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Molina A, Jordá L, Torres MÁ, Martín-Dacal M, Berlanga DJ, Fernández-Calvo P, Gómez-Rubio E, Martín-Santamaría S. Plant cell wall-mediated disease resistance: Current understanding and future perspectives. MOLECULAR PLANT 2024; 17:699-724. [PMID: 38594902 DOI: 10.1016/j.molp.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024]
Abstract
Beyond their function as structural barriers, plant cell walls are essential elements for the adaptation of plants to environmental conditions. Cell walls are dynamic structures whose composition and integrity can be altered in response to environmental challenges and developmental cues. These wall changes are perceived by plant sensors/receptors to trigger adaptative responses during development and upon stress perception. Plant cell wall damage caused by pathogen infection, wounding, or other stresses leads to the release of wall molecules, such as carbohydrates (glycans), that function as damage-associated molecular patterns (DAMPs). DAMPs are perceived by the extracellular ectodomains (ECDs) of pattern recognition receptors (PRRs) to activate pattern-triggered immunity (PTI) and disease resistance. Similarly, glycans released from the walls and extracellular layers of microorganisms interacting with plants are recognized as microbe-associated molecular patterns (MAMPs) by specific ECD-PRRs triggering PTI responses. The number of oligosaccharides DAMPs/MAMPs identified that are perceived by plants has increased in recent years. However, the structural mechanisms underlying glycan recognition by plant PRRs remain limited. Currently, this knowledge is mainly focused on receptors of the LysM-PRR family, which are involved in the perception of various molecules, such as chitooligosaccharides from fungi and lipo-chitooligosaccharides (i.e., Nod/MYC factors from bacteria and mycorrhiza, respectively) that trigger differential physiological responses. Nevertheless, additional families of plant PRRs have recently been implicated in oligosaccharide/polysaccharide recognition. These include receptor kinases (RKs) with leucine-rich repeat and Malectin domains in their ECDs (LRR-MAL RKs), Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE group (CrRLK1L) with Malectin-like domains in their ECDs, as well as wall-associated kinases, lectin-RKs, and LRR-extensins. The characterization of structural basis of glycans recognition by these new plant receptors will shed light on their similarities with those of mammalians involved in glycan perception. The gained knowledge holds the potential to facilitate the development of sustainable, glycan-based crop protection solutions.
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Affiliation(s)
- Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, Madrid, Spain.
| | - Lucía Jordá
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, Madrid, Spain.
| | - Miguel Ángel Torres
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, Madrid, Spain
| | - Marina Martín-Dacal
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, Madrid, Spain
| | - Diego José Berlanga
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, Madrid, Spain
| | - Patricia Fernández-Calvo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain
| | - Elena Gómez-Rubio
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Sonsoles Martín-Santamaría
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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2
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Lynn SC, Dunwell JM, Whitehouse AB, Cockerton HM. Genetic loci associated with tissue-specific resistance to powdery mildew in octoploid strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2024; 15:1376061. [PMID: 38742212 PMCID: PMC11089197 DOI: 10.3389/fpls.2024.1376061] [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: 01/24/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Powdery mildew is one of the most problematic diseases in strawberry production. To date, few commercial strawberry cultivars are deemed to have complete resistance and as such, an extensive spray programme must be implemented to control the pathogen. Here, a large-scale field experiment was used to determine the powdery mildew resistance status of leaf and fruit tissues across a diverse panel of strawberry genotypes. This phenotypic data was used to identify Quantitative Trait Nucleotides (QTN) associated with tissue-specific powdery mildew resistance. In total, six stable QTN were found to be associated with foliar resistance, with one QTN on chromosome 7D associated with a 61% increase in resistance. In contrast to the foliage results, there were no QTN associated with fruit disease resistance and there was a high level of resistance observed on strawberry fruit, with no genetic correlation observed between fruit and foliar symptoms, indicating a tissue-specific response. Beyond the identification of genetic loci, we also demonstrate that genomic selection can lead to rapid gains in foliar resistance across genotypes, with the potential to capture >50% of the genetic foliage resistance present in the population. To date, breeding of robust powdery mildew resistance in strawberry has been impeded by the quantitative nature of natural resistance and a lack of knowledge relating to the genetic control of the trait. These results address this shortfall, through providing the community with a wealth of information that could be utilized for genomic informed breeding, implementation of which could deliver a natural resistance strategy for combatting powdery mildew.
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Affiliation(s)
- Samantha C. Lynn
- Genetics, Genomics and Breeding, National Institute of Agricultural Botany (NIAB), Kent, United Kingdom
- Crop Science, University of Reading, Reading, United Kingdom
| | - Jim M. Dunwell
- Crop Science, University of Reading, Reading, United Kingdom
| | - Adam B. Whitehouse
- Genetics, Genomics and Breeding, National Institute of Agricultural Botany (NIAB), Kent, United Kingdom
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Lee HK, Santiago J. Structural insights of cell wall integrity signaling during development and immunity. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102455. [PMID: 37739866 DOI: 10.1016/j.pbi.2023.102455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/12/2023] [Accepted: 08/25/2023] [Indexed: 09/24/2023]
Abstract
A communication system between plant cells and their surrounding cell wall is required to coordinate development, immunity, and the integration of environmental cues. This communication network is facilitated by a large pool of membrane- and cell-wall-anchored proteins that can potentially interact with the matrix or its fragments, promoting cell wall patterning or eliciting cellular responses that may lead to changes in the architecture and chemistry of the wall. A mechanistic understanding of how these receptors and cell wall proteins recognize and interact with cell wall epitopes would be key to a better understanding of all plant processes that require cell wall remodeling such as expansion, morphogenesis, and defense responses. This review focuses on the latest developments in structurally and biochemically characterized receptors and protein complexes implicated in reading and regulating cell wall integrity and immunity.
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Affiliation(s)
- Hyun Kyung Lee
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Julia Santiago
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland.
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Zou S, Xu Y, Li Q, Wei Y, Zhang Y, Tang D. Wheat powdery mildew resistance: from gene identification to immunity deployment. FRONTIERS IN PLANT SCIENCE 2023; 14:1269498. [PMID: 37790783 PMCID: PMC10544919 DOI: 10.3389/fpls.2023.1269498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023]
Abstract
Powdery mildew is one of the most devastating diseases on wheat and is caused by the obligate biotrophic phytopathogen Blumeria graminis f. sp. tritici (Bgt). Due to the complexity of the large genome of wheat and its close relatives, the identification of powdery mildew resistance genes had been hampered for a long time until recent progress in large-scale sequencing, genomics, and rapid gene isolation techniques. Here, we describe and summarize the current advances in wheat powdery mildew resistance, emphasizing the most recent discoveries about the identification of genes conferring powdery mildew resistance and the similarity, diversity and molecular function of those genes. Multilayered resistance to powdery mildew in wheat could be used for counteracting Bgt, including durable, broad spectrum but partial resistance, as well as race-specific and mostly complete resistance mediated by nucleotide-binding and leucine rich repeat domain (NLR) proteins. In addition to the above mentioned layers, manipulation of susceptibility (S) and negative regulator genes may represent another layer that can be used for durable and broad-spectrum resistance in wheat. We propose that it is promising to develop effective and durable strategies to combat powdery mildew in wheat by simultaneous deployment of multilayered immunity.
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Affiliation(s)
| | | | | | | | | | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
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5
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Chiriţoiu GN, Munteanu CV, Şulea TA, Spiridon L, Petrescu AJ, Jandus C, Romero P, Petrescu ŞM. Methionine oxidation selectively enhances T cell reactivity against a melanoma antigen. iScience 2023; 26:107205. [PMID: 37485346 PMCID: PMC10362274 DOI: 10.1016/j.isci.2023.107205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/02/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
The impact of the peptide amino acids side-chain modifications on the immunological recognition has been scarcely explored. We investigate here the effect of methionine oxidation on the antigenicity of the melanoma immunodominant peptide 369-YMDGTMSQV-377 (YMD). Using CD8+ T cell activation assays, we found that the antigenicity of the sulfoxide form is higher when compared to the YMD peptide. This is consistent with free energy computations performed on HLA-A∗02:01/YMD/TCR complex showing that this is lowered upon oxidation, paired with a steep increase in order at atomic level. Oxidized YMD forms were identified at the melanoma cell surface by LC-MS/MS analysis. These results demonstrate that methionine oxidation in the antigenic peptides may generate altered peptide ligands with increased antigenicity, and that this oxidation may occur in vivo, opening up the possibility that high-affinity CD8+ T cells might be naturally primed in the course of melanoma progression, as a result of immunosurveillance.
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Affiliation(s)
- Gabriela N. Chiriţoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031 Bucharest, Romania
| | - Cristian V.A. Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Splaiul Independenței 296, 060031 Bucharest, Romania
| | - Teodor A. Şulea
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Splaiul Independenței 296, 060031 Bucharest, Romania
| | - Laurenţiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Splaiul Independenței 296, 060031 Bucharest, Romania
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Splaiul Independenței 296, 060031 Bucharest, Romania
| | - Camilla Jandus
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Epalinges, Switzerland
| | - Pedro Romero
- Departement of Oncology, UNIL-CHUV, University of Lausanne, Epalinges, Switzerland
| | - Ştefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031 Bucharest, Romania
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Kanapin A, Rozhmina T, Bankin M, Surkova S, Duk M, Osyagina E, Samsonova M. Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration. Int J Mol Sci 2022; 23:ijms232314536. [PMID: 36498863 PMCID: PMC9738745 DOI: 10.3390/ijms232314536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection.
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Affiliation(s)
- Alexander Kanapin
- Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Tatyana Rozhmina
- Laboratory of Breeding Technologies, Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Mikhail Bankin
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Svetlana Surkova
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Duk
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia
| | - Ekaterina Osyagina
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-812-290-9645
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Chen L, Song B, Yu C, Zhang J, Zhang J, Bi R, Li X, Ren X, Zhu Y, Yao D, Song Y, Yang S, Zhao R. Identifying Soybean Pod Borer ( Leguminivora glycinivorella) Resistance QTLs and the Mechanism of Induced Defense Using Linkage Mapping and RNA-Seq Analysis. Int J Mol Sci 2022; 23:ijms231810910. [PMID: 36142822 PMCID: PMC9504297 DOI: 10.3390/ijms231810910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
The soybean pod borer (Leguminivora glycinivorella) (SPB) is a major cause of soybean (Glycine max L.) yield losses in northeast Asia, thus it is desirable to elucidate the resistance mechanisms involved in soybean response to the SPB. However, few studies have mapped SPB-resistant quantitative trait loci (QTLs) and deciphered the response mechanism in soybean. Here, we selected two soybean varieties, JY93 (SPB-resistant) and K6 (SPB-sensitive), to construct F2 and F2:3 populations for QTL mapping and collected pod shells before and after SPB larvae chewed on the two parents to perform RNA-Seq, which can identify stable QTLs and explore the response mechanism of soybean to the SPB. The results show that four QTLs underlying SPB damage to seeds were detected on chromosomes 4, 9, 13, and 15. Among them, qESP-9-1 was scanned in all environments, hence it can be considered a stable QTL. All QTLs explained 0.79 to 6.09% of the phenotypic variation. Meanwhile, 2298 and 3509 DEGs were identified for JY93 and K6, respectively, after the SPB attack, and most of these genes were upregulated. Gene Ontology enrichment results indicated that the SPB-induced and differently expressed genes in both parents are involved in biological processes such as wound response, signal transduction, immune response, and phytohormone pathways. Interestingly, secondary metabolic processes such as flavonoid synthesis were only significantly enriched in the upregulated genes of JY93 after SPB chewing compared with K6. Finally, we identified 18 candidate genes related to soybean pod borer resistance through the integration of QTL mapping and RNA-Seq analysis. Seven of these genes had similar expression patterns to the mapping parents in four additional soybean germplasm after feeding by the SPB. These results provide additional knowledge of the early response and induced defense mechanisms against the SPB in soybean, which could help in breeding SPB-resistant soybean accessions.
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Affiliation(s)
- Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Baixing Song
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Cheng Yu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun 130118, China
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Department Biology, University of British Columbia-Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Rui Bi
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Yanyu Zhu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Yang Song
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (S.Y.); (R.Z.)
| | - Rengui Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (S.Y.); (R.Z.)
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Cui Z, Xue C, Mei Q, Xuan Y. Malectin Domain Protein Kinase (MDPK) Promotes Rice Resistance to Sheath Blight via IDD12, IDD13, and IDD14. Int J Mol Sci 2022; 23:ijms23158214. [PMID: 35897795 PMCID: PMC9331740 DOI: 10.3390/ijms23158214] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 02/05/2023] Open
Abstract
Sheath blight (ShB) caused by Rhizoctonia solani is a major disease of rice, seriously affecting yield; however, the molecular defense mechanism against ShB remains unclear. A previous transcriptome analysis of rice identified that R. solani inoculation significantly induced MDPK. Genetic studies using MDPK RNAi and overexpressing plants identified that MDPK positively regulates ShB resistance. This MDPK protein was found localized in the endoplasmic reticulum (ER) and Golgi apparatus. Yeast one-hybrid assay, electrophoresis mobility shift assay (EMSA), and chromatin immunoprecipitation (ChIP) showed that the intermediate domain proteins IDD12, IDD13, and IDD14 bind to the MDPK promoter. Moreover, IDD14 was found to interact with IDD12 and IDD13 to form a transcription complex to activate MDPK expression. The three IDDs demonstrated an additive effect on MDPK activation. Further genetic studies showed that the IDD13 and IDD14 single mutants were more susceptible to ShB but not IDD12, while IDD12, IDD13, and IDD14 overexpressing plants were less susceptible than the wild-type plants. The IDD12, IDD13, and IDD14 mutants also proved the additive effect of the three IDDs on MDPK expression, which regulates ShB resistance in rice. Notably, MDPK overexpression maintained normal yield levels in rice. Thus, our study proves that IDD12, IDD13, and IDD14 activate MDPK to enhance ShB resistance in rice. These results improve our knowledge of rice defense mechanisms and provide a valuable marker for resistance breeding.
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Affiliation(s)
- Zhibo Cui
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; (Z.C.); (C.X.)
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Caiyun Xue
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; (Z.C.); (C.X.)
| | - Qiong Mei
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; (Z.C.); (C.X.)
- Correspondence: (Q.M.); (Y.X.); Tel.: +86-24-88342065 (Q.M. &Y.X.)
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; (Z.C.); (C.X.)
- Correspondence: (Q.M.); (Y.X.); Tel.: +86-24-88342065 (Q.M. &Y.X.)
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9
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Serra O, de Sousa RM, Guimarães JB, Matos J, Vicente P, de Sousa ML, Simões F. Genome-wide clonal variability in European pear "Rocha" using high-throughput sequencing. HORTICULTURE RESEARCH 2022; 9:uhac111. [PMID: 38486834 PMCID: PMC10939347 DOI: 10.1093/hr/uhac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/27/2022] [Indexed: 03/17/2024]
Abstract
Pears (Pyrus) are one of the most economically important fruits worldwide. The Pyrus genus is characterized by a high degree of genetic variability between species and interspecific hybrids, and several studies have been performed to assess this variability for both cultivated and wild accessions. These studies have mostly been limited by the resolving power of traditional molecular markers, although in the recent past the availability of reference genome sequences or SNP arrays for pear have enhanced the capability of high-resolution genomics studies. These tools can also be applied to better understand the intra-varietal (or clonal) variability in pear. Here we report the first high resolution genomics analysis of a pear clonal population using whole genome sequencing (WGS). Results showed unique signatures for the accumulation of mutations and transposable element insertions in each clone, which are likely related to their history of propagation and cultivation. The nucleotide diversity remained low in the clonal collection with the exception of few genomic windows, suggesting that balancing selection may be occurring. These windows included mainly genes related to plant fertility. Regions with higher mutational load were partially associated with transcription factors, probably reflecting the distinctive phenotypes in the collection. The annotation of variants also revealed the theoretical disruption of relevant genes in pear. Taken together, the results from this study show that pear clones accumulate mutations differently, and that those mutations can play a role on pear phenotypes, meaning that the study of pear clonal populations can be relevant in genetic studies, mainly when comparing with traditional association studies.
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Affiliation(s)
- Octávio Serra
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Banco Português de Germoplasma Vegetal (BPGV), Quinta de S. José, S. Pedro de Merelim 4700-859 Braga, Portugal
| | - Rui Maia de Sousa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estação Nacional de Fruticultura Vieira Natividade (ENFVN), Estrada de Leiria 2460-059 Alcobaça, Portugal
| | - Joana Bagoin Guimarães
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - José Matos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, 2780-159 Oeiras, Portugal
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia Vicente
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estação Nacional de Fruticultura Vieira Natividade (ENFVN), Estrada de Leiria 2460-059 Alcobaça, Portugal
| | - Miguel Leão de Sousa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estação Nacional de Fruticultura Vieira Natividade (ENFVN), Estrada de Leiria 2460-059 Alcobaça, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, 2780-159 Oeiras, Portugal
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Receptor-mediated nonhost resistance in plants. Essays Biochem 2022; 66:435-445. [PMID: 35388900 PMCID: PMC9528085 DOI: 10.1042/ebc20210080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 01/23/2023]
Abstract
Nonhost resistance (NHR) is a plant immune response that prevents many microorganisms in the plant's environment from pathogenicity against the plant. Since successful pathogens have adapted to overcome the immune systems of their host, the durable nature of NHR has potential in the management of plant disease. At present, there is genetic and molecular evidence that the underlying molecular mechanisms of NHR are similar to the plant immune responses that occur in host plants following infection by adapted pathogens. We consider that the molecular basis of NHR is multilayered, conferred by physicochemical barriers and defense responses that are induced following molecular recognition events. Moreover, the relative contribution of each component may depend on evolutionary distances between host and nonhost plants of given pathogen species. This mini-review has focused on the current knowledge of plant NHR, especially the recognition of non-adapted pathogens by nonhost plants at the cellular level. Recent gains in understanding the roles of plasma membrane-localized pattern-recognition receptors (PRRs) and the cytoplasmic nucleotide-binding leucine-rich repeat receptors (NLRs) associated with these processes, as well as the genes involved, are summarized. Finally, we provide a theoretical perspective on the durability of receptor-mediated NHR and its practical potential as an innovative strategy for crop protection against pathogens.
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Martin EC, Spiridon L, Goverse A, Petrescu AJ. NLRexpress-A bundle of machine learning motif predictors-Reveals motif stability underlying plant Nod-like receptors diversity. FRONTIERS IN PLANT SCIENCE 2022; 13:975888. [PMID: 36186050 PMCID: PMC9519389 DOI: 10.3389/fpls.2022.975888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/19/2022] [Indexed: 05/13/2023]
Abstract
Examination of a collection of over 80,000 Plant Nod-like receptors (NLRs) revealed an overwhelming sequence diversity underlying functional specificity of pathogen detection, signaling and cooperativity. The NLR canonical building blocks-CC/TIR/RPW8, NBS and LRR-contain, however, a number of conserved sequence motifs showing a significant degree of invariance amongst different NLR groups. To identify these motifs we developed NLRexpress-a bundle of 17 machine learning (ML)-based predictors, able to swiftly and precisely detect CC, TIR, NBS, and LRR motifs while minimizing computing time without accuracy losses-aimed as an instrument scalable for screening overall proteomes, transcriptomes or genomes for identifying integral NLRs and discriminating them against incomplete sequences lacking key motifs. These predictors were further used to screen a subset of ∼34,000 regular plant NLR sequences. Motifs were analyzed using unsupervised ML techniques to assess the structural correlations hidden underneath pattern variabilities. Both the NB-ARC switch domain which admittedly is the most conserved region of NLRs and the highly diverse LRR domain with its vastly variable lengths and repeat irregularities-show well-defined relations between motif subclasses, highlighting the importance of structural invariance in shaping NLR sequence diversity. The online NLRexpress webserver can be accessed at https://nlrexpress.biochim.ro.
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Affiliation(s)
- Eliza C. Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Andrei-José Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- *Correspondence: Andrei-José Petrescu,
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Capador-Barreto HD, Bernhardsson C, Milesi P, Vos I, Lundén K, Wu HX, Karlsson B, Ingvarsson PK, Stenlid J, Elfstrand M. Killing two enemies with one stone? Genomics of resistance to two sympatric pathogens in Norway spruce. Mol Ecol 2021; 30:4433-4447. [PMID: 34218489 DOI: 10.1111/mec.16058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 12/31/2022]
Abstract
Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.
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Affiliation(s)
- Hernán D Capador-Barreto
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carolina Bernhardsson
- Uppsala Biocentre, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ingrid Vos
- Forestry Research Institute of Sweden (Skogforsk), Ekebo, Sweden
| | - Karl Lundén
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Bo Karlsson
- Forestry Research Institute of Sweden (Skogforsk), Ekebo, Sweden
| | - Pär K Ingvarsson
- Uppsala Biocentre, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Stenlid
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Malin Elfstrand
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Biotechnological Resources to Increase Disease-Resistance by Improving Plant Immunity: A Sustainable Approach to Save Cereal Crop Production. PLANTS 2021; 10:plants10061146. [PMID: 34199861 PMCID: PMC8229257 DOI: 10.3390/plants10061146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/17/2021] [Accepted: 05/29/2021] [Indexed: 12/16/2022]
Abstract
Plant diseases are globally causing substantial losses in staple crop production, undermining the urgent goal of a 60% increase needed to meet the food demand, a task made more challenging by the climate changes. Main consequences concern the reduction of food amount and quality. Crop diseases also compromise food safety due to the presence of pesticides and/or toxins. Nowadays, biotechnology represents our best resource both for protecting crop yield and for a science-based increased sustainability in agriculture. Over the last decades, agricultural biotechnologies have made important progress based on the diffusion of new, fast and efficient technologies, offering a broad spectrum of options for understanding plant molecular mechanisms and breeding. This knowledge is accelerating the identification of key resistance traits to be rapidly and efficiently transferred and applied in crop breeding programs. This review gathers examples of how disease resistance may be implemented in cereals by exploiting a combination of basic research derived knowledge with fast and precise genetic engineering techniques. Priming and/or boosting the immune system in crops represent a sustainable, rapid and effective way to save part of the global harvest currently lost to diseases and to prevent food contamination.
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Saur IML, Hückelhoven R. Recognition and defence of plant-infecting fungal pathogens. JOURNAL OF PLANT PHYSIOLOGY 2021; 256:153324. [PMID: 33249386 DOI: 10.1016/j.jplph.2020.153324] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
Attempted infections of plants with fungi result in diverse outcomes ranging from symptom-less resistance to severe disease and even death of infected plants. The deleterious effect on crop yield have led to intense focus on the cellular and molecular mechanisms that explain the difference between resistance and susceptibility. This research has uncovered plant resistance or susceptibility genes that explain either dominant or recessive inheritance of plant resistance with many of them coding for receptors that recognize pathogen invasion. Approaches based on cell biology and phytochemistry have contributed to identifying factors that halt an invading fungal pathogen from further invasion into or between plant cells. Plant chemical defence compounds, antifungal proteins and structural reinforcement of cell walls appear to slow down fungal growth or even prevent fungal penetration in resistant plants. Additionally, the hypersensitive response, in which a few cells undergo a strong local immune reaction, including programmed cell death at the site of infection, stops in particular biotrophic fungi from spreading into surrounding tissue. In this review, we give a general overview of plant recognition and defence of fungal parasites tracing back to the early 20th century with a special focus on Triticeae and on the progress that was made in the last 30 years.
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Affiliation(s)
- Isabel M L Saur
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
| | - Ralph Hückelhoven
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Ramann-Straße 2, 85354 Freising, Germany.
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15
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Panstruga R, Moscou MJ. What is the Molecular Basis of Nonhost Resistance? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1253-1264. [PMID: 32808862 DOI: 10.1094/mpmi-06-20-0161-cr] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.Nonhost resistance is typically considered the ability of a plant species to repel all attempts of a pathogen species to colonize it and reproduce on it. Based on this common definition, nonhost resistance is presumed to be very durable and, thus, of great interest for its potential use in agriculture. Despite considerable research efforts, the molecular basis of this type of plant immunity remains nebulous. We here stress the fact that "nonhost resistance" is a phenomenological rather than a mechanistic concept that comprises more facets than typically considered. We further argue that nonhost resistance essentially relies on the very same genes and pathways as other types of plant immunity, of which some may act as bottlenecks for particular pathogens on a given plant species or under certain conditions. Thus, in our view, the frequently used term "nonhost genes" is misleading and should be avoided. Depending on the plant-pathogen combination, nonhost resistance may involve the recognition of pathogen effectors by host immune sensor proteins, which might give rise to host shifts or host range expansions due to evolutionary-conditioned gains and losses in respective armories. Thus, the extent of nonhost resistance also defines pathogen host ranges. In some instances, immune-related genes can be transferred across plant species to boost defense, resulting in augmented disease resistance. We discuss future routes for deepening our understanding of nonhost resistance and argue that the confusing term "nonhost resistance" should be used more cautiously in the light of a holistic view of plant immunity.
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Affiliation(s)
- Ralph Panstruga
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Worringer Weg 1, 52056 Aachen, Germany
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, United Kingdom
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Bartholomé J, Brachi B, Marçais B, Mougou-Hamdane A, Bodénès C, Plomion C, Robin C, Desprez-Loustau ML. The genetics of exapted resistance to two exotic pathogens in pedunculate oak. THE NEW PHYTOLOGIST 2020; 226:1088-1103. [PMID: 31711257 DOI: 10.1111/nph.16319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 11/05/2019] [Indexed: 05/16/2023]
Abstract
Exotic pathogens cause severe damage in natural populations in the absence of coevolutionary dynamics with their hosts. However, some resistance to such pathogens may occur in naive populations. The objective of this study was to investigate the genetics of this so-called 'exapted' resistance to two pathogens of Asian origin (Erysiphe alphitoides and Phytophthora cinnamomi) in European oak. Host-pathogen compatibility was assessed by recording infection success and pathogen growth in a full-sib family of Quercus robur under controlled and natural conditions. Two high-resolution genetic maps anchored on the reference genome were used to study the genetic architecture of resistance and to identify positional candidate genes. Two genomic regions, each containing six strong and stable quantitative trait loci (QTLs) accounting for 12-19% of the phenotypic variation, were mainly associated with E. alphitoides infection. Candidate genes, especially genes encoding receptor-like-kinases and galactinol synthases, were identified in these regions. The three QTLs associated with P. cinnamomi infection did not colocate with QTLs found for E. alphitoides. These findings provide evidence that exapted resistance to E. alphitoides and P. cinnamomi is present in Q. robur and suggest that the underlying molecular mechanisms involve genes encoding proteins with extracellular signaling functions.
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Affiliation(s)
- Jérôme Bartholomé
- BIOGECO, INRA, Université de Bordeaux, 69 route d'Arcachon, Cestas, 33610, France
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, 34398, France
- CIRAD, UMR AGAP, TA A-108 / 03 - Avenue Agropolis, Montpellier, 34398, France
| | - Benjamin Brachi
- BIOGECO, INRA, Université de Bordeaux, 69 route d'Arcachon, Cestas, 33610, France
| | - Benoit Marçais
- IAM, INRA, Université de Lorraine, Champenoux, Nancy, 54000, France
| | - Amira Mougou-Hamdane
- BIOGECO, INRA, Université de Bordeaux, 69 route d'Arcachon, Cestas, 33610, France
- Institut National Agronomique de Tunisie, Université de Carthage, 43 avenue Charles Nicolle Cité el Mahrajène, Tunis, 1082, Tunisia
| | - Catherine Bodénès
- BIOGECO, INRA, Université de Bordeaux, 69 route d'Arcachon, Cestas, 33610, France
| | - Christophe Plomion
- BIOGECO, INRA, Université de Bordeaux, 69 route d'Arcachon, Cestas, 33610, France
| | - Cécile Robin
- BIOGECO, INRA, Université de Bordeaux, 69 route d'Arcachon, Cestas, 33610, France
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Devi SJSR, Singh K, Umakanth B, Vishalakshi B, Rao KVS, Suneel B, Sharma SK, Kadambari GKM, Prasad MS, Senguttvel P, Syamaladevi DP, Madhav MS. Identification and Characterization of a Large Effect QTL from Oryza glumaepatula Revealed Pi68(t) as Putative Candidate Gene for Rice Blast Resistance. RICE (NEW YORK, N.Y.) 2020; 13:17. [PMID: 32166467 PMCID: PMC7067966 DOI: 10.1186/s12284-020-00378-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/02/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Field resistance is often effective and durable as compared to vertical resistance. The introgression line (INGR15002) derived from O. glumaepatula has proven broad spectrum field resistance for both leaf and neck blast. RESULTS Quantitative Trait Loci (QTL) analysis of INGR15002, led to the identification of two major QTL - qBL3 contributing about 34% and 32% phenotypic variance towards leaf and neck blast resistance, respectively and qBL7 contributing about 25% of phenotypic variance for leaf blast. Further, qBL3 was fine mapped, narrowed down to 300 kb region and a linked SNP maker was identified. By combining mapping with microarray analysis, a candidate gene, Os03g0281466 (malectin-serine threonine kinase), was identified in the fine mapped region and named as Pi68(t). The nucleotide variations in the coding as well as upstream region of the gene was identified through cloning and sequence analysis of Pi68(t) alleles. These significant variations led to the non-synonymous changes in the protein as well as variations (presence/absence) in four important motifs (W-box element; MYC element; TCP element; BIHD1OS) at promoter region those are associated with resistance and susceptible reactions. The effect of qBL3 was validated by its introgression into BPT5204 (susceptible variety) through marker-assisted selection and progeny exhibiting resistance to both leaf and neck blast was identified. Further, the utility of linked markers of Pi68(t) in the blast breeding programs was demonstrated in elite germplasm lines. CONCLUSIONS This is the first report on the identification and characterization of major effect QTL from O. glumaepatula, which led to the identification of a putative candidate gene, Pi68(t), which confers field resistance to leaf as well as neck blast in rice.
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Affiliation(s)
- S. J. S. Rama Devi
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - Kuldeep Singh
- Department of Plant Breeding and Genetics, P.A.U, Ludhiana, Punjab India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- School of Agricultural Biotechnology, P.A.U, Ludhiana, Punjab India
| | - B. Umakanth
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - B. Vishalakshi
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | | | - B. Suneel
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - S. K. Sharma
- Plant Pathology Division, ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
- Plant Pathology Division, Indian Institute of Rice Research, Hyderabad-30, India
| | | | - M. S. Prasad
- Plant Pathology Division, ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - P. Senguttvel
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - Divya P. Syamaladevi
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - M. S. Madhav
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
- Crop Improvement Section, IIRR, Hyderabad, 500 030 India
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LRRpredictor-A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers. Genes (Basel) 2020; 11:genes11030286. [PMID: 32182725 PMCID: PMC7140858 DOI: 10.3390/genes11030286] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022] Open
Abstract
Leucine-rich-repeats (LRRs) belong to an archaic procaryal protein architecture that is widely involved in protein-protein interactions. In eukaryotes, LRR domains developed into key recognition modules in many innate immune receptor classes. Due to the high sequence variability imposed by recognition specificity, precise repeat delineation is often difficult especially in plant NOD-like Receptors (NLRs) notorious for showing far larger irregularities. To address this problem, we introduce here LRRpredictor, a method based on an ensemble of estimators designed to better identify LRR motifs in general but particularly adapted for handling more irregular LRR environments, thus allowing to compensate for the scarcity of structural data on NLR proteins. The extrapolation capacity tested on a set of annotated LRR domains from six immune receptor classes shows the ability of LRRpredictor to recover all previously defined specific motif consensuses and to extend the LRR motif coverage over annotated LRR domains. This analysis confirms the increased variability of LRR motifs in plant and vertebrate NLRs when compared to extracellular receptors, consistent with previous studies. Hence, LRRpredictor is able to provide novel insights into the diversification of LRR domains and a robust support for structure-informed analyses of LRRs in immune receptor functioning.
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Abstract
Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.
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20
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Hunt M, Banerjee S, Surana P, Liu M, Fuerst G, Mathioni S, Meyers BC, Nettleton D, Wise RP. Small RNA discovery in the interaction between barley and the powdery mildew pathogen. BMC Genomics 2019; 20:610. [PMID: 31345162 PMCID: PMC6657096 DOI: 10.1186/s12864-019-5947-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/30/2019] [Indexed: 01/04/2023] Open
Abstract
Background Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, barley (Hordeum vulgare) to explore fungal and plant sRNAs expressed during Bgh infection of barley leaf epidermal cells. Results RNA was isolated from four fast-neutron immune-signaling mutants and their progenitor over a time course representing key stages of Bgh infection, including appressorium formation, penetration of epidermal cells, and development of haustorial feeding structures. The Cereal Introduction (CI) 16151 progenitor carries the resistance allele Mla6, while Bgh isolate 5874 harbors the AVRa6 avirulence effector, resulting in an incompatible interaction. Parallel Analysis of RNA Ends (PARE) was used to verify sRNAs with likely transcript targets in both barley and Bgh. Bgh sRNAs are predicted to regulate effectors, metabolic genes, and translation-related genes. Barley sRNAs are predicted to influence the accumulation of transcripts that encode auxin response factors, NAC transcription factors, homeodomain transcription factors, and several splicing factors. We also identified phasing small interfering RNAs (phasiRNAs) in barley that overlap transcripts that encode receptor-like kinases (RLKs) and nucleotide-binding, leucine-rich domain proteins (NLRs). Conclusions These data suggest that Bgh sRNAs regulate gene expression in metabolism, translation-related, and pathogen effectors. PARE-validated targets of predicted Bgh milRNAs include both EKA (effectors homologous to AVRk1 and AVRa10) and CSEP (candidate secreted effector protein) families. We also identified barley phasiRNAs and miRNAs in response to Bgh infection. These include phasiRNA loci that overlap with a significant proportion of receptor-like kinases, suggesting an additional sRNA control mechanism may be active in barley leaves as opposed to predominant R-gene phasiRNA overlap in many eudicots. In addition, we identified conserved miRNAs, novel miRNA candidates, and barley genome mapped sRNAs that have PARE validated transcript targets in barley. The miRNA target transcripts are enriched in transcription factors, signaling-related proteins, and photosynthesis-related proteins. Together these results suggest both barley and Bgh control metabolism and infection-related responses via the specific accumulation and targeting of genes via sRNAs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5947-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matt Hunt
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA.,Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA
| | - Sagnik Banerjee
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Priyanka Surana
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Meiling Liu
- Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.,Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA
| | - Greg Fuerst
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA
| | - Sandra Mathioni
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.,Division of Plant Sciences, University of Missouri - Columbia, 52 Agriculture Lab, Columbia, MO, 65211, USA
| | - Dan Nettleton
- Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.,Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA
| | - Roger P Wise
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA. .,Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA. .,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA. .,Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA.
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Janáková E, Jakobson I, Peusha H, Abrouk M, Škopová M, Šimková H, Šafář J, Vrána J, Doležel J, Järve K, Valárik M. Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1061-1072. [PMID: 30535646 PMCID: PMC6449310 DOI: 10.1007/s00122-018-3259-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
A segment of Triticum militinae chromosome 7G harbors a gene(s) conferring powdery mildew resistance which is effective at both the seedling and the adult plant stages when transferred into bread wheat (T. aestivum). The introgressed segment replaces a piece of wheat chromosome arm 4AL. An analysis of segregating materials generated to positionally clone the gene highlighted that in a plant heterozygous for the introgression segment, only limited recombination occurs between the introgressed region and bread wheat 4A. Nevertheless, 75 genetic markers were successfully placed within the region, thereby confining the gene to a 0.012 cM window along the 4AL arm. In a background lacking the Ph1 locus, the localized rate of recombination was raised 33-fold, enabling the reduction in the length of the region containing the resistance gene to a 480 kbp stretch harboring 12 predicted genes. The substituted segment in the reference sequence of bread wheat cv. Chinese Spring is longer (640 kbp) and harbors 16 genes. A comparison of the segments' sequences revealed a high degree of divergence with respect to both their gene content and nucleotide sequence. Of the 12 T. militinae genes, only four have a homolog in cv. Chinese Spring. Possible candidate genes for the resistance have been identified based on function predicted from their sequence.
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Affiliation(s)
- Eva Janáková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Irena Jakobson
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Hilma Peusha
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Michael Abrouk
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Monika Škopová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Limagrain Central Europe Cereals, s.r.o., Hrubčice 111, 79821, Bedihošť, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Kadri Järve
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Miroslav Valárik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
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Fonseca JP, Mysore KS. Genes involved in nonhost disease resistance as a key to engineer durable resistance in crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 279:108-116. [PMID: 30709487 DOI: 10.1016/j.plantsci.2018.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/28/2018] [Accepted: 07/06/2018] [Indexed: 05/25/2023]
Abstract
Most potential pathogens fail to establish virulence for a plethora of plants found in nature. This intrinsic property to resist pathogen virulence displayed by organisms without triggering canonical resistance (R) genes has been termed nonhost resistance (NHR). While host resistance involves recognition of pathogen elicitors such as avirulence factors by bona fide R proteins, mechanism of NHR seems less obvious, often involving more than one gene. We can generally describe NHR in two steps: 1) pre-invasive resistance, either passive or active, which can restrict the pathogen from entering the host, and 2) post-invasive resistance, an active defense response that often results in hypersensitive response like programmed cell death and reactive oxygen species accumulation. While PAMP-triggered-immunity (PTI) is generally effective against nonhost pathogens, effector-triggered-immunity (ETI) can be effective against both host and nonhost pathogens. Prolonged interactions between adapted pathogens and their resistant host plants results in co-evolution, which can lead to new pathogen strains that can be virulent and cause disease on supposedly resistant host. In this context, engineering durable resistance by manipulating genes involved in NHR is an attractive approach for sustainable agriculture. Several genes involved in NHR have been characterized for their role in plant defense. In this review, we report genes involved in NHR identified to date and highlight a few examples where genes involved in NHR have been used to confer resistance in crop plants against economically important diseases.
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Hu P, Liu J, Xu J, Zhou C, Cao S, Zhou W, Huang Z, Yuan S, Wang X, Xiao J, Zhang R, Wang H, Zhang S, Xing L, Cao A. A malectin-like/leucine-rich repeat receptor protein kinase gene, RLK-V, regulates powdery mildew resistance in wheat. MOLECULAR PLANT PATHOLOGY 2018; 19:2561-2574. [PMID: 30030900 PMCID: PMC6637979 DOI: 10.1111/mpp.12729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 05/21/2023]
Abstract
Pattern recognition receptors (PRRs) can trigger plant immunity through the recognition of pathogen-associated molecular patterns. In this study, we report that a malectin-like/leucine-rich repeat receptor protein kinase gene, RLK-V, from Haynaldia villosa putatively acts as a PRR to positively regulate powdery mildew resistance caused by Blumeria graminis f. sp. tritici (Bgt) in wheat. RLK-V has two alternatively spliced transcripts corresponding to an intact RLK-V1.1 and a truncated RLK-V1.2 caused by intron retention. Expression analysis showed that both transcripts could be up-regulated by Bgt in resistant materials, whereas the functional RLK-V1.1 was expressed only after Bgt inoculation. Promoter activity assays indicated that RLK-V could respond to Bgt even in susceptible wheat. Silencing of RLK-V in Pm21-carrying resistant materials resulted in compromised resistance to Bgt. In addition, over-expression of RLK-V1.1 in Pm21-lacking susceptible Yangmai158 and SM-1 by single-cell transient expression and stable transformation in Yangmai158 could improve powdery mildew resistance. We propose that RLK-V regulates basal resistance to powdery mildew, which is also required for broad-spectrum resistance mediated by the Pm21 gene. Over-expression of RLK-V1.1 could trigger cell death in Nicotiana benthamiana, and RLK-V1.1 transgenic wheat accumulated more reactive oxygen species and displayed a stronger hypersensitive response than did the recipient, which led to enhanced Bgt resistance. However, constitutive activation of RLK-V1.1 resulted in the abnormal growth of transgenic plants.
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Affiliation(s)
- Ping Hu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
- Henan Collaborative Innovation Center of Modern Biological BreedingHenan Institute of Science and Technology453003China
| | - Jiaqian Liu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Jiefei Xu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Chuanyu Zhou
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Shuqi Cao
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Weihao Zhou
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Zhenpu Huang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Sufan Yuan
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Xiue Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Jin Xiao
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Ruiqi Zhang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Haiyan Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Shouzhong Zhang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
| | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm EnhancementCytogenetics Institute, Nanjing Agricultural University/JCIC‐MCPNanjing210095China
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Pan Y, Liu Z, Rocheleau H, Fauteux F, Wang Y, McCartney C, Ouellet T. Transcriptome dynamics associated with resistance and susceptibility against fusarium head blight in four wheat genotypes. BMC Genomics 2018; 19:642. [PMID: 30157778 PMCID: PMC6116500 DOI: 10.1186/s12864-018-5012-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/14/2018] [Indexed: 02/07/2023] Open
Abstract
Background Fusarium head blight (FHB) of wheat in North America is caused mostly by the fungal pathogen Fusarium graminearum (Fg). Upon exposure to Fg, wheat initiates a series of cellular responses involving massive transcriptional reprogramming. In this study, we analyzed transcriptomics data of four wheat genotypes (Nyubai, Wuhan 1, HC374, and Shaw), at 2 and 4 days post inoculation (dpi) with Fg, using RNA-seq technology. Results A total of 37,772 differentially expressed genes (DEGs) were identified, 28,961 from wheat and 8811 from the pathogen. The susceptible genotype Shaw exhibited the highest number of host and pathogen DEGs, including 2270 DEGs associating with FHB susceptibility. Protein serine/threonine kinases and LRR-RK were associated with susceptibility at 2 dpi, while several ethylene-responsive, WRKY, Myb, bZIP and NAC-domain containing transcription factors were associated with susceptibility at 4 dpi. In the three resistant genotypes, 220 DEGs were associated with resistance. Glutathione S-transferase (GST), membrane proteins and distinct LRR-RKs were associated with FHB resistance across the three genotypes. Genes with unique, high up-regulation by Fg in Wuhan 1 were mostly transiently expressed at 2 dpi, while many defense-associated genes were up-regulated at both 2 and 4 dpi in Nyubai; the majority of unique genes up-regulated in HC374 were detected at 4 dpi only. In the pathogen, most genes showed increased expression between 2 and 4 dpi in all genotypes, with stronger levels in the susceptible host; however two pectate lyases and a hydrolase were expressed higher at 2 dpi, and acetyltransferase activity was highly enriched at 4 dpi. Conclusions There was an early up-regulation of LRR-RKs, different between susceptible and resistant genotypes; subsequently, distinct sets of genes associated with defense response were up-regulated. Differences in expression profiles among the resistant genotypes indicate genotype-specific defense mechanisms. This study also shows a greater resemblance in transcriptomics of HC374 to Nyubai, consistent with their sharing of two FHB resistance QTLs on 3BS and 5AS, compared to Wuhan 1 which carries one QTL on 2DL in common with HC374. Electronic supplementary material The online version of this article (10.1186/s12864-018-5012-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youlian Pan
- Digital Technologies Research Centre, NRC, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada.
| | - Ziying Liu
- Digital Technologies Research Centre, NRC, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Hélène Rocheleau
- Ottawa Research and Development Centre, AAFC, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - François Fauteux
- Digital Technologies Research Centre, NRC, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Yunli Wang
- Digital Technologies Research Centre, NRC, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Curt McCartney
- Morden Research and Development Centre, AAFC, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, AAFC, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
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25
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Pan Y, Liu Z, Rocheleau H, Fauteux F, Wang Y, McCartney C, Ouellet T. Transcriptome dynamics associated with resistance and susceptibility against fusarium head blight in four wheat genotypes. BMC Genomics 2018. [PMID: 30157778 DOI: 10.1186/s12864-018-5012-5013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Fusarium head blight (FHB) of wheat in North America is caused mostly by the fungal pathogen Fusarium graminearum (Fg). Upon exposure to Fg, wheat initiates a series of cellular responses involving massive transcriptional reprogramming. In this study, we analyzed transcriptomics data of four wheat genotypes (Nyubai, Wuhan 1, HC374, and Shaw), at 2 and 4 days post inoculation (dpi) with Fg, using RNA-seq technology. RESULTS A total of 37,772 differentially expressed genes (DEGs) were identified, 28,961 from wheat and 8811 from the pathogen. The susceptible genotype Shaw exhibited the highest number of host and pathogen DEGs, including 2270 DEGs associating with FHB susceptibility. Protein serine/threonine kinases and LRR-RK were associated with susceptibility at 2 dpi, while several ethylene-responsive, WRKY, Myb, bZIP and NAC-domain containing transcription factors were associated with susceptibility at 4 dpi. In the three resistant genotypes, 220 DEGs were associated with resistance. Glutathione S-transferase (GST), membrane proteins and distinct LRR-RKs were associated with FHB resistance across the three genotypes. Genes with unique, high up-regulation by Fg in Wuhan 1 were mostly transiently expressed at 2 dpi, while many defense-associated genes were up-regulated at both 2 and 4 dpi in Nyubai; the majority of unique genes up-regulated in HC374 were detected at 4 dpi only. In the pathogen, most genes showed increased expression between 2 and 4 dpi in all genotypes, with stronger levels in the susceptible host; however two pectate lyases and a hydrolase were expressed higher at 2 dpi, and acetyltransferase activity was highly enriched at 4 dpi. CONCLUSIONS There was an early up-regulation of LRR-RKs, different between susceptible and resistant genotypes; subsequently, distinct sets of genes associated with defense response were up-regulated. Differences in expression profiles among the resistant genotypes indicate genotype-specific defense mechanisms. This study also shows a greater resemblance in transcriptomics of HC374 to Nyubai, consistent with their sharing of two FHB resistance QTLs on 3BS and 5AS, compared to Wuhan 1 which carries one QTL on 2DL in common with HC374.
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Affiliation(s)
- Youlian Pan
- Digital Technologies Research Centre, NRC, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada.
| | - Ziying Liu
- Digital Technologies Research Centre, NRC, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Hélène Rocheleau
- Ottawa Research and Development Centre, AAFC, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - François Fauteux
- Digital Technologies Research Centre, NRC, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Yunli Wang
- Digital Technologies Research Centre, NRC, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Curt McCartney
- Morden Research and Development Centre, AAFC, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, AAFC, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
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26
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Hu Y, Liang Y, Zhang M, Tan F, Zhong S, Li X, Gong G, Chang X, Shang J, Tang S, Li T, Luo P. Comparative transcriptome profiling of Blumeria graminis f. sp. tritici during compatible and incompatible interactions with sister wheat lines carrying and lacking Pm40. PLoS One 2018; 13:e0198891. [PMID: 29975700 PMCID: PMC6033381 DOI: 10.1371/journal.pone.0198891] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/25/2018] [Indexed: 11/18/2022] Open
Abstract
Blumeria graminis f. sp. tritici (Bgt) is an obligate biotrophic fungus that causes wheat powdery mildew, which is a devastating disease in wheat. However, little is known about the pathogenesis of this fungus, and differences in the pathogenesis of the same pathogen at various resistance levels in hosts have not been determined. In the present study, leaf tissues of both Pm40-expressing hexaploid wheat line L658 and its Pm40-deficient sister line L958 were harvested at 0 (without inoculation), 6, 12, 24, 48 and 72 hours post-inoculation (hpi) with Bgt race 15 and then subjected to RNA sequencing (RNA-seq). In addition, we also observed changes in fungal growth morphology at the aforementioned time points. There was a high correlation between percentage of reads mapped to the Bgt reference genome and biomass of the fungus within the leaf tissue during the growth process. The percentage of mapped reads of Bgt in compatible interactions was significantly higher (at the p<0.05 level) than that of reads in incompatible interactions from 24 to 72 hpi. Further functional annotations indicated that expression levels of genes encoding H+-transporting ATPase, putative secreted effector proteins (PSEPs) and heat shock proteins (HSPs) were significantly up-regulated in compatible interactions compared with these levels in incompatible interactions, particularly at 72 hpi. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that genes involved in the endocytosis pathway were also enriched in compatible interactions. Overall, genes encoding H+-transporting ATPase, PSEPs and HSPs possibly played crucial roles in successfully establishing the pathogenesis of compatible interactions during late stages of inoculation. The study results also indicated that endocytosis is likely to play a potential role in Bgt in establishing compatible interactions.
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Affiliation(s)
- Yuting Hu
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yinping Liang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min Zhang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Feiquan Tan
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengfu Zhong
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xin Li
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoshu Gong
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Chang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Shang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengwen Tang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tao Li
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peigao Luo
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
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Künstler A, Bacsó R, Albert R, Barna B, Király Z, Hafez YM, Fodor J, Schwarczinger I, Király L. Superoxide (O 2.-) accumulation contributes to symptomless (type I) nonhost resistance of plants to biotrophic pathogens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 128:115-125. [PMID: 29775863 DOI: 10.1016/j.plaphy.2018.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/04/2018] [Accepted: 05/06/2018] [Indexed: 06/08/2023]
Abstract
Nonhost resistance is the most common form of disease resistance exhibited by plants against most pathogenic microorganisms. Type I nonhost resistance is symptomless (i.e. no macroscopically visible cell/tissue death), implying an early halt of pathogen growth. The timing/speed of defences is much more rapid during type I nonhost resistance than during type II nonhost and host ("gene-for-gene") resistance associated with a hypersensitive response (localized necrosis, HR). However, the mechanism(s) underlying symptomless (type I) nonhost resistance is not entirely understood. Here we assessed accumulation dynamics of the reactive oxygen species superoxide (O2.-) during interactions of plants with a range of biotrophic and hemibiotrophic pathogens resulting in susceptibility, symptomless nonhost resistance or host resistance with HR. Our results show that the timing of macroscopically detectable superoxide accumulation (1-4 days after inoculation, DAI) is always associated with the speed of the defense response (symptomless nonhost resistance vs. host resistance with HR) in inoculated leaves. The relatively early (1 DAI) superoxide accumulation during symptomless nonhost resistance of barley to wheat powdery mildew (Blumeria graminis f. sp. tritici) is localized to mesophyll chloroplasts of inoculated leaves and coupled to enhanced NADPH oxidase (EC 1.6.3.1) activity and transient increases in expression of genes regulating superoxide levels and cell death (superoxide dismutase, HvSOD1 and BAX inhibitor-1, HvBI-1). Importantly, the partial suppression of symptomless nonhost resistance of barley to wheat powdery mildew by heat shock (49 °C, 45 s) and antioxidant (SOD and catalase) treatments points to a functional role of superoxide in symptomless (type I) nonhost resistance.
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Affiliation(s)
- András Künstler
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary
| | - Renáta Bacsó
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary
| | - Réka Albert
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary
| | - Balázs Barna
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary
| | - Zoltán Király
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary
| | - Yaser Mohamed Hafez
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary
| | - József Fodor
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary
| | - Ildikó Schwarczinger
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary
| | - Lóránt Király
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1022 Budapest, Herman Ottó str. 15, Hungary.
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Transient Overexpression of HvSERK2 Improves Barley Resistance to Powdery Mildew. Int J Mol Sci 2018; 19:ijms19041226. [PMID: 29670014 PMCID: PMC5979413 DOI: 10.3390/ijms19041226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/14/2018] [Accepted: 04/15/2018] [Indexed: 01/03/2023] Open
Abstract
Somatic embryogenesis receptor-like kinases (SERKs) play an essential role in plant response to pathogen infection. Here we identified three SERK genes (HvSERK1/2/3) from barley, and aimed to determine their implication in defense responses to barley powdery mildew (Bgh). Although HvSERK1/2/3 share the characteristic domains of the SERK family, only HvSERK2 was significantly induced in barley leaves during Bgh infection. The expression of HvSERK2 was rapidly induced by hydrogen peroxide (H2O2) treatment, but not by treatment with salicylic acid (SA), methyl jasmonate (MeJA), ethephon (ETH), or abscisic acid (ABA). Bioinformatics analysis of the cloned HvSERK2 promoter revealed that it contains several elements responsible for defense responses against pathogens. Promoter functional analysis showed that the HvSERK2 promoter was induced by Bgh and H2O2. Subcellular localization analysis of HvSERK2 indicated that it is mainly located on the plasma membrane. Transient overexpression of HvSERK2 in epidermal cells of the susceptible barley cultivar Hua 30 reduced the Bgh haustorium index from 58.6% to 43.2%. This study suggests that the HvSERK2 gene plays a positive role in the improvement of barley resistance to powdery mildew, and provides new insight into the function of SERK genes in the biotic stress response of plants.
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Delventhal R, Rajaraman J, Stefanato FL, Rehman S, Aghnoum R, McGrann GRD, Bolger M, Usadel B, Hedley PE, Boyd L, Niks RE, Schweizer P, Schaffrath U. A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley. BMC PLANT BIOLOGY 2017; 17:232. [PMID: 29202692 PMCID: PMC5715502 DOI: 10.1186/s12870-017-1178-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/15/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Nonhost resistance (NHR) protects plants against a vast number of non-adapted pathogens which implicates a potential exploitation as source for novel disease resistance strategies. Aiming at a fundamental understanding of NHR a global analysis of transcriptome reprogramming in the economically important Triticeae cereals wheat and barley, comparing host and nonhost interactions in three major fungal pathosystems responsible for powdery mildew (Blumeria graminis ff. ssp.), cereal blast (Magnaporthe sp.) and leaf rust (Puccinia sp.) diseases, was performed. RESULTS In each pathosystem a significant transcriptome reprogramming by adapted- or non-adapted pathogen isolates was observed, with considerable overlap between Blumeria, Magnaporthe and Puccinia. Small subsets of these general pathogen-regulated genes were identified as differentially regulated between host and corresponding nonhost interactions, indicating a fine-tuning of the general pathogen response during the course of co-evolution. Additionally, the host- or nonhost-related responses were rather specific for each pair of adapted and non-adapted isolates, indicating that the nonhost resistance-related responses were to a great extent pathosystem-specific. This pathosystem-specific reprogramming may reflect different resistance mechanisms operating against non-adapted pathogens with different lifestyles, or equally, different co-option of the hosts by the adapted isolates to create an optimal environment for infection. To compare the transcriptional reprogramming between wheat and barley, putative orthologues were identified. Within the wheat and barley general pathogen-regulated genes, temporal expression profiles of orthologues looked similar, indicating conserved general responses in Triticeae against fungal attack. However, the comparison of orthologues differentially expressed between host and nonhost interactions revealed fewer commonalities between wheat and barley, but rather suggested different host or nonhost responses in the two cereal species. CONCLUSIONS Taken together, our results suggest independent co-evolutionary forces acting on host pathosystems mirrored by barley- or wheat-specific nonhost responses. As a result of evolutionary processes, at least for the pathosystems investigated, NHR appears to rely on rather specific plant responses.
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Affiliation(s)
- Rhoda Delventhal
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Jeyaraman Rajaraman
- Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Francesca L. Stefanato
- Department of Disease and Stress Biology, John Innes Centre, Norwich Research Park, Colney Lane, Colney, Norwich, Norfolk, NR4 7UH UK
- Present address: Molecular microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Sajid Rehman
- Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
- Present address: Biodiversity and Integrated Gene Management Program (BIGM), International Center for Agriculture Research in the Dry Areas, Rabat, Morocco
| | - Reza Aghnoum
- Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
- Present address: Seed and Plant Improvement Research Department, Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Mashhad, Iran
| | - Graham R. D. McGrann
- Department of Disease and Stress Biology, John Innes Centre, Norwich Research Park, Colney Lane, Colney, Norwich, Norfolk, NR4 7UH UK
| | - Marie Bolger
- Institute of Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52056 Aachen, Germany
| | - Björn Usadel
- Institute of Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52056 Aachen, Germany
| | - Pete E. Hedley
- The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA UK
| | - Lesley Boyd
- NIAB, Huntingdon Road, Cambridge, CB3 0LE UK
| | - Rients E. Niks
- Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Patrick Schweizer
- Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
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