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Sun X, Lei R, Zhang H, Chen W, Jia Q, Guo X, Zhang Y, Wu P, Wang X. Rapid and sensitive detection of two fungal pathogens in soybeans using the recombinase polymerase amplification/CRISPR-Cas12a method for potential on-site disease diagnosis. PEST MANAGEMENT SCIENCE 2024; 80:1168-1181. [PMID: 37874890 DOI: 10.1002/ps.7847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 10/08/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Diaporthe aspalathi and Diaporthe caulivora are two of the fungal pathogens causing soybean stem canker (SSC) in soybean, which is one of the most widespread diseases in soybean growing regions and can cause 100% loss of yield. Current methods for the detection of fungal pathogens, including morphological identification and molecular detection, are mostly limited by the need for professional laboratories and staff. To develop a detection method for potential on-site diagnosis for two of the fungal pathogens causing SSC, we designed a rapid assay combining recombinase polymerase amplification (RPA) and CRISPR-Cas12a-based diagnostics to specifically detect D. aspalathi and D. caulivora. RESULTS The translation elongation factor 1-alpha gene was employed as the target gene to evaluate the specificity and sensitivity of this assay. The RPA/CRISPR-Cas12a system has excellent specificity to distinguish D. aspalathi and D. caulivora from closely related species. The sensitivities of RPA/CRISPR-Cas12a-based fluorescence detection and lateral flow assay for D. aspalathi and D. caulivora are 14.5 copies and 24.6 copies, respectively. This assay can detect hyphae in inoculated soybean stems at 12 days after inoculation and has a recovery as high as 86% for hyphae-spiked soybean seed powder. The total time from DNA extraction to detection was not more than 60 min. CONCLUSION The method developed for rapid detection of plant pathogens includes DNA extraction with magnetic beads or rapid DNA extraction, isothermal nucleic acid amplification at 39 °C, CRISPR-Cas12a cleavage reaction at 37 °C, and lateral flow assay or endpoint fluorescence visualization at room temperature. The RPA and CRISPR-Cas12a reagents can be preloaded in the microcentrifuge tube to simplify the procedures in the field. Both RPA and CRISPR-Cas12a reaction can be realized on a portable incubator, and the results are visualized using lateral flow strips or portable flashlight. This method requires minimal equipment and operator training, and has promising applications for rapid on-site disease screening, port inspection, or controlling fungal pathogen transmission in crop. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiwen Sun
- Chinese Academy of Inspection and Quarantine, Beijing, China
- Shenyang Agricultural University, Shenyang, China
| | - Rong Lei
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | | | - Wujian Chen
- Technical Center of Hangzhou Customs, Hangzhou, China
| | - Qianwen Jia
- School of Life and Health, Dalian University, Dalian, China
| | - Xing Guo
- School of Life and Health, Dalian University, Dalian, China
| | - Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Pinshan Wu
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xinyi Wang
- School of Life and Health, Dalian University, Dalian, China
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Mena E, Reboledo G, Stewart S, Montesano M, Ponce de León I. Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance against Diaporthe caulivora. Sci Rep 2023; 13:13061. [PMID: 37567886 PMCID: PMC10421924 DOI: 10.1038/s41598-023-39695-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Soybean stem canker (SSC) caused by the fungal pathogen Diaporthe caulivora is an important disease affecting soybean production worldwide. However, limited information related to the molecular mechanisms underlying soybean resistance to Diaporthe species is available. In the present work, we analyzed the defense responses to D. caulivora in the soybean genotypes Williams and Génesis 5601. The results showed that compared to Williams, Génesis 5601 is more resistant to fungal infection evidenced by significantly smaller lesion length, reduced disease severity and pathogen biomass. Transcriptional profiling was performed in untreated plants and in D. caulivora-inoculated and control-treated tissues at 8 and 48 h post inoculation (hpi). In total, 2.322 and 1.855 genes were differentially expressed in Génesis 5601 and Williams, respectively. Interestingly, Génesis 5601 exhibited a significantly higher number of upregulated genes compared to Williams at 8 hpi, 1.028 versus 434 genes. Resistance to D. caulivora was associated with defense activation through transcriptional reprogramming mediating perception of the pathogen by receptors, biosynthesis of phenylpropanoids, hormone signaling, small heat shock proteins and pathogenesis related (PR) genes. These findings provide novel insights into soybean defense mechanisms leading to host resistance against D. caulivora, and generate a foundation for the development of resistant SSC varieties within soybean breeding programs.
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Affiliation(s)
- Eilyn Mena
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Silvina Stewart
- Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay
| | - Marcos Montesano
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Laboratorio de Fisiología Vegetal, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Inés Ponce de León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
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Petrović K, Šućur Elez J, Crnković M, Krsmanović S, Rajković M, Kuzmanović B, Malenčić Đ. The Biochemical Response of Soybean Cultivars Infected by Diaporthe Species Complex. PLANTS (BASEL, SWITZERLAND) 2023; 12:2896. [PMID: 37631108 PMCID: PMC10457839 DOI: 10.3390/plants12162896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023]
Abstract
Oxidative stress in soybean plants infected with Diaporthe isolates was evaluated in order to select (1) the least aggressive inoculation method, (2) to determine the most aggressive Diaporthe isolate, and (3) to determine the most tolerant soybean cultivar to this isolate. Based on the present malondialdehyde (MDA) content, the main end product of the lipid peroxidation process, and the biomarker for oxidative stress, the mycelium contact method was chosen as the least aggressive inoculation method, compared to the toothpick method and plug method. The activity of the antioxidant enzymes (superoxide-dismutase (SOD), catalase (CAT), and peroxidase (PX)), the reduced glutathione (GSH) content, and the level of lipid peroxidation (LP) were measured in soybean cv. Sava infected by five different Diaporthe species (DPM1F-D. aspalathi, DPC/KR19-D. caulivora, DPC004NY15-D. eres, 18-DIA-SOY-14-D. gulyae, and PL157A-D. longicolla). The most pathogenic Diaporthe species to cv. Sava was D. eres. The screening of the antioxidant enzymes activity in the leaves of 12 different soybean cultivars (Altona, Atlas, Capital, Chico, CX134, Favorit, Lakota, McCall, Morsoy, Strain, Rubin, and Victoria) infected with D. eres by the mycelium contact inoculation method showed that Capital, McCall, and Morsoy were the cultivars with the highest tolerance to D. eres, followed by Chico, Favorit, Lakota, and Rubin. The most sensitive cultivars were Atlas, CX134, Victoria, and Strain.
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Affiliation(s)
- Kristina Petrović
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, 21000 Novi Sad, Serbia; (K.P.); (S.K.); (M.R.)
- Breeding Department, Maize Research Institute, 11185 Belgrade, Serbia
- BioSense Institute, University of Novi Sad, 21101 Novi Sad, Serbia
| | - Jovana Šućur Elez
- Department of Field and Vegetable Crops, Faculty of Agriculture, University of Novi Sad, 21000 Novi Sad, Serbia; (M.C.); (B.K.); (Đ.M.)
| | - Marina Crnković
- Department of Field and Vegetable Crops, Faculty of Agriculture, University of Novi Sad, 21000 Novi Sad, Serbia; (M.C.); (B.K.); (Đ.M.)
| | - Slobodan Krsmanović
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, 21000 Novi Sad, Serbia; (K.P.); (S.K.); (M.R.)
- Sector for Plant Nutrition, Agromarket BiH, 76300 Bijeljina, Bosnia and Herzegovina
| | - Miloš Rajković
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, 21000 Novi Sad, Serbia; (K.P.); (S.K.); (M.R.)
- Department for Research and Development in Agriculture, Institute of Medicinal Plant Research “Dr. Josif Pančić”, 11000 Belgrade, Serbia
| | - Boris Kuzmanović
- Department of Field and Vegetable Crops, Faculty of Agriculture, University of Novi Sad, 21000 Novi Sad, Serbia; (M.C.); (B.K.); (Đ.M.)
| | - Đorđe Malenčić
- Department of Field and Vegetable Crops, Faculty of Agriculture, University of Novi Sad, 21000 Novi Sad, Serbia; (M.C.); (B.K.); (Đ.M.)
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The genome of a Far Eastern isolate of Diaporthe caulivora, a soybean fungal pathogen. Appl Microbiol Biotechnol 2023; 107:1311-1327. [PMID: 36650392 DOI: 10.1007/s00253-023-12370-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/26/2022] [Accepted: 12/31/2022] [Indexed: 01/19/2023]
Abstract
Diaporthe caulivora is an economically important fungal pathogen and a causal agent of soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of D. caulivora was sequenced, assembled, and announced. Assembly quality was enough for advanced annotation, including prediction of potential disease-related genes encoding virulence factors and molecular determinants contributing to pathogen-host selection, interactions, and adaptation. Comparative analysis of 15 Diaporthe species was conducted regarding general genome properties, collinearity, and proteomes, and included detailed investigation of interspersed repeats. A notable feature of this analysis is a high recombinant variability of Diaporthe genomes, determined by the number and distribution of interspersed repeats, which also proved to be responsible for the diversity of GC content and genome size. This variability is assumed the main determinant of the divergence of Diaporthe genomes. A Bayesian multi-gene phylogeny was inferred for the 15 Diaporthe species on the basis of twenty thousand polymorphic sites of > 100 orthologous genes using independently adjusted evolutionary models. This allowed for the most accurate determination of evolutionary relationships and species boundaries for effective reporting about these plant pathogens. The evidence, obtained by different genome analysis techniques, implies the host-independent evolution of Diaporthe species. KEY POINTS: • The genome of a Far Eastern isolate of D. caulivora was announced. • A high degree of recombinant variability determines genomic divergence in Diaporthe genus. • The multi-gene phylogeny implies host-independent evolution of Diaporthe species.
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Zhao X, Li K, Zheng S, Yang J, Chen C, Zheng X, Wang Y, Ye W. Diaporthe Diversity and Pathogenicity Revealed from a Broad Survey of Soybean Stem Blight in China. PLANT DISEASE 2022; 106:2892-2903. [PMID: 35412334 DOI: 10.1094/pdis-12-21-2785-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Many species in the fungal Diaporthe (anamorph Phomopsis) genus have become a group of the most important pathogens that cause seed decay, stem and pot blight, and stem canker in soybean production worldwide, resulting in significant yield loss. Due to increased disease prevalence but a lack of research, we performed an extensive field survey to isolate and identify the Diaporthe species associated with soybean stem blight in six provinces of China between 2019 and 2020. A total of 92 Diaporthe isolates were identified based on morphological and multilocus phylogenetic analysis and classified into six species: D. longicolla, D. unshiuensis, D. sojae, D. caulivora, D. tectonigena, and an unknown Diaporthe sp. The most frequently identified species was D. longicolla with 57 isolates. High genetic diversity was observed for the D. longicolla isolates, and haplotype network analysis revealed a mixed structure among the population in the six provinces. In comparative pathogenicity assays, different virulence levels were observed among the 92 Diaporthe isolates. The results of this study provide new insights into the Diaporthe spp. associated with soybean stem blight in China and can help in the development of effective management strategies.
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Affiliation(s)
- Xiaolin Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kainan Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Sujiao Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jin Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Changjun Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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Lin F, Chhapekar SS, Vieira CC, Da Silva MP, Rojas A, Lee D, Liu N, Pardo EM, Lee YC, Dong Z, Pinheiro JB, Ploper LD, Rupe J, Chen P, Wang D, Nguyen HT. Breeding for disease resistance in soybean: a global perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3773-3872. [PMID: 35790543 PMCID: PMC9729162 DOI: 10.1007/s00122-022-04101-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/11/2022] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.
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Affiliation(s)
- Feng Lin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Sushil Satish Chhapekar
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Caio Canella Vieira
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Marcos Paulo Da Silva
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Dongho Lee
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Nianxi Liu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Esteban Mariano Pardo
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - Yi-Chen Lee
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Zhimin Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Jose Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ/USP), PO Box 9, Piracicaba, SP 13418-900 Brazil
| | - Leonardo Daniel Ploper
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - John Rupe
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Pengyin Chen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
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Mena E, Garaycochea S, Stewart S, Montesano M, Ponce De León I. Comparative genomics of plant pathogenic Diaporthe species and transcriptomics of Diaporthe caulivora during host infection reveal insights into pathogenic strategies of the genus. BMC Genomics 2022; 23:175. [PMID: 35240994 PMCID: PMC8896106 DOI: 10.1186/s12864-022-08413-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Background Diaporthe caulivora is a fungal pathogen causing stem canker in soybean worldwide. The generation of genomic and transcriptomic information of this ascomycete, together with a comparative genomic approach with other pathogens of this genus, will contribute to get insights into the molecular basis of pathogenicity strategies used by D. caulivora and other Diaporthe species. Results In the present work, the nuclear genome of D. caulivora isolate (D57) was resolved, and a comprehensive annotation based on gene expression and genomic analysis is provided. Diaporthe caulivora D57 has an estimated size of 57,86 Mb and contains 18,385 predicted protein-coding genes, from which 1501 encode predicted secreted proteins. A large array of D. caulivora genes encoding secreted pathogenicity-related proteins was identified, including carbohydrate-active enzymes (CAZymes), necrosis-inducing proteins, oxidoreductases, proteases and effector candidates. Comparative genomics with other plant pathogenic Diaporthe species revealed a core secretome present in all Diaporthe species as well as Diaporthe-specific and D. caulivora-specific secreted proteins. Transcriptional profiling during early soybean infection stages showed differential expression of 2659 D. caulivora genes. Expression patterns of upregulated genes and gene ontology enrichment analysis revealed that host infection strategies depends on plant cell wall degradation and modification, detoxification of compounds, transporter activities and toxin production. Increased expression of effectors candidates suggests that D. caulivora pathogenicity also rely on plant defense evasion. A high proportion of the upregulated genes correspond to the core secretome and are represented in the pathogen-host interaction (PHI) database, which is consistent with their potential roles in pathogenic strategies of the genus Diaporthe. Conclusions Our findings give novel and relevant insights into the molecular traits involved in pathogenicity of D. caulivora towards soybean plants. Some of these traits are in common with other Diaporthe pathogens with different host specificity, while others are species-specific. Our analyses also highlight the importance to have a deeper understanding of pathogenicity functions among Diaporthe pathogens and their interference with plant defense activation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08413-y.
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Affiliation(s)
- Eilyn Mena
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, CP 11600, Montevideo, Uruguay
| | - Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Las Brujas, Ruta 48 Km 10, Canelones, Uruguay
| | - Silvina Stewart
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa Cultivos de Secano, Estación Experimental La Estanzuela, Ruta 50 km 11, 70000, Colonia, Uruguay
| | - Marcos Montesano
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, CP 11600, Montevideo, Uruguay.,Laboratorio de Fisiología Vegetal, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, CP 11400, Montevideo, Uruguay
| | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, CP 11600, Montevideo, Uruguay.
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Ferreira EGC, Marcelino-Guimarães FC. Mapping Major Disease Resistance Genes in Soybean by Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:313-340. [PMID: 35641772 DOI: 10.1007/978-1-0716-2237-7_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soybean is one of the most valuable agricultural crops in the world. Besides, this legume is constantly attacked by a wide range of pathogens (fungi, bacteria, viruses, and nematodes) compromising yield and increasing production costs. One of the major disease management strategies is the genetic resistance provided by single genes and quantitative trait loci (QTL). Identifying the genomic regions underlying the resistance against these pathogens on soybean is one of the first steps performed by molecular breeders. In the past, genetic mapping studies have been widely used to discover these genomic regions. However, over the last decade, advances in next-generation sequencing technologies and their subsequent cost decreasing led to the development of cost-effective approaches to high-throughput genotyping. Thus, genome-wide association studies applying thousands of SNPs in large sets composed of diverse soybean accessions have been successfully done. In this chapter, a comprehensive review of the majority of GWAS for soybean diseases published since this approach was developed is provided. Important diseases caused by Heterodera glycines, Phytophthora sojae, and Sclerotinia sclerotiorum have been the focus of the several GWAS. However, other bacterial and fungi diseases also have been targets of GWAS. As such, this GWAS summary can serve as a guide for future studies of these diseases. The protocol begins by describing several considerations about the pathogens and bringing different procedures of molecular characterization of them. Advice to choose the best isolate/race to maximize the discovery of multiple R genes or to directly map an effective R gene is provided. A summary of protocols, methods, and tools to phenotyping the soybean panel is given to several diseases. We also give details of options of DNA extraction protocols and genotyping methods, and we describe parameters of SNP quality to soybean data. Websites and their online tools to obtain genotypic and phenotypic data for thousands of soybean accessions are highlighted. Finally, we report several tricks and tips in Subheading 4, especially related to composing the soybean panel as well as generating and analyzing the phenotype data. We hope this protocol will be helpful to achieve GWAS success in identifying resistance genes on soybean.
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K N, Dubey SC, Kamil D. Diversity analysis of different Diaporthe ( Phomopsis) species and development of molecular marker to identify quarantine important species Phomopsis phaseolorum. 3 Biotech 2022; 12:31. [PMID: 35070621 PMCID: PMC8714617 DOI: 10.1007/s13205-021-03075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 10/09/2021] [Indexed: 01/03/2023] Open
Abstract
The genus Diaporthe Nitschke (Phomopsis Sacc. & Harter) infect various agricultural and horticultural important crops and cause diseases such as damping off, leaf spots, blights, canker, dieback, wilt, root and fruit rots. P. vexans, P. helianthi and P. phaseolorum are the important species within genus causing huge yield and economic loss. Being primarily seed borne it also hinders import and export of germplasm and seeds. Therefore, extensive characterization is required to diagnose and manage the disease. Seventeen isolates collected from ITCC, IARI and ICAR-NBPGR belonging to eight species were morphological and molecularly characterized and diversity was analyzed. Several morphological and cultural characters were studied and analyzed. Due to lack of sufficient morphological variation to identify/differentiate species, molecular characterization using house-keeping genes, internal transcriber spacer (ITS) was carried out. ITS produced amplicon of ~ 600 bp in the isolates of Phomopsis and phylogenetic tree obtained revealed that isolates of a species belonging same geographic region had more sequence similarity than isolates belonging to different geographic regions this might be due to population adaption under varied environments. Development of EF-1alpha-based marker specific to P. phaseolorum helps in easily detection of pathogen in quarantine stations. In addition, species of Phomopsis were previously named based on host association which has led to misidentification and proliferation of species. Cross pathogenicity of isolates on three important hosts, brinjal, soybean and chilli revealed its broad host range and naming only basis of host association is unjustified.
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Affiliation(s)
- Nishmitha K
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Deeba Kamil
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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10
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Pérez-Pizá MC, Grijalba PE, Cejas E, Chamorro Garcés JC, Ferreyra M, Zilli C, Vallecorsa P, Santa-Cruz D, Yannarelli G, Prevosto L, Balestrasse K. Effects of non-thermal plasma technology on Diaporthe longicolla cultures and mechanisms involved. PEST MANAGEMENT SCIENCE 2021; 77:2068-2077. [PMID: 33342044 DOI: 10.1002/ps.6234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 12/09/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The Diaporthe/Phomopsis complex (D/P) is a group of soybean seed-borne fungi. The use of chemical fungicides, either for seed treatment or during the crop cycle, is the most adopted practice for treating fungal diseases caused by this complex. Worldwide, there is a search for alternative seed treatments that are less harmful to the environment than chemicals. Non-thermal plasma (NTP) is a novel seed treatment technology for pathogen removal. This research aimed to evaluate the effects of NTP on the in vitro performance of pure cultures of Diaporthe longicolla and elucidate the mechanisms underlying these effects. RESULTS Active D. longicolla mycelium, growing in vitro, was exposed to different NTP treatments, employing a dielectric barrier discharge arrangement with different carrier gases (N2 or O2 ). Fungal growth, fresh biomass and colony appearance were negatively affected by plasma treatments (TN3 and TO3). Lipid peroxidation and antioxidant activities were higher in plasma-treated colonies comparison with non-exposed colonies (control). Fungal asexual spores (conidia) were also exposed to NTP, showing high susceptibility. CONCLUSION Exposure of D. longicolla colonies to NTP severely compromised fungal biology. Ozone production during treatment and lipid peroxidation of fungal cell membranes appeared to be involved in the observed effects. © 2020 Society of Chemical Industry.
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Affiliation(s)
- María C Pérez-Pizá
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Facultad de Agronomía, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo E Grijalba
- Cátedra de Fitopatología, Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires, Facultad de Agronomía, Buenos Aires, Argentina
| | - Ezequiel Cejas
- Departamento de Ingeniería Electromecánica, Grupo de Descargas Eléctricas, Facultad Regional Venado Tuerto, Universidad Tecnológica Nacional, CONICET, Venado Tuerto, Argentina
| | - Juan C Chamorro Garcés
- Departamento de Ingeniería Electromecánica, Grupo de Descargas Eléctricas, Facultad Regional Venado Tuerto, Universidad Tecnológica Nacional, CONICET, Venado Tuerto, Argentina
| | - Matías Ferreyra
- Departamento de Ingeniería Electromecánica, Grupo de Descargas Eléctricas, Facultad Regional Venado Tuerto, Universidad Tecnológica Nacional, CONICET, Venado Tuerto, Argentina
| | - Carla Zilli
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Facultad de Agronomía, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo Vallecorsa
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Facultad de Agronomía, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Santa-Cruz
- Laboratorio de Regulación Génica y Células Madre, Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMeTTyB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Gustavo Yannarelli
- Laboratorio de Regulación Génica y Células Madre, Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMeTTyB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Leandro Prevosto
- Departamento de Ingeniería Electromecánica, Grupo de Descargas Eléctricas, Facultad Regional Venado Tuerto, Universidad Tecnológica Nacional, CONICET, Venado Tuerto, Argentina
| | - Karina Balestrasse
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Facultad de Agronomía, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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11
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Huda-Shakirah AR, Kee YJ, Wong KL, Zakaria L, Mohd MH. Diaporthe species causing stem gray blight of red-fleshed dragon fruit (Hylocereus polyrhizus) in Malaysia. Sci Rep 2021; 11:3907. [PMID: 33594187 PMCID: PMC7887222 DOI: 10.1038/s41598-021-83551-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
This study aimed to characterize the new fungal disease on the stem of red-fleshed dragon fruit (Hylocereus polyrhizus) in Malaysia, which is known as gray blight through morphological, molecular and pathogenicity analyses. Nine fungal isolates were isolated from nine blighted stems of H. polyrhizus. Based on morphological characteristics, DNA sequences and phylogeny (ITS, TEF1-α, and β-tubulin), the fungal isolates were identified as Diaporthe arecae, D. eugeniae, D. hongkongensis, D. phaseolorum, and D. tectonendophytica. Six isolates recovered from the Cameron Highlands, Pahang belonged to D. eugeniae (DF1 and DF3), D. hongkongensis (DF9), D. phaseolorum (DF2 and DF12), and D. tectonendophytica (DF7), whereas three isolates from Bukit Kor, Terengganu were recognized as D. arecae (DFP3), D. eugeniae (DFP4), and D. tectonendophytica (DFP2). Diaporthe eugeniae and D. tectonendophytica were found in both Pahang and Terengganu, D. phaseolorum and D. hongkongensis in Pahang, whereas D. arecae only in Terengganu. The role of the Diaporthe isolates in causing stem gray blight of H. polyrhizus was confirmed. To date, only D. phaseolorum has been previously reported on Hylocereus undatus. This is the first report on D. arecae, D. eugeniae, D. hongkongensis, D. phaseolorum, and D. tectonendophytica causing stem gray blight of H. polyrhizus worldwide.
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Affiliation(s)
| | - Yee Jia Kee
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Kak Leong Wong
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Latiffah Zakaria
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Masratul Hawa Mohd
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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12
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Książkiewicz M, Rychel-Bielska S, Plewiński P, Nuc M, Irzykowski W, Jędryczka M, Krajewski P. The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes. Int J Mol Sci 2021; 22:ijms22020574. [PMID: 33430123 PMCID: PMC7827158 DOI: 10.3390/ijms22020574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 01/10/2023] Open
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) is a grain legume crop that is advantageous in animal nutrition due to its high protein content; however, livestock grazing on stubble may develop a lupinosis disease that is related to toxins produced by a pathogenic fungus, Diaporthe toxica. Two major unlinked alleles, Phr1 and PhtjR, confer L. angustifolius resistance to this fungus. Besides the introduction of these alleles into modern cultivars, the molecular mechanisms underlying resistance remained unsolved. In this study, resistant and susceptible lines were subjected to differential gene expression profiling in response to D. toxica inoculation, spanning the progress of the infection from the early to latent phases. High-throughput sequencing of stem transcriptome and PCR quantification of selected genes were performed. Gene Ontology term analysis revealed that an early (24 h) response in the resistant germplasm encompassed activation of genes controlling reactive oxygen species and oxylipin biosynthesis, whereas in the susceptible germplasm, it comprised induction of xyloglucan endotransglucosylases/hydrolases. During the first five days of the infection, the number of genes with significantly altered expressions was about 2.6 times higher in resistant lines than in the susceptible line. Global transcriptome reprogramming involving the activation of defense response genes occurred in lines conferring Phr1 and PhtjR resistance alleles about 4–8 days earlier than in the susceptible germplasm.
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Affiliation(s)
- Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (S.R.-B.); (P.P.)
- Correspondence: ; Tel.: +48-616-550-268
| | - Sandra Rychel-Bielska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (S.R.-B.); (P.P.)
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, 50-363 Wrocław, Poland
| | - Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (S.R.-B.); (P.P.)
| | - Maria Nuc
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (M.N.); (P.K.)
| | - Witold Irzykowski
- Department of Pathogen Genetics and Plant Resistance, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (W.I.); (M.J.)
| | - Małgorzata Jędryczka
- Department of Pathogen Genetics and Plant Resistance, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (W.I.); (M.J.)
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (M.N.); (P.K.)
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13
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Mena E, Stewart S, Montesano M, Ponce de León I. Soybean Stem Canker Caused by Diaporthe caulivora; Pathogen Diversity, Colonization Process, and Plant Defense Activation. FRONTIERS IN PLANT SCIENCE 2020; 10:1733. [PMID: 32117332 PMCID: PMC7011206 DOI: 10.3389/fpls.2019.01733] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 12/09/2019] [Indexed: 05/31/2023]
Abstract
Soybean is an important crop in South America, and its production is limited by fungal diseases caused by species from the genus Diaporthe, including seed decay, pod and stem blight, and soybean stem canker (SSC). In this study, we focused on Diaporthe species isolated from soybean plants with SSC lesions in different parts of Uruguay. Diaporthe diversity was determined by sequencing the internal transcribed spacer (ITS) regions of ribosomal RNA and a partial region of the translation elongation factor 1-alpha gene (TEF1α). Phylogenetic analysis showed that the isolates belong to five defined groups of Diaporthe species, Diaporthe caulivora and Diaporthe longicolla being the most predominant species present in stem canker lesions. Due to the importance of D. caulivora as the causal agent of SSC in the region and other parts of the world, we further characterized the interaction of this pathogen with soybean. Based on genetic diversity of D. caulivora isolates evaluated with inter-sequence single repetition (ISSR), three different isolates were selected for pathogenicity assays. Differences in virulence were observed among the selected D. caulivora isolates on susceptible soybean plants. Further inspection of the infection and colonization process showed that D. caulivora hyphae are associated with trichomes in petioles, leaves, and stems, acting probably as physical adhesion sites of the hyphae. D. caulivora colonized the stem rapidly reaching the phloem and the xylem at 72 h post-inoculation (hpi), and after 96 hpi, the stem was heavily colonized. Infected soybean plants induce reinforcement of the cell walls, evidenced by incorporation of phenolic compounds. In addition, several defense genes were induced in D. caulivora-inoculated stems, including those encoding a pathogenesis-related protein-1 (PR-1), a PR-10, a β-1,3-glucanase, two chitinases, two lipoxygenases, a basic peroxidase, a defensin, a phenylalanine-ammonia lyase, and a chalcone synthase. This study provides new insights into the interaction of soybean with D. caulivora, an important pathogen causing SSC, and provides information on the activation of plant defense responses.
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Affiliation(s)
- Eilyn Mena
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Silvina Stewart
- Sección Protección Vegetal, Instituto Nacional de Investigación Agropecuaria, La Estanzuela, Uruguay
| | - Marcos Montesano
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Laboratorio de Fisiología Vegetal, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Inés Ponce de León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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14
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Maldonado dos Santos JV, Ferreira EGC, Passianotto ALDL, Brumer BB, Santos ABD, Soares RM, Torkamaneh D, Arias CAA, Belzile F, Abdelnoor RV, Marcelino-Guimarães FC. Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development. BMC Genomics 2019; 20:798. [PMID: 31672122 PMCID: PMC6824049 DOI: 10.1186/s12864-019-6139-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/25/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. RESULTS We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. CONCLUSIONS Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.
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Affiliation(s)
- João Vitor Maldonado dos Santos
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
| | | | - André Luiz de Lima Passianotto
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
- Present address: Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2V7 Canada
| | - Bruna Bley Brumer
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
| | - Adriana Brombini Dos Santos
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
| | - Rafael Moreira Soares
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
| | - Davoud Torkamaneh
- Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, G1V 0A6 Canada
| | - Carlos Alberto Arrabal Arias
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
| | - François Belzile
- Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, G1V 0A6 Canada
| | - Ricardo Vilela Abdelnoor
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
| | - Francismar Corrêa Marcelino-Guimarães
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
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15
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Ghimire K, Petrović K, Kontz BJ, Bradley CA, Chilvers MI, Mueller DS, Smith DL, Wise KA, Mathew FM. Inoculation Method Impacts Symptom Development Associated with Diaporthe aspalathi, D. caulivora, and D. longicolla on Soybean (Glycine max). PLANT DISEASE 2019; 103:677-684. [PMID: 30742552 DOI: 10.1094/pdis-06-18-1078-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
One hundred fifty-two Diaporthe isolates were recovered from symptomatic soybean (Glycine max) stems sampled from the U.S. states of Iowa, Indiana, Kentucky, Michigan, and South Dakota. Using morphology and DNA sequencing, isolates were identified as D. aspalathi (8.6%), D. caulivora (24.3%), and D. longicolla (67.1%). Aggressiveness of five isolates each of the three pathogens was studied on cultivars Hawkeye (D. caulivora and D. longicolla) and Bragg (D. aspalathi) using toothpick, stem-wound, mycelium contact, and spore injection inoculation methods in the greenhouse. For D. aspalathi, methods significantly affected disease severity (P < 0.001) and pathogen recovery (P < 0.001). The relative treatment effects (RTE) of stem-wound and toothpick methods were significantly greater than for the other methods. For D. caulivora and D. longicolla, a significant isolate × method interaction affected disease severity (P < 0.05) and pathogen recovery (P < 0.001). Significant differences in RTEs were observed among D. caulivora and D. longicolla isolates only when the stem-wound and toothpick methods were used. Our study has determined that the stem-wound and toothpick methods are reliable to evaluate the three pathogens; however, the significant isolate × method interactions for D. caulivora and D. longicolla indicate that multiple isolates should also be considered for future pathogenicity studies.
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Affiliation(s)
- Krishna Ghimire
- 1 Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
| | - Kristina Petrović
- 1 Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
- 2 Institute of Field and Vegetable Crops, Department of Soybean, Maksima Gorkog 30, Novi Sad 21000, Serbia
| | - Brian J Kontz
- 1 Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
| | - Carl A Bradley
- 3 Department of Plant Pathology, University of Kentucky Research and Education Center, Princeton, KY 42445, U.S.A
| | - Martin I Chilvers
- 4 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Daren S Mueller
- 5 Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Damon L Smith
- 6 Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A.; and
| | - Kiersten A Wise
- 7 Department of Botany and Plant Pathology, West Lafayette, IN 47907, U.S.A
| | - Febina M Mathew
- 1 Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
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16
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Dos Santos TT, de Souza Leite T, de Queiroz CB, de Araújo EF, Pereira OL, de Queiroz MV. High genetic variability in endophytic fungi from the genus Diaporthe isolated from common bean (Phaseolus vulgaris L.) in Brazil. J Appl Microbiol 2016; 120:388-401. [PMID: 26541097 DOI: 10.1111/jam.12985] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/26/2015] [Accepted: 09/07/2015] [Indexed: 01/11/2023]
Abstract
AIMS The goals of the present study were to identify, to analyse the phylogenetic relations and to evaluate the genetic variability in Diaporthe endophytic isolates from common bean. METHODS AND RESULTS Diaporthe sp., D. infecunda and D. phaseolorum strains were identified using multilocus phylogeny (rDNA ITS region; EF1-α, β-tubulin, and calmodulin genes). IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) molecular markers reveal the existence of high genetic variability, especially among D. infecunda isolates. CONCLUSIONS It was concluded that the multilocus phylogenetic approach was more effective than individual analysis of ITS sequences, in identifying the isolates to species level, and that IRAP and REMAP markers can be used for studying the genetic variability in the genus Diaporthe particularly at the intraspecific level. SIGNIFICANCE AND IMPACT OF THE STUDY The combined use of molecular tools such as multilocus phylogenetic approach and molecular markers, as performed in this study, is the best way to distinguish endophytic strains of Diaporthe isolated from common bean (Phaseolus vulgaris L.).
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Affiliation(s)
- T T Dos Santos
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil.,Instituto de Ciências e Tecnologia das Águas, Universidade Federal do Oeste do Pará, Santarém, Brazil
| | - T de Souza Leite
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - C B de Queiroz
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - E F de Araújo
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - O L Pereira
- Department of Phytopathology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - M V de Queiroz
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
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17
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Chang HX, Lipka AE, Domier LL, Hartman GL. Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies. PHYTOPATHOLOGY 2016; 106:1139-1151. [PMID: 27135674 DOI: 10.1094/phyto-01-16-0042-fi] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Genetic resistance is a key strategy for disease management in soybean. Over the last 50 years, soybean germplasm has been phenotyped for resistance to many pathogens, resulting in the development of disease-resistant elite breeding lines and commercial cultivars. While biparental linkage mapping has been used to identify disease resistance loci, genome-wide association studies (GWAS) using high-density and high-quality markers such as single nucleotide polymorphisms (SNPs) has become a powerful tool to associate molecular markers and phenotypes. The objective of our study was to provide a comprehensive understanding of disease resistance in the United States Department of Agriculture Agricultural Research Service Soybean Germplasm Collection by using phenotypic data in the public Germplasm Resources Information Network and public SNP data (SoySNP50K). We identified SNPs significantly associated with disease ratings from one bacterial disease, five fungal diseases, two diseases caused by nematodes, and three viral diseases. We show that leucine-rich repeat (LRR) receptor-like kinases and nucleotide-binding site-LRR candidate resistance genes were enriched within the linkage disequilibrium regions of the significant SNPs. We review and present a global view of soybean resistance loci against multiple diseases and discuss the power and the challenges of using GWAS to discover disease resistance in soybean.
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Affiliation(s)
- Hao-Xun Chang
- All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana
| | - Alexander E Lipka
- All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana
| | - Leslie L Domier
- All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana
| | - Glen L Hartman
- All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana
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18
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Sun S, Kim MY, Van K, Lee YW, Li B, Lee SH. QTLs for resistance to Phomopsis seed decay are associated with days to maturity in soybean (Glycine max). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2029-38. [PMID: 23702513 DOI: 10.1007/s00122-013-2115-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 05/08/2013] [Indexed: 05/28/2023]
Abstract
Phomopsis seed decay (PSD), primarily caused by Phomopsis longicolla, is a major contributor to poor soybean seed quality and significant yield loss, particularly in early maturing soybean genotypes. However, it is not yet known whether PSD resistance is associated with early maturity. This study was conducted to identify quantitative trait loci (QTLs) for resistance to PSD and days to maturity using a recombinant inbred line (RIL) population derived from a cross between the PSD-resistant Taekwangkong and the PSD-susceptible SS2-2. Based on a genetic linkage map incorporating 117 simple sequence repeat markers, QTL analysis revealed two and three QTLs conferring PSD resistance and days to maturity, respectively, in the RIL population. Two QTLs (PSD-6-1 and PSD-10-2) for PSD resistance were identified in the intervals of Satt100-Satt460 and Sat_038-Satt243 on chromosomes 6 and 10, respectively. Two QTLs explained phenotypic variances in PSD resistance of 46.3 and 14.1 %, respectively. At the PSD-6-1 QTL, the PSD-resistant cultivar Taekwangkong contributed the allele with negative effect decreasing the infection rate of PSD and this QTL does not overlap with any previously reported loci for PSD resistance in other soybean genotypes. Among the three QTLs for days to maturity, two (Mat-6-2 and Mat-10-3) were located at positions similar to the PSD-resistance QTLs. The identification of the QTLs linked to both PSD resistance and days to maturity indicates a biological correlation between these two traits. The newly identified QTL for resistance to PSD associated with days to maturity in Taekwangkong will help improve soybean resistance to P. longicolla.
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Affiliation(s)
- Suli Sun
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul, The Republic of Korea
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Schilder AMC, Erincik O, Castlebury L, Rossman A, Ellis MA. Characterization of Phomopsis spp. Infecting Grapevines in the Great Lakes Region of North America. PLANT DISEASE 2005; 89:755-762. [PMID: 30791247 DOI: 10.1094/pd-89-0755] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Seventy-five isolates of Phomopsis were obtained from grapes (Vitis spp.) with Phomopsis cane and leaf spot symptoms in Ohio, Michigan, New York, Pennsylvania, Maryland, and Ontario (Canada). Four isolates from California and one from Europe were also included in the study. Isolates were grouped on the basis of DNA sequences from intron regions in the translation elongation factor 1-α and calmodulin genes. According to DNA sequence comparisons with the type isolate, all isolates except two (OH-48 and CAL-5) were determined to be P. viticola, confirming the etiology of this disease in the Great Lakes region. Thirty representative isolates were evaluated for mycelial growth rate in vitro, conidial size, and pathogenicity on grapevine (Vitis interspecific hybrid 'Seyval') leaves and internodes. A subsample of 13 isolates was also evaluated for pathogenicity on fruit and rachises. All isolates of P. viticola caused disease on grape but differed in virulence. Among P. viticola isolates, virulence on leaves and internodes was positively correlated, and virulence on fruit and rachises was positively correlated, but there was no relationship between ratings on vegetative versus reproductive grape tissues. Some isolates that were not virulent on leaves or internodes were highly virulent on fruit and rachises and vice versa, indicating some specialization with respect to host tissues. However, differences were mostly of a quantitative nature, which makes it difficult if not impossible to assign biotypes. Among P. viticola isolates, virulence on fruit and rachises was positively correlated with mycelial growth rate in vitro. For the two isolates that were not P. viticola, the internal transcribed spacer regions of the nuclear ribosomal DNA were sequenced for identification purposes. Based on the best match available in GenBank, CAL-5 was determined to be close to Diaporthe phaseolorum, while the sequence of OH-48 matched that of Phomopsis sp. from Eucommia ulmoides in China. Both isolates had shorter alpha conidia and significantly higher mycelial growth rates than the P. viticola isolates, and were not or only slightly pathogenic to Vitis interspecific hybrid 'Seyval'.
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Affiliation(s)
- A M C Schilder
- Department of Plant Pathology, Michigan State University, East Lansing 48824
| | - O Erincik
- Department of Plant Pathology, Ohio State University, Wooster 44691
| | - L Castlebury
- Systemic Botany and Mycology, USDA-ARS, Beltsville, MD 20705
| | - A Rossman
- Systemic Botany and Mycology, USDA-ARS, Beltsville, MD 20705
| | - M A Ellis
- Department of Plant Pathology, Ohio State University, Wooster 44691
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Svetaz L, Tapia A, López SN, Furlán RLE, Petenatti E, Pioli R, Schmeda-Hirschmann G, Zacchino SA. Antifungal chalcones and new caffeic acid esters from Zuccagnia punctata acting against soybean infecting fungi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2004; 52:3297-300. [PMID: 15161186 DOI: 10.1021/jf035213x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The crude methanolic extract of Zuccagnia punctata was active toward the fungal pathogens of soybean Phomopsis longicolla and Colletotrichum truncatum. Assay guided fractionation led to the isolation of two chalcones, one flavanone and a new caffeoyl ester derivative as the compounds responsible for the antifungal activity. Another new caffeoyl ester derivative was isolated from the antifungal chloroform extract but proved to be inactive against the soybean infecting fungi up to 50 microg/mL
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Affiliation(s)
- Laura Svetaz
- Pharmacognosy, School of Biochemical and Pharmaceutical Sciences, National University of Rosario, Suipacha 531, 2000-Rosario, Argentina
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