382 DOI: 10.3390/plants11081008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 12/02/2022]
Abstract
Potato (Solanum tuberosum L.) is an important food crop worldwide, and potato cyst nematodes (PCNs) are among the most serious pests. The identification of disease resistance genes and molecular markers for PCN infestation can aid in crop improvement research programs against PCN infestation. In the present study, we used high-throughput RNA sequencing to investigate the comprehensive resistance mechanisms induced by PCN infestation in the resistant cultivar Kufri Swarna and the susceptible cultivar Kufri Jyoti. PCN infestation induced 791 differentially expressed genes in resistant cultivar Kufri Swarna, comprising 438 upregulated and 353 downregulated genes. In susceptible cultivar Kufri Jyoti, 2225 differentially expressed genes were induced, comprising 1247 upregulated and 978 downregulated genes. We identified several disease resistance genes (KIN) and transcription factors (WRKY, HMG, and MYB) that were upregulated in resistant Kufri Swarna. The differentially expressed genes from several enriched KEGG pathways, including MAPK signaling, contributed to the disease resistance in Kufri Swarna. Functional network analysis showed that several cell wall biogenesis genes were induced in Kufri Swarna in response to infestation. This is the first study to identify underlying resistance mechanisms against PCN and host interaction in Indian potato varieties.
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Goode K, Mitchum MG. Pattern-triggered immunity against root-knot nematode infection: A minireview. PHYSIOLOGIA PLANTARUM 2022; 174:e13680. [PMID: 35362104 PMCID: PMC9322311 DOI: 10.1111/ppl.13680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/15/2022] [Accepted: 03/28/2022] [Indexed: 05/24/2023]
Abstract
Pattern-triggered immunity (PTI) is the basal level of defense a plant has against pathogens. In the case of root-knot nematodes (RKN), PTI relies on the recognition of nematode-associated molecular patterns (NAMPs) for activation. Nematodes have successfully overcome PTI many times by evolving effector proteins to combat PTI responses. As a result, much study has focused on effector-triggered immunity (ETI). Here, we highlight recent advances in our understanding of PTI against RKN. A new interest in understanding PTI in response to RKN infection shows that understanding the basal defense responses RKN have overcome provides critical insight into what mechanisms the effectors have evolved to target in the host plant.
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Affiliation(s)
- Kelly Goode
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGeorgiaUSA
| | - Melissa G. Mitchum
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensGeorgiaUSA
- Department of Plant PathologyUniversity of GeorgiaAthensGeorgiaUSA
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8
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Dong J, Hudson ME. WI12 Rhg1 interacts with DELLAs and mediates soybean cyst nematode resistance through hormone pathways. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:283-296. [PMID: 34532941 PMCID: PMC8753364 DOI: 10.1111/pbi.13709] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/08/2021] [Accepted: 09/10/2021] [Indexed: 05/19/2023]
Abstract
The soybean cyst nematode (SCN) is one of the most important causes of soybean yield loss. The major source of genetic resistance to SCN is the Rhg1 repeat, a tandem copy number polymorphism of three genes. The roles of these genes are only partially understood. Moreover, nematode populations virulent on Rhg1-carrying soybeans are becoming more common, increasing the need to understand the most successful genetic resistance mechanism. Here, we show that a Rhg1-locus gene (Glyma.18G02270) encoding a wound-inducible protein (WI12Rhg1 ) is needed for SCN resistance. Furthermore, knockout of WI12Rhg1 reduces the expression of DELLA18, and the expression of WI12Rhg1 is itself induced by either JA, SA or GA. The content of the defence hormone SA is significantly lower whilst GA12 and GA53 are increased in WI12Rhg1 knockout roots compared with unedited hairy roots. We find that WI12Rhg1 directly interacts with DELLA18 (Glyma.18G040000) in yeast and plants and that double knockout of DELLA18 and its homeolog DELLA11 (Glyma.11G216500) significantly reduces SCN resistance and alters the root morphology. As DELLA proteins are implicated in hormone signalling, we explored the content of defence hormones (JA and SA) in DELLA knockout and unedited roots, finding reduced levels of JA and SA after the knockout of DELLA. Additionally, the treatment of DELLA-knockout roots with JA or SA rescues SCN resistance lost by the knockout. Meanwhile, the SCN resistance of unedited roots decreases after the treatment with GA, but increases with JA or SA. Our findings highlight the critical roles of WI12Rhg1 and DELLA proteins in SCN resistance through interconnection with hormone signalling.
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Affiliation(s)
- Jia Dong
- Department of Crop SciencesUniversity of Illinois Urbana‐ChampaignUrbanaILUSA
| | - Matthew E. Hudson
- Department of Crop SciencesUniversity of Illinois Urbana‐ChampaignUrbanaILUSA
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Khoei MA, Karimi M, Karamian R, Amini S, Soorni A. Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L. FRONTIERS IN PLANT SCIENCE 2021; 12:779597. [PMID: 34956274 PMCID: PMC8705754 DOI: 10.3389/fpls.2021.779597] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/08/2021] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) is a major plant protein source and oilseed crop. However, plant-parasitic nematodes (PPNs) affect its annual yield. In the current study, in order to better understand the regulation of defense mechanism against PPNs in soybean, we investigated the role of long non-coding RNAs (lncRNAs) in response to two nematode species, Heterodera glycines (SCN: soybean cyst nematode) and Rotylenchulus reniformis (reniform). To this end, two publicly available RNA-seq data sets (SCN data set and RAD: reniform-associated data set) were employed to discover the lncRNAome profile of soybean under SCN and reniform infection, respectively. Upon identification of unannotated transcripts in these data sets, a seven-step pipeline was utilized to sieve these transcripts, which ended up in 384 and 283 potential lncRNAs in SCN data set and RAD, respectively. These transcripts were then used to predict cis and trans nematode-related targets in soybean genome. Computational prediction of target genes function, some of which were also among differentially expressed genes, revealed the involvement of putative nematode-responsive genes as well as enrichment of multiple stress responses in both data sets. Finally, 15 and six lncRNAs were proposed to be involved in microRNA-mediated regulation of gene expression in soybean in response to SNC and reniform infection, respectively. Collectively, this study provides a novel insight into the signaling and regulatory network of soybean-pathogen interactions and opens a new window for further research.
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Affiliation(s)
| | | | - Roya Karamian
- Department of Biology, Faculty of Sciences, Bu-Ali Sina University, Hamedan, Iran
| | | | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Kamali S, Javadmanesh A, Stelinski LL, Kyndt T, Seifi A, Cheniany M, Zaki-Aghl M, Hosseini M, Heydarpour M, Asili J, Karimi J. Beneficial worm allies warn plants of parasite attack below-ground and reduce above-ground herbivore preference and performance. Mol Ecol 2021; 31:691-712. [PMID: 34706125 DOI: 10.1111/mec.16254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 11/29/2022]
Abstract
Antagonistic interactions among different functional guilds of nematodes have been recognized for quite some time, but the underlying explanatory mechanisms are unclear. We investigated responses of tomato (Solanum lycopersicum) to two functional guilds of nematodes-plant parasite (Meloidogyne javanica) and entomopathogens (Heterorhabditis bacteriophora, Steinernema feltiae below-ground, and S. carpocapsae)-as well as a leaf mining insect (Tuta absoluta) above-ground. Our results indicate that entomopathogenic nematodes (EPNs): (1) reduced root knot nematode (RKN) infestation below-ground, (2) reduced herbivore (T. absoluta) host preference and performance above-ground, and (3) induced overlapping plant defence responses by rapidly activating polyphenol oxidase and guaiacol peroxidase activity in roots, but simultaneously suppressing this activity in above-ground tissues. Concurrently, we investigated potential plant signalling mechanisms underlying these interactions using transcriptome analyses. We found that both entomopathogens and plant parasites triggered immune responses in plant roots with shared gene expression. Secondary metabolite transcripts induced in response to the two nematode functional guilds were generally overlapping and showed an analogous profile of regulation. Likewise, we show that EPNs modulate plant defence against RKN invasion, in part, by suppressing active expression of antioxidant enzymes. Inoculations of roots with EPN triggered an immune response in tomato via upregulated phenylpropanoid metabolism and synthesis of protease inhibitors in plant tissues, which may explain decreased egg laying and developmental performance exhibited by herbivores on EPN-inoculated plants. Furthermore, changes induced in the volatile organic compound-related transcriptome indicated that M. javanica and/or S. carpocapsae inoculation of plants triggered both direct and indirect defences. Our results support the hypothesis that plants "mistake" subterranean EPNs for parasites, and these otherwise beneficial worms activate a battery of plant defences associated with systemic acquired resistance and/or induced systemic resistance with concomitant antagonistic effects on temporally co-occurring subterranean plant pathogenic nematodes and terrestrial herbivores.
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Affiliation(s)
- Shokoofeh Kamali
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Lukasz L Stelinski
- Department of Entomology and Nematology, University of Florida Citrus Research and Education Center, Lake Alfred, Florida, USA
| | - Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Alireza Seifi
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Monireh Cheniany
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Zaki-Aghl
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mojtaba Hosseini
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahyar Heydarpour
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Javad Asili
- Department of Pharmacognosy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Javad Karimi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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11
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Godinho Mendes RA, Basso MF, Fernandes de Araújo J, Paes de Melo B, Lima RN, Ribeiro TP, da Silva Mattos V, Saliba Albuquerque EV, Grossi-de-Sa M, Dessaune Tameirao SN, da Rocha Fragoso R, Mattar da Silva MC, Vignols F, Fernandez D, Grossi-de-Sa MF. Minc00344 and Mj-NULG1a effectors interact with GmHub10 protein to promote the soybean parasitism by Meloidogyne incognita and M. javanica. Exp Parasitol 2021; 229:108153. [PMID: 34508716 DOI: 10.1016/j.exppara.2021.108153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 05/31/2021] [Accepted: 08/28/2021] [Indexed: 10/24/2022]
Abstract
Several economically important crops are susceptible to root-knot nematode (RKNs). Meloidogyne incognita and M. javanica are the two most reported species from the RKN complex, causing damage to several crops worldwide. The successful outcome of the Meloidogyne-plant interaction is associated with molecular factors secreted by the nematode to suppress the plant's immune response and promote nematode parasitism. In contrast, several plant factors are associated with defense against nematode infection. In this study, we identified and characterized the specific interaction of Minc00344 and Mj-NULG1a effectors with soybean GmHub10 (Glyma.19G008200) protein in vitro and in vivo. An Arabidopsis thaliana T-DNA mutant of AtHub10 (AT3G27960, an orthologous gene of GmHub10) showed higher susceptibility to M. incognita. Thus, since soybean and A. thaliana Hub10 proteins are involved in pollen tube growth and indirect activation of the defense response, our data suggest that effector-Hub10 interactions could be associated with an increase in plant susceptibility. These findings indicate the potential of these effector proteins to develop new biotechnological tools based on RNA interference and the overexpression of engineered Hub10 proteins for the efficient management of RKN in crops.
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Affiliation(s)
- Reneida Aparecida Godinho Mendes
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70297-400, Brazil; Federal University of Brasília, Brasília-DF, 70910-900, Brazil
| | - Marcos Fernando Basso
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70297-400, Brazil; National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brazil
| | | | - Bruno Paes de Melo
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70297-400, Brazil; Federal University of Viçosa, Viçosa-MG, 36570-900, Brazil
| | - Rayane Nunes Lima
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70297-400, Brazil
| | | | | | | | - Maira Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70297-400, Brazil; IRD, Cirad, Univ Montpellier, IPME, 911, Avenue Agropolis, 34394, Montpellier Cedex 5, France
| | | | | | - Maria Cristina Mattar da Silva
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70297-400, Brazil; National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brazil
| | - Florence Vignols
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/Université de Montpellier/SupAgro, Montpellier, France
| | - Diana Fernandez
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70297-400, Brazil; IRD, Cirad, Univ Montpellier, IPME, 911, Avenue Agropolis, 34394, Montpellier Cedex 5, France; National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brazil
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70297-400, Brazil; Catholic University of Brasília, Brasília-DF, 71966-700, Brazil; National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brazil.
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12
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Oosterbeek M, Lozano-Torres JL, Bakker J, Goverse A. Sedentary Plant-Parasitic Nematodes Alter Auxin Homeostasis via Multiple Strategies. FRONTIERS IN PLANT SCIENCE 2021; 12:668548. [PMID: 34122488 PMCID: PMC8193132 DOI: 10.3389/fpls.2021.668548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Sedentary endoparasites such as cyst and root-knot nematodes infect many important food crops and are major agro-economical pests worldwide. These plant-parasitic nematodes exploit endogenous molecular and physiological pathways in the roots of their host to establish unique feeding structures. These structures function as highly active transfer cells and metabolic sinks and are essential for the parasites' growth and reproduction. Plant hormones like indole-3-acetic acid (IAA) are a fundamental component in the formation of these feeding complexes. However, their underlying molecular and biochemical mechanisms are still elusive despite recent advances in the field. This review presents a comprehensive overview of known functions of various auxins in plant-parasitic nematode infection sites, based on a systematic analysis of current literature. We evaluate multiple aspects involved in auxin homeostasis in plants, including anabolism, catabolism, transport, and signalling. From these analyses, a picture emerges that plant-parasitic nematodes have evolved multiple strategies to manipulate auxin homeostasis to establish a successful parasitic relationship with their host. Additionally, there appears to be a potential role for auxins other than IAA in plant-parasitic nematode infections that might be of interest to be further elucidated.
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13
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Kofsky J, Zhang H, Song BH. Novel resistance strategies to soybean cyst nematode (SCN) in wild soybean. Sci Rep 2021; 11:7967. [PMID: 33846373 PMCID: PMC8041904 DOI: 10.1038/s41598-021-86793-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is the most damaging soybean pest worldwide and management of SCN remains challenging. The current SCN resistant soybean cultivars, mainly developed from the cultivated soybean gene pool, are losing resistance due to SCN race shifts. The domestication process and modern breeding practices of soybean cultivars often involve strong selection for desired agronomic traits, and thus, decreased genetic variation in modern cultivars, which consequently resulted in limited sources of SCN resistance. Wild soybean (Glycine soja) is the wild ancestor of cultivated soybean (Glycine max) and it's gene pool is indisputably more diverse than G. max. Our aim is to identify novel resistant genetic resources from wild soybean for the development of new SCN resistant cultivars. In this study, resistance response to HG type 2.5.7 (race 5) of SCN was investigated in a newly identified SCN resistant ecotype, NRS100. To understand the resistance mechanism in this ecotype, we compared RNA seq-based transcriptomes of NRS100 with two SCN-susceptible accessions of G. soja and G. max, as well as an extensively studied SCN resistant cultivar, Peking, under both control and nematode J2-treated conditions. The proposed mechanisms of resistance in NRS100 includes the suppression of the jasmonic acid (JA) signaling pathway in order to allow for salicylic acid (SA) signaling-activated resistance response and polyamine synthesis to promote structural integrity of root cell walls. Our study identifies a set of novel candidate genes and associated pathways involved in SCN resistance and the finding provides insight into the mechanism of SCN resistance in wild soybean, advancing the understanding of resistance and the use of wild soybean-sourced resistance for soybean improvement.
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Affiliation(s)
- Janice Kofsky
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Hengyou Zhang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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14
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Alekcevetch JC, de Lima Passianotto AL, Ferreira EGC, Dos Santos AB, da Silva DCG, Dias WP, Belzile F, Abdelnoor RV, Marcelino-Guimarães FC. Genome-wide association study for resistance to the Meloidogyne javanica causing root-knot nematode in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:777-792. [PMID: 33469696 DOI: 10.1007/s00122-020-03723-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/03/2020] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE A locus on chromosome 13, containing multiple TIR-NB-LRR genes and SNPs associated with M. javanica resistance, was identified using a combination of GWAS, resequencing, genetic mapping and expression profiling. Meloidogyne javanica, a root-knot nematode, is an important problem in soybean-growing areas, leading to severe yield losses. Some accessions have been identified carrying resistance loci to this nematode. In this study, a set of 317 soybean accessions was characterized for resistance to M. javanica. A genome-wide association study was performed using SNPs from genotyping-by-sequencing, and a region of 29.2 kb on chromosome 13 was identified. An analysis of haplotypes showed that SNPs were able to discriminate between susceptible and resistant accessions, with 25 accessions sharing the haplotype associated with resistance. Furthermore, five accessions that exhibited resistance without carrying this haplotype may carry different loci conferring resistance to M. javanica. We also conducted the screening of the SNPs in the USDA soybean germplasm, revealing that several soybean accessions previously reported as resistant to other nematodes also shared the resistance haplotype on chromosome 13. Two SNP-based TaqMan® assays were developed and validated in two panels of soybean cultivars and in biparental populations. In silico analysis of the region associated with resistance identified the occurrence of genes with structural similarity with classical major resistance genes (NBS-LRR genes). Specifically, several nonsynonymous SNPs were observed in Glyma.13g194800 and Glyma.13g194900. The expression profile of these candidate genes demonstrated that the two gene models were up-regulated in the resistance source PI 505,099 after nematode infection. Overall, the SNPs associated with resistance and the genes identified constitute an important tool for introgression of resistance to the root-knot nematode by marker-assisted selection in soybean breeding programs.
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Affiliation(s)
| | | | | | - Adriana Brombini Dos Santos
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass road, Warta County, PR, Brazil
| | - Danielle Cristina Gregório da Silva
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass road, Warta County, PR, Brazil
| | - Waldir Pereira Dias
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass road, Warta County, PR, Brazil
| | - François Belzile
- Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Ricardo Vilela Abdelnoor
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass road, Warta County, PR, Brazil
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15
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Hromadová D, Soukup A, Tylová E. Arabinogalactan Proteins in Plant Roots - An Update on Possible Functions. FRONTIERS IN PLANT SCIENCE 2021; 12:674010. [PMID: 34079573 PMCID: PMC8165308 DOI: 10.3389/fpls.2021.674010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/19/2021] [Indexed: 05/05/2023]
Abstract
Responsiveness to environmental conditions and developmental plasticity of root systems are crucial determinants of plant fitness. These processes are interconnected at a cellular level with cell wall properties and cell surface signaling, which involve arabinogalactan proteins (AGPs) as essential components. AGPs are cell-wall localized glycoproteins, often GPI-anchored, which participate in root functions at many levels. They are involved in cell expansion and differentiation, regulation of root growth, interactions with other organisms, and environmental response. Due to the complexity of cell wall functional and regulatory networks, and despite the large amount of experimental data, the exact molecular mechanisms of AGP-action are still largely unknown. This dynamically evolving field of root biology is summarized in the present review.
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16
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Mota APZ, Fernandez D, Arraes FBM, Petitot AS, de Melo BP, de Sa MEL, Grynberg P, Saraiva MAP, Guimaraes PM, Brasileiro ACM, Albuquerque EVS, Danchin EGJ, Grossi-de-Sa MF. Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics. Mol Genet Genomics 2020; 295:1063-1078. [PMID: 32333171 DOI: 10.1007/s00438-020-01677-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/04/2020] [Indexed: 01/11/2023]
Abstract
Root-knot nematodes (RKNs, genus Meloidogyne) affect a large number of crops causing severe yield losses worldwide, more specifically in tropical and sub-tropical regions. Several plant species display high resistance levels to Meloidogyne, but a general view of the plant immune molecular responses underlying resistance to RKNs is still lacking. Combining comparative genomics with differential gene expression analysis may allow the identification of widely conserved plant genes involved in RKN resistance. To identify genes that are evolutionary conserved across plant species, we used OrthoFinder to compared the predicted proteome of 22 plant species, including important crops, spanning 214 Myr of plant evolution. Overall, we identified 35,238 protein orthogroups, of which 6,132 were evolutionarily conserved and universal to all the 22 plant species (PLAnts Common Orthogroups-PLACO). To identify host genes responsive to RKN infection, we analyzed the RNA-seq transcriptome data from RKN-resistant genotypes of a peanut wild relative (Arachis stenosperma), coffee (Coffea arabica L.), soybean (Glycine max L.), and African rice (Oryza glaberrima Steud.) challenged by Meloidogyne spp. using EdgeR and DESeq tools, and we found 2,597 (O. glaberrima), 743 (C. arabica), 665 (A. stenosperma), and 653 (G. max) differentially expressed genes (DEGs) during the resistance response to the nematode. DEGs' classification into the previously characterized 35,238 protein orthogroups allowed identifying 17 orthogroups containing at least one DEG of each resistant Arachis, coffee, soybean, and rice genotype analyzed. Orthogroups contain 364 DEGs related to signaling, secondary metabolite production, cell wall-related functions, peptide transport, transcription regulation, and plant defense, thus revealing evolutionarily conserved RKN-responsive genes. Interestingly, the 17 DEGs-containing orthogroups (belonging to the PLACO) were also universal to the 22 plant species studied, suggesting that these core genes may be involved in ancestrally conserved immune responses triggered by RKN infection. The comparative genomic approach that we used here represents a promising predictive tool for the identification of other core plant defense-related genes of broad interest that are involved in different plant-pathogen interactions.
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Affiliation(s)
- Ana Paula Zotta Mota
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília-DF, Brazil
- Departamento de Biologia Celular e Molecular, UFRGS, Porto Alegre-RS, Brazil
| | - Diana Fernandez
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília-DF, Brazil
- IRD, Cirad, Univ Montpellier, IPME, 911, Montpellier, France
| | - Fabricio B M Arraes
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília-DF, Brazil
- Departamento de Biologia Celular e Molecular, UFRGS, Porto Alegre-RS, Brazil
| | | | - Bruno Paes de Melo
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília-DF, Brazil
- Departamento de Bioquímica e Biologia Molecular/Bioagro, UFV, Viçosa-MG, Brazil
| | - Maria E Lisei de Sa
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília-DF, Brazil
- Empresa de Pesquisa Agropecuária de Minas Gerais, EPAMIG, Uberaba-MG, Brazil
| | | | | | | | | | | | | | - Maria Fatima Grossi-de-Sa
- EMBRAPA Recursos Genéticos e Biotecnologia, Brasília-DF, Brazil.
- Universidade Católica de Brasília, Brasília-DF, Brazil.
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17
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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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18
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Seiml-Buchinger VV, Matveeva EM. Expression and Functional Characteristics of Genes in the Globodera rostochiensis Woll. Potato Cyst Nematode at Different Stages of Its Life Cycle. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019030142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Jones P, Garcia BJ, Furches A, Tuskan GA, Jacobson D. Plant Host-Associated Mechanisms for Microbial Selection. FRONTIERS IN PLANT SCIENCE 2019; 10:862. [PMID: 31333701 PMCID: PMC6618679 DOI: 10.3389/fpls.2019.00862] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/14/2019] [Indexed: 05/18/2023]
Abstract
Plants serve as host to numerous microorganisms. The members of these microbial communities interact among each other and with the plant, and there is increasing evidence to suggest that the microbial community may promote plant growth, improve drought tolerance, facilitate pathogen defense and even assist in environmental remediation. Therefore, it is important to better understand the mechanisms that influence the composition and structure of microbial communities, and what role the host may play in the recruitment and control of its microbiome. In particular, there is a growing body of research to suggest that plant defense systems not only provide a layer of protection against pathogens but may also actively manage the composition of the overall microbiome. In this review, we provide an overview of the current research into mechanisms employed by the plant host to select for and control its microbiome. We specifically review recent research that expands upon the role of keystone microbial species, phytohormones, and abiotic stress, and in how they relate to plant driven dynamic microbial structuring.
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Affiliation(s)
- Piet Jones
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Benjamin J. Garcia
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
| | - Anna Furches
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Gerald A. Tuskan
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
- *Correspondence: Daniel Jacobson
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20
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Bozbuga R, Lilley CJ, Knox JP, Urwin PE. Host-specific signatures of the cell wall changes induced by the plant parasitic nematode, Meloidogyne incognita. Sci Rep 2018; 8:17302. [PMID: 30470775 PMCID: PMC6251906 DOI: 10.1038/s41598-018-35529-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/29/2018] [Indexed: 11/10/2022] Open
Abstract
Root-knot nematodes (Meloidogyne spp.) are an important group of plant parasitic nematodes that induce within host plant roots unique feeding site structures, termed giant cells, which supply nutrient flow to the nematode. A comparative in situ analysis of cell wall polysaccharides in the giant cells of three host species (Arabidopsis, maize and aduki bean) infected with Meloidogyne incognita has been carried out. Features common to giant cell walls of all three species include the presence of high-esterified pectic homogalacturonan, xyloglucan and pectic arabinan. The species-specific presence of xylan and mixed-linkage glucan (MLG) epitopes in giant cell walls of maize reflected that host’s taxonomic group. The LM5 galactan and LM21 mannan epitopes were not detected in the giant cell walls of aduki bean but were detected in Arabidopsis and maize giant cell walls. The LM2 arabinogalactan-protein epitope was notable for its apparent global variations in root cell walls as a response to infection across the three host species. Additionally, a set of Arabidopsis cell wall mutants were used to determine any impacts of altered cell wall structures on M. incognita infection. Disruption of the arabinogalactan-protein 8 gene had the greatest impact and resulted in an increased infection rate.
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Affiliation(s)
- Refik Bozbuga
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, Leeds, United Kingdom
| | - Catherine J Lilley
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, Leeds, United Kingdom
| | - J Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, Leeds, United Kingdom
| | - Peter E Urwin
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, Leeds, United Kingdom.
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21
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Rauwane ME, Odeny DA, Millar I, Rey C, Rees J. The early transcriptome response of cassava (Manihot esculenta Crantz) to mealybug (Phenacoccus manihoti) feeding. PLoS One 2018; 13:e0202541. [PMID: 30133510 PMCID: PMC6105004 DOI: 10.1371/journal.pone.0202541] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/06/2018] [Indexed: 11/18/2022] Open
Abstract
The mealybug, Phenacoccus manihoti, is a leading pest of cassava (Manihot esculenta Crantz), damaging this crop globally. Although the biological control of this mealybug using natural predators has been established, resistance breeding remains an important means of control. Understanding plant responses to insect herbivory, by determining and identifying differentially expressed genes (DEGs), is a vital step towards the understanding of molecular mechanisms of defence responses in plants and the development of resistant cultivars by gene editing. Morphological and molecular analysis confirmed the mealybug identity as Phenacoccus manihoti (Matile-Ferrero). The transcriptome response of the green mite resistant cassava genotype AR23.1 was compared to P40/1 with no known resistance at 24 and 72 hours of mealybug infestation compared to non-infested mock. A total of 301 and 206 genes were differentially expressed at 24 and 72 of mealybug infestation for AR23.1 and P40/1 genotypes respectively, using a log2 fold change and P-value ≤ 0.05. Gene ontology functional classification revealed an enrichment of genes in the secondary metabolic process category in AR23.1 in comparison with P40/1, while genes in the regulation of molecular function, cellular component biogenesis and electron carrier categories were more significantly enriched in P40/1 than in AR23.1. Biological pathway analysis, based on KEGG, revealed a significant enrichment of plant-pathogen interaction and plant hormonal signal transduction pathways for a cohort of up-regulated and down-regulated DEGs in both genotypes. Defence-related genes such as 2-oxogluterate, gibberellin oxidase and terpene synthase proteins were only induced in genotype AR23.1 and not in P40/1, and subsequently validated by RT-qPCR. The study revealed a difference in response to mealybug infestation in the two genotypes studied, with AR23.1 showing a higher number of differentially expressed transcripts post mealybug infestation at 24 and 72 hours. Candidate defence-related genes that were overexpressed in the AR23.1 genotype post mealybug infestation will be useful in future functional studies towards the control of mealybugs.
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Affiliation(s)
- Molemi E. Rauwane
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
- University of the Witwatersrand, Johannesburg, South Africa
| | | | - Ian Millar
- Biosystematics Division, Plant Protection Research Institute, Agricultural Research Council, Queenswood, Pretoria, South Africa
| | - Chrissie Rey
- University of the Witwatersrand, Johannesburg, South Africa
| | - Jasper Rees
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
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Wang X, Cheng C, Zhang K, Tian Z, Xu J, Yang S, Lou Q, Li J, Chen JF. Comparative transcriptomics reveals suppressed expression of genes related to auxin and the cell cycle contributes to the resistance of cucumber against Meloidogyne incognita. BMC Genomics 2018; 19:583. [PMID: 30075750 PMCID: PMC6090858 DOI: 10.1186/s12864-018-4979-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/31/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infection, the exact regulation mechanism of M. incognita-resistance in cucumber remains elusive. Verification of an introgression line, 'IL10-1', with M. incognita-resistance provides the opportunity to unravel the resistance mechanism of cucumber against M. incognita. RESULTS In the present study, analyses of physiological responses and transcriptional events between IL10-1 (resistant line) and CC3 (susceptible line) were conducted after M. incognita infection. Physiological observations showed abnormal development of giant cells and M. incognita in IL10-1, which were the primary differences compared with CC3. Furthermore, Gene ontology (GO) analysis revealed that genes encoding cell wall proteins were up-regulated in IL10-1 and that the highly expressed lipid transfer protein gene (Csa6G410090) might be the principal regulator of this up-regulation. Simultaneously, analyses of gene expression profiles revealed more auxin-related genes were suppressed in IL10-1 than in those of CC3, which corresponded with the lower level of indole acetic acid (IAA) in the roots of IL10-1 than in those of CC3. Additionally, poor nucleus development as a clear indication of abnormal giant cells in IL10-1 was related to inhibition of the cell cycle. Of those genes related to the cell cycle, the F-box domain Skp2-like genes were down-regulated in IL10-1, whereas more of these genes were up-regulated in CC3. CONCLUSIONS All of these findings indicate that suppressed expression of genes related to auxin and the cell cycle and highly expressed cell wall proteins play important roles in the abnormal development of giant cells, which hinders the development of M. incognita, thereby causing resistance to M. incognita in IL10-1. Knowledge from this research will provide a useful foundation for developing effective strategies in M. incognita-resistance breeding.
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Affiliation(s)
- Xing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhen Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jian Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shuqiong Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jin-Feng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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Ali MA, Anjam MS, Nawaz MA, Lam HM, Chung G. Signal Transduction in Plant⁻Nematode Interactions. Int J Mol Sci 2018; 19:ijms19061648. [PMID: 29865232 PMCID: PMC6032140 DOI: 10.3390/ijms19061648] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/26/2018] [Accepted: 05/29/2018] [Indexed: 12/26/2022] Open
Abstract
To successfully invade and infect their host plants, plant parasitic nematodes (PPNs) need to evolve molecular mechanisms to overcome the defense responses from the plants. Nematode-associated molecular patterns (NAMPs), including ascarosides and certain proteins, while instrumental in enabling the infection, can be perceived by the host plants, which then initiate a signaling cascade leading to the induction of basal defense responses. To combat host resistance, some nematodes can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling and also modulate the hosts’ gene expression patterns to facilitate the establishment of nematode feeding sites (NFSs). In this review, we summarized all the known signaling pathways involved in plant–nematode interactions. Specifically, we placed particular focus on the effector proteins from PPNs that mimic the signaling of the defense responses in host plants. Furthermore, we gave an updated overview of the regulation by PPNs of different host defense pathways such as salicylic acid (SA)/jasmonic acid (JA), auxin, and cytokinin and reactive oxygen species (ROS) signaling to facilitate their parasitic successes in plants. This review will enhance the understanding of the molecular signaling pathways involved in both compatible and incompatible plant–nematode interactions.
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Affiliation(s)
- Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan.
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Muhammad Shahzad Anjam
- Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan 66000, Pakistan.
| | | | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
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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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Ling J, Mao Z, Zhai M, Zeng F, Yang Y, Xie B. Transcriptome profiling of Cucumis metuliferus infected by Meloidogyne incognita provides new insights into putative defense regulatory network in Cucurbitaceae. Sci Rep 2017; 7:3544. [PMID: 28615634 PMCID: PMC5471208 DOI: 10.1038/s41598-017-03563-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/02/2017] [Indexed: 12/27/2022] Open
Abstract
Root-knot nematodes (RKN) represent extensive challenges to Cucurbitaceae crops. However, Cucumis metuliferus (Cm) is known to be resistant to Meloidogyne incognita (Mi) infections. Thus, analysis of differentially expressed genes may lead to a comprehensive gene expression profiling of the incompatible Cm-Mi interaction. In this study, the time-course transcriptome of Cm against Mi infection was monitored using RNA-Seq. More than 170000 transcripts were examined in Cm roots, and 2430 genes were subsequently identified as differentially expressed in response to Mi infection. Based on function annotation and orthologs finding, the potential mechanism of transcriptional factor, cytoskeleton, pathogen-related genes and plant hormone were assessed at the transcription level. A comparison of gene expression levels between Mi-infected Cm and cucumber plants revealed that cytoskeleton-related genes are key regulators of Cm resistance to Mi. We herein discuss the dual nature of cytoskeleton-related genes in the susceptibility and resistance of plant hosts to Mi. Our observations provide novel insights into the responses of Cm to Mi at the transcriptome level. The data generated in this study may be useful for elucidating the mechanism underlying resistance to RKNs in cucurbitaceous crops.
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Affiliation(s)
- Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Mingjuan Zhai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Feng Zeng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China.
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Cavaiuolo M, Cocetta G, Spadafora ND, Müller CT, Rogers HJ, Ferrante A. Gene expression analysis of rocket salad under pre-harvest and postharvest stresses: A transcriptomic resource for Diplotaxis tenuifolia. PLoS One 2017; 12:e0178119. [PMID: 28558066 PMCID: PMC5448768 DOI: 10.1371/journal.pone.0178119] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/07/2017] [Indexed: 11/25/2022] Open
Abstract
Diplotaxis tenuifolia L. is of important economic value in the fresh-cut industry for its nutraceutical and sensorial properties. However, information on the molecular mechanisms conferring tolerance of harvested leaves to pre- and postharvest stresses during processing and shelf-life have never been investigated. Here, we provide the first transcriptomic resource of rocket by de novo RNA sequencing assembly, functional annotation and stress-induced expression analysis of 33874 transcripts. Transcriptomic changes in leaves subjected to commercially-relevant pre-harvest (salinity, heat and nitrogen starvation) and postharvest stresses (cold, dehydration, dark, wounding) known to affect quality and shelf-life were analysed 24h after stress treatment, a timing relevant to subsequent processing of salad leaves. Transcription factors and genes involved in plant growth regulator signaling, autophagy, senescence and glucosinolate metabolism were the most affected by the stresses. Hundreds of genes with unknown function but uniquely expressed under stress were identified, providing candidates to investigate stress responses in rocket. Dehydration and wounding had the greatest effect on the transcriptome and different stresses elicited changes in the expression of genes related to overlapping groups of hormones. These data will allow development of approaches targeted at improving stress tolerance, quality and shelf-life of rocket with direct applications in the fresh-cut industries.
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Affiliation(s)
- Marina Cavaiuolo
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Milano, Italy
| | - Giacomo Cocetta
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Milano, Italy
| | | | | | - Hilary J. Rogers
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Milano, Italy
- * E-mail:
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27
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Guimaraes LA, Mota APZ, Araujo ACG, de Alencar Figueiredo LF, Pereira BM, de Passos Saraiva MA, Silva RB, Danchin EGJ, Guimaraes PM, Brasileiro ACM. Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene. PLANT MOLECULAR BIOLOGY 2017; 94:79-96. [PMID: 28243841 PMCID: PMC5437183 DOI: 10.1007/s11103-017-0594-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/13/2017] [Indexed: 05/08/2023]
Abstract
Expansins are plant cell wall-loosening proteins involved in adaptive responses to environmental stimuli and various developmental processes. The first genome-wide analysis of the expansin superfamily in the Arachis genus identified 40 members in A. duranensis and 44 in A. ipaënsis, the wild progenitors of cultivated peanut (A. hypogaea). These expansins were further characterized regarding their subfamily classification, distribution along the genomes, duplication events, molecular structure, and phylogeny. A RNA-seq expression analysis in different Arachis species showed that the majority of these expansins are modulated in response to diverse stresses such as water deficit, root-knot nematode (RKN) infection, and UV exposure, with an expansin-like B gene (AraEXLB8) displaying a highly distinct stress-responsive expression profile. Further analysis of the AraEXLB8 coding sequences showed high conservation across the Arachis genotypes, with eight haplotypes identified. The modulation of AraEXLB8 expression in response to the aforementioned stresses was confirmed by qRT-PCR analysis in distinct Arachis genotypes, whilst in situ hybridization revealed transcripts in different root tissues according to the stress imposed. The overexpression of AraEXLB8 in soybean (Glycine max) composite plants remarkably decreased the number of galls in transformed hairy roots inoculated with RKN. This study improves the current understanding of the molecular evolution, divergence, and gene expression of expansins in Arachis, and provides molecular and functional insights into the role of expansin-like B, the less-studied plant expansin subfamily.
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Affiliation(s)
- Larissa Arrais Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | - Ana Paula Zotta Mota
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Claudia Guerra Araujo
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
| | | | - Bruna Medeiros Pereira
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | | | - Raquel Bispo Silva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRA, University of Nice Sophia Antipolis, CNRS, 06900, Sophia Antipolis, France
| | - Patricia Messenberg Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Final W5 Norte, Brasília, DF, CP 02372, Brazil
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Petitot AS, Kyndt T, Haidar R, Dereeper A, Collin M, de Almeida Engler J, Gheysen G, Fernandez D. Transcriptomic and histological responses of African rice (Oryza glaberrima) to Meloidogyne graminicola provide new insights into root-knot nematode resistance in monocots. ANNALS OF BOTANY 2017; 119:885-899. [PMID: 28334204 PMCID: PMC5604615 DOI: 10.1093/aob/mcw256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/24/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS The root-knot nematode Meloidogyne graminicola is responsible for production losses in rice ( Oryza sativa ) in Asia and Latin America. The accession TOG5681 of African rice, O. glaberrima , presents improved resistance to several biotic and abiotic factors, including nematodes. The aim of this study was to assess the cytological and molecular mechanisms underlying nematode resistance in this accession. METHODS Penetration and development in M. graminicola in TOG5681 and the susceptible O. sativa genotype 'Nipponbare' were compared by microscopic observation of infected roots and histological analysis of galls. In parallel, host molecular responses to M. graminicola were assessed by root transcriptome profiling at 2, 4 and 8 d post-infection (dpi). Specific treatments with hormone inhibitors were conducted in TOG5681 to assess the impact of the jasmonic acid and salicylic acid pathways on nematode penetration and reproduction. KEY RESULTS Penetration and development of M. graminicola juveniles were reduced in the resistant TOG5681 in comparison with the susceptible accession, with degeneration of giant cells observed in the resistant genotype from 15 dpi onwards. Transcriptome changes were observed as early as 2 dpi, with genes predicted to be involved in defence responses, phenylpropanoid and hormone pathways strongly induced in TOG5681, in contrast to 'Nipponbare'. No specific hormonal pathway could be identified as the major determinant of resistance in the rice-nematode incompatible interaction. Candidate genes proposed as involved in resistance to M. graminicola in TOG5681 were identified based on their expression pattern and quantitative trait locus (QTL) position, including chalcone synthase, isoflavone reductase, phenylalanine ammonia lyase, WRKY62 transcription factor, thionin, stripe rust resistance protein, thaumatins and ATPase3. CONCLUSIONS This study provides a novel set of candidate genes for O. glaberrima resistance to nematodes and highlights the rice- M. graminicola pathosystem as a model to study plant-nematode incompatible interactions.
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Affiliation(s)
- Anne-Sophie Petitot
- Institut de Recherche pour le Développement, UMR 186 IPME (IRD-UM2-Cirad) 911, avenue Agropolis, BP 64501 34394 Montpellier Cedex 5, France
| | - Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Rana Haidar
- Institut de Recherche pour le Développement, UMR 186 IPME (IRD-UM2-Cirad) 911, avenue Agropolis, BP 64501 34394 Montpellier Cedex 5, France
| | - Alexis Dereeper
- Institut de Recherche pour le Développement, UMR 186 IPME (IRD-UM2-Cirad) 911, avenue Agropolis, BP 64501 34394 Montpellier Cedex 5, France
| | - Myriam Collin
- UMR 232 DIADE (IRD-UM2-Cirad) 911, avenue Agropolis BP 64501, 34394 Montpellier Cedex 5, France
| | - Janice de Almeida Engler
- Institut National de la Recherche Agronomique, UMR IBSV INRA/CNRS/UNS, 400, Route de Chappes BP167, 06903 Sophia Antipolis Cedex, France
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Diana Fernandez
- Institut de Recherche pour le Développement, UMR 186 IPME (IRD-UM2-Cirad) 911, avenue Agropolis, BP 64501 34394 Montpellier Cedex 5, France
- For correspondence. E-mail
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Castañeda NEN, Alves GSC, Almeida RM, Amorim EP, Fortes Ferreira C, Togawa RC, Costa MMDC, Grynberg P, Santos JRP, Cares JE, Miller RNG. Gene expression analysis in Musa acuminata during compatible interactions with Meloidogyne incognita. ANNALS OF BOTANY 2017; 119:915-930. [PMID: 28130221 PMCID: PMC5604581 DOI: 10.1093/aob/mcw272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/01/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Endoparasitic root-knot nematodes (RKNs) ( Meloidogyne spp.) cause considerable losses in banana ( Musa spp.), with Meloidogyne incognita a predominant species in Cavendish sub-group bananas. This study investigates the root transcriptome in Musa acuminata genotypes 4297-06 (AA) and Cavendish Grande Naine (CAV; AAA) during early compatible interactions with M. incognita . METHODS Roots were analysed by brightfield light microscopy over a 35 d period to examine nematode penetration and morphological cell transformation. RNA samples were extracted 3, 7 and 10 days after inoculation (DAI) with nematode J2 juveniles, and cDNA libraries were sequenced using lllumina HiSeq technology. Sequences were mapped to the M. acuminata ssp. malaccensis var. Pahang genome sequence, differentially expressed genes (DEGs) identified and transcript representation determined by gene set enrichment and pathway mapping. KEY RESULTS Microscopic analysis revealed a life cycle of M. incognita completing in 24 d in CAV and 27 d in 4279-06. Comparable numbers of DEGs were up- and downregulated in each genotype, with potential involvement of many in early host defence responses involving reactive oxygen species and jasmonate/ethylene signalling. DEGs revealed concomitant auxin metabolism and cell wall modification processes likely to be involved in giant cell formation. Notable transcripts related to host defence included those coding for leucine-rich repeat receptor-like serine/threonine-protein kinases, peroxidases, thaumatin-like pathogenesis-related proteins, and DREB, ERF, MYB, NAC and WRKY transcription factors. Transcripts related to giant cell development included indole acetic acid-amido synthetase GH3.8 genes, involved in auxin metabolism, as well as genes encoding expansins and hydrolases, involved in cell wall modification. CONCLUSIONS Expression analysis in M. acuminata during compatible interactions with RKNs provides insights into genes modulated during infection and giant cell formation. Increased understanding of both defence responses to limit parasitism during compatible interactions and effector-targeted host genes in this complex interaction will facilitate the development of genetic improvement measures for RKNs.
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Affiliation(s)
| | | | - Rosane Mansan Almeida
- Universidade de Brasília, Instituto de Ciências Biológicas, CEP 70910-900, Brasilia, DF, Brazil
| | - Edson Perito Amorim
- Embrapa Cassava and Tropical Fruits, CEP 44380-000, Cruz das Almas, BA, Brazil
| | | | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70770-917, Brasília, DF, Brazil
| | - Marcos Mota Do Carmo Costa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70770-917, Brasília, DF, Brazil
| | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70770-917, Brasília, DF, Brazil
| | | | - Juvenil Enrique Cares
- Universidade de Brasília, Instituto de Ciências Biológicas, CEP 70910-900, Brasilia, DF, Brazil
| | - Robert Neil Gerard Miller
- Universidade de Brasília, Instituto de Ciências Biológicas, CEP 70910-900, Brasilia, DF, Brazil
- For correspondence. E-mail
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Ali MA, Azeem F, Li H, Bohlmann H. Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1699. [PMID: 29046680 PMCID: PMC5632807 DOI: 10.3389/fpls.2017.01699] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/15/2017] [Indexed: 05/03/2023]
Abstract
Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS) and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.
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Affiliation(s)
- Muhammad A. Ali
- Department of Plant Pathology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- *Correspondence: Muhammad A. Ali ;
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hongjie Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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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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Nath M, Bhatt D, Prasad R, Gill SS, Anjum NA, Tuteja N. Reactive Oxygen Species Generation-Scavenging and Signaling during Plant-Arbuscular Mycorrhizal and Piriformospora indica Interaction under Stress Condition. FRONTIERS IN PLANT SCIENCE 2016; 7:1574. [PMID: 27818671 PMCID: PMC5073151 DOI: 10.3389/fpls.2016.01574] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/06/2016] [Indexed: 05/18/2023]
Abstract
A defined balance between the generation and scavenging of reactive oxygen species (ROS) is essential to utilize ROS as an adaptive defense response of plants under biotic and abiotic stress conditions. Moreover, ROS are not only a major determinant of stress response but also act as signaling molecule that regulates various cellular processes including plant-microbe interaction. In particular, rhizosphere constitutes the biologically dynamic zone for plant-microbe interactions which forms a mutual link leading to reciprocal signaling in both the partners. Among plant-microbe interactions, symbiotic associations of arbuscular mycorrhizal fungi (AMF) and arbuscular mycorrhizal-like fungus especially Piriformospora indica with plants are well known to improve plant growth by alleviating the stress-impacts and consequently enhance the plant fitness. AMF and P. indica colonization mainly enhances ROS-metabolism, maintains ROS-homeostasis, and thereby averts higher ROS-level accrued inhibition in plant cellular processes and plant growth and survival under stressful environments. This article summarizes the major outcomes of the recent reports on the ROS-generation, scavenging and signaling in biotic-abiotic stressed plants with AMF and P. indica colonization. Overall, a detailed exploration of ROS-signature kinetics during plant-AMF/P. indica interaction can help in designing innovative strategies for improving plant health and productivity under stress conditions.
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Affiliation(s)
- Manoj Nath
- Amity Institute of Microbial Technology, Amity University Uttar PradeshNoida, India
- *Correspondence: Manoj Nath, Narendra Tuteja,
| | - Deepesh Bhatt
- Department of Biotechnology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Veer Narmad South Gujarat UniversitySurat, India
| | - Ram Prasad
- Amity Institute of Microbial Technology, Amity University Uttar PradeshNoida, India
| | - Sarvajeet S. Gill
- Stress Physiology and Molecular Biology Laboratory, Centre for Biotechnology, Maharshi Dayanand UniversityRohtak, India
| | - Naser A. Anjum
- Centre for Environmental and Marine Studies and Department of Chemistry, University of AveiroAveiro, Portugal
| | - Narendra Tuteja
- Amity Institute of Microbial Technology, Amity University Uttar PradeshNoida, India
- *Correspondence: Manoj Nath, Narendra Tuteja,
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Schouteden N, De Waele D, Panis B, Vos CM. Arbuscular Mycorrhizal Fungi for the Biocontrol of Plant-Parasitic Nematodes: A Review of the Mechanisms Involved. Front Microbiol 2015; 6:1280. [PMID: 26635750 PMCID: PMC4646980 DOI: 10.3389/fmicb.2015.01280] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/31/2015] [Indexed: 11/26/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate root symbionts that can protect their host plant against biotic stress factors such as plant-parasitic nematode (PPN) infection. PPN consist of a wide range of species with different life styles that can cause major damage in many important crops worldwide. Various mechanisms have been proposed to play a role in the biocontrol effect of AMF against PPN. This review presents an overview of the different mechanisms that have been proposed, and discusses into more detail the plausibility of their involvement in the biocontrol against PPN specifically. The proposed mechanisms include enhanced plant tolerance, direct competition for nutrients and space, induced systemic resistance (ISR) and altered rhizosphere interactions. Recent studies have emphasized the importance of ISR in biocontrol and are increasingly placing rhizosphere effects on the foreground as well, both of which will be the focal point of this review. Though AMF are not yet widely used in conventional agriculture, recent data help to develop a better insight into the modes of action, which will eventually lead toward future field applications of AMF against PPN. The scientific community has entered an exciting era that provides the tools to actually unravel the underlying molecular mechanisms, making this a timely opportunity for a review of our current knowledge and the challenges ahead.
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Affiliation(s)
- Nele Schouteden
- Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Dirk De Waele
- Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Heverlee, Belgium
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Bart Panis
- Bioversity International, Heverlee, Belgium
| | - Christine M. Vos
- Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, Belgium
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Gent, Belgium
- Commonwealth Scientific and Industrial Research Organisation Agriculture, Queensland Bioscience Precinct, Brisbane, QLD, Australia
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Kong LA, Wu DQ, Huang WK, Peng H, Wang GF, Cui JK, Liu SM, Li ZG, Yang J, Peng DL. Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis. BMC Genomics 2015; 16:801. [PMID: 26475271 PMCID: PMC4609135 DOI: 10.1186/s12864-015-2037-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background Cereal cyst nematode Heterodera avenae, an important soil-borne pathogen in wheat, causes numerous annual yield losses worldwide, and use of resistant cultivars is the best strategy for control. However, target genes are not readily available for breeding resistant cultivars. Therefore, comparative transcriptomic analyses were performed to identify more applicable resistance genes for cultivar breeding. Methods The developing nematodes within roots were stained with acid fuchsin solution. Transcriptome assemblies and redundancy filteration were obtained by Trinity, TGI Clustering Tool and BLASTN, respectively. Gene Ontology annotation was yielded by Blast2GO program, and metabolic pathways of transcripts were analyzed by Path_finder. The ROS levels were determined by luminol-chemiluminescence assay. The transcriptional gene expression profiles were obtained by quantitative RT-PCR. Results The RNA-sequencing was performed using an incompatible wheat cultivar VP1620 and a compatible control cultivar WEN19 infected with H. avenae at 24 h, 3 d and 8 d. Infection assays showed that VP1620 failed to block penetration of H. avenae but disturbed the transition of developmental stages, leading to a significant reduction in cyst formation. Two types of expression profiles were established to predict candidate resistance genes after developing a novel strategy to generate clean RNA-seq data by removing the transcripts of H. avenae within the raw data before assembly. Using the uncoordinated expression profiles with transcript abundance as a standard, 424 candidate resistance genes were identified, including 302 overlapping genes and 122 VP1620-specific genes. Genes with similar expression patterns were further classified according to the scales of changed transcript abundances, and 182 genes were rescued as supplementary candidate resistance genes. Functional characterizations revealed that diverse defense-related pathways were responsible for wheat resistance against H. avenae. Moreover, phospholipase was involved in many defense-related pathways and localized in the connection position. Furthermore, strong bursts of reactive oxygen species (ROS) within VP1620 roots infected with H. avenae were induced at 24 h and 3 d, and eight ROS-producing genes were significantly upregulated, including three class III peroxidase and five lipoxygenase genes. Conclusions Large-scale identification of wheat resistance genes were processed by comparative transcriptomic analysis. Functional characterization showed that phospholipases associated with ROS production played vital roles in early defense responses to H. avenae via involvement in diverse defense-related pathways as a hub switch. This study is the first to investigate the early defense responses of wheat against H. avenae, not only provides applicable candidate resistance genes for breeding novel wheat cultivars, but also enables a better understanding of the defense mechanisms of wheat against H. avenae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2037-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ling-An Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Du-Qing Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Wen-Kun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Gao-Feng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Jiang-Kuan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Shi-Ming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Zhi-Gang Li
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, 100193, China.
| | - Jun Yang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, 100193, China.
| | - De-Liang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Villeth GRC, Carmo LST, Silva LP, Fontes W, Grynberg P, Saraiva M, Brasileiro ACM, Carneiro RMD, Oliveira JTA, Grossi-de-Sá MF, Mehta A. Cowpea-Meloidogyne incognita
interaction: Root proteomic analysis during early stages of nematode infection. Proteomics 2015; 15:1746-59. [DOI: 10.1002/pmic.201400561] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/13/2015] [Accepted: 02/26/2015] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia; Brasília DF Brazil
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Brasileiro ACM, Morgante CV, Araujo ACG, Leal-Bertioli SCM, Silva AK, Martins ACQ, Vinson CC, Santos CMR, Bonfim O, Togawa RC, Saraiva MAP, Bertioli DJ, Guimaraes PM. Transcriptome Profiling of Wild Arachis from Water-Limited Environments Uncovers Drought Tolerance Candidate Genes. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:1876-1892. [PMID: 26752807 PMCID: PMC4695501 DOI: 10.1007/s11105-015-0882-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Peanut (Arachis hypogaea L.) is an important legume cultivated mostly in drought-prone areas where its productivity can be limited by water scarcity. The development of more drought-tolerant varieties is, therefore, a priority for peanut breeding programs worldwide. In contrast to cultivated peanut, wild relatives have a broader genetic diversity and constitute a rich source of resistance/tolerance alleles to biotic and abiotic stresses. The present study takes advantage of this diversity to identify drought-responsive genes by analyzing the expression profile of two wild species, Arachis duranensis and Arachis magna (AA and BB genomes, respectively), in response to progressive water deficit in soil. Data analysis from leaves and roots of A. duranensis (454 sequencing) and A. magna (suppression subtractive hybridization (SSH)) stressed and control complementary DNA (cDNA) libraries revealed several differentially expressed genes in silico, and 44 of them were selected for further validation by quantitative RT-PCR (qRT-PCR). This allowed the identification of drought-responsive candidate genes, such as Expansin, Nitrilase, NAC, and bZIP transcription factors, displaying significant levels of differential expression during stress imposition in both species. This is the first report on identification of differentially expressed genes under drought stress and recovery in wild Arachis species. The generated transcriptome data, besides being a valuable resource for gene discovery, will allow the characterization of new alleles and development of molecular markers associated with drought responses in peanut. These together constitute important tools for the peanut breeding program and also contribute to a better comprehension of gene modulation in response to water deficit and rehydration.
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Affiliation(s)
- Ana C. M. Brasileiro
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Carolina V. Morgante
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
- />Embrapa Semiárido, Petrolina, PE Brazil
| | - Ana C. G. Araujo
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Soraya C. M. Leal-Bertioli
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Amanda K. Silva
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Andressa C. Q. Martins
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Christina C. Vinson
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Candice M. R. Santos
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
- />CONAB, Brasília, DF Brazil
| | - Orzenil Bonfim
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Roberto C. Togawa
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | - Mario A. P. Saraiva
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
| | | | - Patricia M. Guimaraes
- />Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, 02372 Final W5 Norte, Brasília, DF Brazil
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Postnikova OA, Hult M, Shao J, Skantar A, Nemchinov LG. Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita. PLoS One 2015; 10:e0118269. [PMID: 25710378 PMCID: PMC4339843 DOI: 10.1371/journal.pone.0118269] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/12/2015] [Indexed: 12/02/2022] Open
Abstract
Nematodes are one of the major limiting factors in alfalfa production. Root-knot nematodes (RKN, Meloidogyne spp.) are widely distributed and economically important sedentary endoparasites of agricultural crops and they may inflict significant damage to alfalfa fields. As of today, no studies have been published on global gene expression profiling in alfalfa infected with RKN or any other plant parasitic nematode. Very little information is available about molecular mechanisms that contribute to pathogenesis and defense responses in alfalfa against these pests and specifically against RKN. In this work, we performed root transcriptome analysis of resistant (cv. Moapa 69) and susceptible (cv. Lahontan) alfalfa cultivars infected with RKN Meloidogyne incognita, widespread root-knot nematode species and a major pest worldwide. A total of 1,701,622,580 pair-end reads were generated on an Illumina Hi-Seq 2000 platform from the roots of both cultivars and assembled into 45,595 and 47,590 transcripts in cvs Moapa 69 and Lahontan, respectively. Bioinformatic analysis revealed a number of common and unique genes that were differentially expressed in susceptible and resistant lines as a result of nematode infection. Although the susceptible cultivar showed a more pronounced defense response to the infection, feeding sites were successfully established in its roots. Characteristically, basal gene expression levels under normal conditions differed between the two cultivars as well, which may confer advantage to one of the genotypes toward resistance to nematodes. Differentially expressed genes were subsequently assigned to known Gene Ontology categories to predict their functional roles and associated biological processes. Real-time PCR validated expression changes in genes arbitrarily selected for experimental confirmation. Candidate genes that contribute to protection against M. incognita in alfalfa were proposed and alfalfa-nematode interactions with respect to resistance are discussed.
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Affiliation(s)
- Olga A. Postnikova
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Maria Hult
- USDA-ARS, Beltsville Agricultural Research Center, Nematology Laboratory, Beltsville, Maryland, United States of America
| | - Jonathan Shao
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Andrea Skantar
- USDA-ARS, Beltsville Agricultural Research Center, Nematology Laboratory, Beltsville, Maryland, United States of America
| | - Lev G. Nemchinov
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
- * E-mail:
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Davies LJ, Brown CR, Elling AA. Calcium is involved in the R Mc1 (blb)-mediated hypersensitive response against Meloidogyne chitwoodi in potato. PLANT CELL REPORTS 2015; 34:167-77. [PMID: 25315813 DOI: 10.1007/s00299-014-1697-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/29/2014] [Accepted: 10/07/2014] [Indexed: 05/08/2023]
Abstract
Functional characterization of the Columbia root-knot nematode resistance gene R Mc1 ( blb ) in potato revealed the R gene-mediated resistance is dependent on a hypersensitive response and involves calcium. The resistance (R) gene R Mc1(blb) confers resistance against the plant-parasitic nematode, Meloidogyne chitwoodi. Avirulent and virulent nematodes were used to functionally characterize the R Mc1(blb)-mediated resistance mechanism in potato (Solanum tuberosum). Histological observations indicated a hypersensitive response (HR) occurred during avirulent nematode infection. This was confirmed by quantifying reactive oxygen species activity in response to avirulent and virulent M. chitwoodi. To gain an insight into the signal transduction pathways mediating the R Mc1(blb)-induced HR, chemical inhibitors were utilized. Inhibiting Ca(2+) channels caused a significant reduction in electrolyte leakage, an indicator of cell death. Labeling with a Ca(2+)-sensitive dye revealed high Ca(2+) levels in the root cells surrounding avirulent nematodes. Furthermore, the calcium-dependent protein kinase (CDPK), StCDPK4 had a higher transcript level in R Mc1(blb) potato roots infected with avirulent nematodes in comparison to roots infected with virulent M. chitwoodi. The results of this study indicate Ca(2+) plays a role in the R Mc1(blb)-mediated resistance against M. chitwoodi in potato.
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Affiliation(s)
- Laura J Davies
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
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Okada K, Abe H, Arimura GI. Jasmonates induce both defense responses and communication in monocotyledonous and dicotyledonous plants. PLANT & CELL PHYSIOLOGY 2015; 56:16-27. [PMID: 25378688 DOI: 10.1093/pcp/pcu158] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Jasmonic acid (JA) and its derivatives (jasmonates, JAs) are phytohormones with essential roles in plant defense against pathogenesis and herbivorous arthropods. Both the up- and down-regulation of defense responses are dependent on signaling pathways mediated by JAs as well as other stress hormones (e.g. salicylic acid), generally those involving the transcriptional and post-transcriptional regulation of transcription factors via protein modification and epigenetic regulation. In addition to the typical model plant Arabidopsis (a dicotyledon), advances in genetics research have made rice a model monocot in which innovative pest control traits can be introduced and whose JA signaling pathway can be studied. In this review, we introduce the dynamic functions of JAs in plant defense strategy using defensive substances (e.g. indole alkaloids and terpenoid phytoalexins) and airborne signals (e.g. green leaf volatiles and volatile terpenes) in response to biotrophic and necrotrophic pathogens as well as above-ground and below-ground herbivores. We then discuss the important issue of how the mutualism of herbivorous arthropods with viruses or bacteria can cause cross-talk between JA and other phytohormones to counter the defense systems.
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Affiliation(s)
- Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Hiroshi Abe
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, 305-0074 Japan
| | - Gen-ichiro Arimura
- Department of Biological Science & Technology, Faculty of Industrial Science & Technology, Tokyo University of Science, Tokyo, 125-8585 Japan
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Kyndt T, Fernandez D, Gheysen G. Plant-parasitic nematode infections in rice: molecular and cellular insights. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:135-53. [PMID: 24906129 DOI: 10.1146/annurev-phyto-102313-050111] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Being one of the major staple foods in the world, and an interesting model monocot plant, rice (Oryza sativa L.) has recently received attention from molecular nematologists studying the cellular and molecular aspects of the interaction between this crop and plant-parasitic nematodes. In this review, we highlight recent advances in this field, with a focus on the best-studied root-knot nematodes. Histological studies have revealed the cellular changes inside root-knot nematode-induced feeding sites, both in the compatible interaction with Oryza sativa and the incompatible interaction with the related species Oryza glaberrima. After comparing the published data from transcriptome analyses, mutant studies, and exogenous hormone applications, we provide a comprehensive model showing the role and interaction of plant hormone pathways in defense of this monocot crop against root nematodes, where jasmonate seems to play a key role. Finally, recent evidence indicates that effectors secreted from rice-infecting nematodes can suppress plant defense.
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Affiliation(s)
- Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium; ,
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