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Santhanam P, Labbé C, Tremblay V, Bélanger RR. A rapid molecular diagnostic tool to discriminate alleles of avirulence genes and haplotypes of Phytophthora sojae using high-resolution melting analysis. MOLECULAR PLANT PATHOLOGY 2024; 25:e13406. [PMID: 38009407 PMCID: PMC10799203 DOI: 10.1111/mpp.13406] [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: 04/29/2023] [Revised: 10/02/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023]
Abstract
Effectors encoded by avirulence genes (Avr) interact with the Phytophthora sojae resistance gene (Rps) products to generate incompatible interactions. The virulence profile of P. sojae is rapidly evolving as a result of the large-scale deployment of Rps genes in soybean. For a successful exploitation of Rps genes, it is recommended that soybean growers use cultivars containing the Rps genes corresponding to Avr genes present in P. sojae populations present in their fields. Determination of the virulence profile of P. sojae isolates is critical for the selection of soybean cultivars. High-resolution melting curve (HRM) analysis is a powerful tool, first applied in medicine, for detecting mutations with potential applications in different biological fields. Here, we report the development of an HRM protocol, as an original approach to discriminate effectors, to differentiate P. sojae haplotypes for six Avr genes. An HRM assay was performed on 24 P. sojae isolates with different haplotypes collected from soybean fields across Canada. The results clearly confirmed that the HRM assay discriminated different virulence genotypes. Moreover, the HRM assay was able to differentiate multiple haplotypes representing small allelic variations. HRM-based prediction was validated by phenotyping assays. This HRM assay provides a unique, cost-effective and efficient tool to predict virulence pathotypes associated with six different Avr (1b, 1c, 1d, 1k, 3a and 6) genes from P. sojae, which can be applied in the deployment of appropriate Rps genes in soybean fields.
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Affiliation(s)
- Parthasarathy Santhanam
- Département de PhytologieUniversité LavalQuebecQuebecCanada
- Present address:
Agriculture Agri‐Food Canada, MRDCMordenManitobaCanada
| | - Caroline Labbé
- Département de PhytologieUniversité LavalQuebecQuebecCanada
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2
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McCoy AG, Belanger RR, Bradley CA, Cerritos-Garcia DG, Garnica VC, Giesler LJ, Grijalba PE, Guillin E, Henriquez MA, Kim YM, Malvick DK, Matthiesen RL, Mideros SX, Noel ZA, Robertson AE, Roth MG, Schmidt CL, Smith DL, Sparks AH, Telenko DEP, Tremblay V, Wally O, Chilvers MI. A global-temporal analysis on Phytophthora sojae resistance-gene efficacy. Nat Commun 2023; 14:6043. [PMID: 37758723 PMCID: PMC10533513 DOI: 10.1038/s41467-023-41321-7] [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: 02/10/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Plant disease resistance genes are widely used in agriculture to reduce disease outbreaks and epidemics and ensure global food security. In soybean, Rps (Resistance to Phytophthora sojae) genes are used to manage Phytophthora sojae, a major oomycete pathogen that causes Phytophthora stem and root rot (PRR) worldwide. This study aims to identify temporal changes in P. sojae pathotype complexity, diversity, and Rps gene efficacy. Pathotype data was collected from 5121 isolates of P. sojae, derived from 29 surveys conducted between 1990 and 2019 across the United States, Argentina, Canada, and China. This systematic review shows a loss of efficacy of specific Rps genes utilized for disease management and a significant increase in the pathotype diversity of isolates over time. This study finds that the most widely deployed Rps genes used to manage PRR globally, Rps1a, Rps1c and Rps1k, are no longer effective for PRR management in the United States, Argentina, and Canada. This systematic review emphasizes the need to widely introduce new sources of resistance to P. sojae, such as Rps3a, Rps6, or Rps11, into commercial cultivars to effectively manage PRR going forward.
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Affiliation(s)
| | | | | | | | | | | | | | - Eduardo Guillin
- Instituto Nacional de Tecnologia Agropecuaria, Buenos Aires, Argentina
| | | | - Yong Min Kim
- Agriculture and Agri-Food Canada, Brandon, Manitoba, Canada
| | | | | | | | | | | | | | | | | | - Adam H Sparks
- Department of Primary Industries and Regional Development, Perth, WA, Australia
- University of Southern Queensland, Toowoomba, Qld, Australia
| | | | | | - Owen Wally
- Agriculture and Agri-Food Canada, Harrow, ON, Canada
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3
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Madina MH, Santhanam P, Asselin Y, Jaswal R, Bélanger RR. Progress and Challenges in Elucidating the Functional Role of Effectors in the Soybean- Phytophthora sojae Interaction. J Fungi (Basel) 2022; 9:12. [PMID: 36675833 PMCID: PMC9866111 DOI: 10.3390/jof9010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Phytophthora sojae, the agent responsible for stem and root rot, is one of the most damaging plant pathogens of soybean. To establish a compatible-interaction, P. sojae secretes a wide array of effector proteins into the host cell. These effectors have been shown to act either in the apoplastic area or the cytoplasm of the cell to manipulate the host cellular processes in favor of the development of the pathogen. Deciphering effector-plant interactions is important for understanding the role of P. sojae effectors in disease progression and developing approaches to prevent infection. Here, we review the subcellular localization, the host proteins, and the processes associated with P. sojae effectors. We also discuss the emerging topic of effectors in the context of effector-resistance genes interaction, as well as model systems and recent developments in resources and techniques that may provide a better understanding of the soybean-P. sojae interaction.
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Arsenault‐Labrecque G, Santhanam P, Asselin Y, Cinget B, Lebreton A, Labbé C, Belzile F, Gijzen M, Bélanger RR. RXLR effector gene Avr3a from Phytophthora sojae is recognized by Rps8 in soybean. MOLECULAR PLANT PATHOLOGY 2022; 23:693-706. [PMID: 35150190 PMCID: PMC8995065 DOI: 10.1111/mpp.13190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
The use of resistance genes in elite soybean cultivars is one of the most widely used methods to manage Phytophthora sojae. This method relies on effector-triggered immunity, where a Resistant to P. sojae (Rps) gene product from the plant recognizes a specific effector from the pathogen, encoded by an avirulence (Avr) gene. Many Avr genes from P. sojae have been identified in the last decade, allowing a better exploitation of this type of resistance. The objective of the present study was to identify the Avr gene triggering immunity derived from the soybean resistance gene Rps8. The analysis of a segregating F2 progeny coupled with a genotyping-by-sequencing approach led to the identification of a putative Avr8 locus. The investigation of this locus using whole-genome sequencing data from 31 isolates of P. sojae identified Avr3a as the likely candidate for Avr8. Long-read sequencing also revealed that P. sojae isolates can carry up to five copies of the Avr3a gene, compared to the four previously reported. Haplotype and transcriptional analyses showed that amino acid changes and absence of Avr3a transcripts from P. sojae isolates caused changes in virulence towards Rps8. Functional analyses using CRISPR/Cas9 knockout and constitutive expression demonstrated that Rps8 interacted with Avr3a. We also showed that a specific allele of Avr3a is recognized by Rps3a but not Rps8. While Rps3a and Rps8 have been previously described as closely linked, this is the first report of a clear distinction hitherto undefined between these two resistance genes.
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Affiliation(s)
| | | | - Yanick Asselin
- Department of PhytologyUniversité LavalQuébecQuébecCanada
| | | | | | - Caroline Labbé
- Department of PhytologyUniversité LavalQuébecQuébecCanada
| | | | - Mark Gijzen
- Agriculture and Agri‐Food CanadaLondonOntarioCanada
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Belzile F, Jean M, Torkamaneh D, Tardivel A, Lemay MA, Boudhrioua C, Arsenault-Labrecque G, Dussault-Benoit C, Lebreton A, de Ronne M, Tremblay V, Labbé C, O’Donoughue L, St-Amour VTB, Copley T, Fortier E, Ste-Croix DT, Mimee B, Cober E, Rajcan I, Warkentin T, Gagnon É, Legay S, Auclair J, Bélanger R. The SoyaGen Project: Putting Genomics to Work for Soybean Breeders. FRONTIERS IN PLANT SCIENCE 2022; 13:887553. [PMID: 35557742 PMCID: PMC9087807 DOI: 10.3389/fpls.2022.887553] [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: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The SoyaGen project was a collaborative endeavor involving Canadian soybean researchers and breeders from academia and the private sector as well as international collaborators. Its aims were to develop genomics-derived solutions to real-world challenges faced by breeders. Based on the needs expressed by the stakeholders, the research efforts were focused on maximizing realized yield through optimization of maturity and improved disease resistance. The main deliverables related to molecular breeding in soybean will be reviewed here. These include: (1) SNP datasets capturing the genetic diversity within cultivated soybean (both within a worldwide collection of > 1,000 soybean accessions and a subset of 102 short-season accessions (MG0 and earlier) directly relevant to this group); (2) SNP markers for selecting favorable alleles at key maturity genes as well as loci associated with increased resistance to key pathogens and pests (Phytophthora sojae, Heterodera glycines, Sclerotinia sclerotiorum); (3) diagnostic tools to facilitate the identification and mapping of specific pathotypes of P. sojae; and (4) a genomic prediction approach to identify the most promising combinations of parents. As a result of this fruitful collaboration, breeders have gained new tools and approaches to implement molecular, genomics-informed breeding strategies. We believe these tools and approaches are broadly applicable to soybean breeding efforts around the world.
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Affiliation(s)
- François Belzile
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Martine Jean
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Aurélie Tardivel
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Marc-André Lemay
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Chiheb Boudhrioua
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | | | | | - Amandine Lebreton
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Maxime de Ronne
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Vanessa Tremblay
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Caroline Labbé
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
| | - Louise O’Donoughue
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Vincent-Thomas Boucher St-Amour
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Tanya Copley
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Eric Fortier
- Centre de Recherche sur les Grains (CEROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | | | - Benjamin Mimee
- Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, QC, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Tom Warkentin
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Éric Gagnon
- Semences Prograin Inc., Saint-Césaire, QC, Canada
- Sevita Genetics, Inkerman, ON, Canada
| | | | | | - Richard Bélanger
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
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de Ronne M, Santhanam P, Cinget B, Labbé C, Lebreton A, Ye H, Vuong TD, Hu H, Valliyodan B, Edwards D, Nguyen HT, Belzile F, Bélanger R. Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole-genome sequencing reveals a major QTL. THE PLANT GENOME 2022; 15:e20184. [PMID: 34964282 DOI: 10.1002/tpg2.20184] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
In the last decade, more than 70 quantitative trait loci (QTL) related to soybean [Glycine max (L.) Merr.] partial resistance (PR) against Phytophthora sojae have been identified by genome-wide association studies (GWAS). However, most of them have either a minor effect on the resistance level or are specific to a single phenotypic variable or one isolate, thereby limiting their use in breeding programs. In this study, we have used an analytical approach combining (a) the phenotypic characterization of a diverse panel of 357 soybean accessions for resistance to P. sojae captured through a single variable, corrected dry weight; (b) a new hydroponic assay allowing the inoculation of a combination of P. sojae isolates covering the spectrum of commercially relevant Rps genes; and (c) exhaustive genotyping through whole-genome resequencing (WGS). This led to the identification of a novel P. sojae resistance QTL with a relatively major effect compared with the previously reported QTL. The QTL interval, spanning ∼500 kb on chromosome (Chr) 15, does not colocalize with previously reported QTL for P. sojae resistance. Plants carrying the favorable allele at this QTL were 60% more resistant. Eight genes were found to reside in the linkage disequilibrium (LD) block containing the peak single-nucleotide polymorphism (SNP) including Glyma.15G217100, which encodes a major latex protein (MLP)-like protein, with a functional annotation related to pathogen resistance. Expression analysis of Glyma.15G217100 indicated that it was nearly eight times more highly expressed in a group of plant introductions (PIs) carrying the resistant (R) allele compared with those carrying the susceptible (S) allele within a short period after inoculation. These results offer new and valuable options to develop improved soybean cultivars with broad resistance to P. sojae through marker-assisted selection.
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Affiliation(s)
| | | | | | | | | | - Heng Ye
- Division of Plant Sciences and National Center for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Tri D Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, 65211, USA
- Dep. of Agriculture and Environmental Sciences, Lincoln Univ., Jefferson City, MO, 65101, USA
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, 65211, USA
| | - François Belzile
- Dép. de phytologie, Univ. Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Univ. Laval, Québec, Canada
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Hu Y, He Z, Kang Y, Cui L. Mutations in the Promoter and Coding Regions of Avr3a Cause Gain of Virulence of Phytophthora sojae to Rps3a in Soybean. Front Microbiol 2021; 12:759196. [PMID: 34858371 PMCID: PMC8632523 DOI: 10.3389/fmicb.2021.759196] [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: 08/16/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Phytophthora sojae threatens soybean production worldwide, and the cultivation of soybean cultivars carrying Rps genes is the most effective way to control this pathogen. However, DNA mutations in the Avr genes of P. sojae can escape recognization of the corresponding Rps genes, leading to the loss of soybean resistance. In this study, we investigated sequence polymorphism and transcript level of the Avr3a gene in Chinese isolates of P. sojae. Twenty-four mutations resulting in five unique Avr3a alleles were discovered in the Avr3a coding region from 32 P. sojae isolates. The Avr3a transcripts were detectable in the isolates containing Avr3a(I), Avr3a(II), Avr3a(III), and Avr3a(IV) but not in the isolates containing Avr3a(V). Promoter and 5'-UTR sequence analysis revealed eight unique mutations in the promoter region of Avr3a(V), suggesting that the mutations could result in the loss of Avr3a(V) transcription. Virulence tests indicated the isolates containing Avr3a(II) and Avr3a(IV) were virulent, suggesting that the mutations in the coding regions of Avr3a(II) and Avr3a(IV) caused the gain of virulence to Rps3a. Based on DNA mutations of Avr3a in virulent alleles, two SNP markers and one PCR-based marker were developed successfully for detecting the virulence of P. sojae isolates to Rps3a. These findings provide new insights into escape mechanisms of Avr3a and effective support for accurate pathotype identification of P. sojae using molecular methods.
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Affiliation(s)
- Yanhong Hu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Zhihua He
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yebin Kang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Linkai Cui
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
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Tremblay V, McLaren DL, Kim YM, Strelkov SE, Conner RL, Wally O, Bélanger RR. Molecular Assessment of Pathotype Diversity of Phytophthora sojae in Canada Highlights Declining Sources of Resistance in Soybean. PLANT DISEASE 2021; 105:4006-4013. [PMID: 34161124 DOI: 10.1094/pdis-04-21-0762-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The large-scale deployment of resistance to Phytophthora sojae (Rps) genes in soybean has led to the rapid evolution of the virulence profile (pathotype) of P. sojae populations. Determining the pathotypes of P. sojae isolates is important in selecting soybean germplasm carrying the proper Rps, but this process is fastidious and requires specific expertise. In this work, we used a molecular assay to assess the pathotypes of P. sojae isolates obtained throughout the provinces of Québec, Ontario, and Manitoba. In preliminary assays, the molecular tool showed equivalent prediction of the pathotypes as a phenotyping assay and proved to be much faster to apply while eliminating intermediate values. Upon analysis of nearly 300 isolates, 24 different pathotypes were detected in Québec and Ontario, compared with only eight in Manitoba, where soybean culture is more recent. Pathotypes 1a, 1c, and 1d was predominant in Québec, while 1a, 1b, 1c, 1d, and 1k pathotypes were the most common in Manitoba. Overall, the results showed that 98 and 86% of the isolates carried pathotype 1a or 1c, respectively, suggesting that Rps1a and Rps1c were no longer effective in Canada. Based on the history of soybean varieties used in surveyed fields, it was found that 84% of them contained Rps genes that were no longer resistant against the pathotypes of the isolates found in the fields. While highlighting an easier and more precise option to assess pathotypes, this study presents the first pan-Canadian survey of P. sojae and stresses the importance of carefully managing the declining sources of resistance.
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Affiliation(s)
- Vanessa Tremblay
- Centre de Recherche en Innovation des Végétaux, Université Laval, Québec, G1V 0A6 Canada
| | - Debra L McLaren
- Agriculture and Agri-Food Canada, Brandon Research and Development Centre, Brandon, Manitoba, R7A 5Y3 Canada
| | - Yong Min Kim
- Agriculture and Agri-Food Canada, Brandon Research and Development Centre, Brandon, Manitoba, R7A 5Y3 Canada
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5 Canada
| | - Robert L Conner
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, Manitoba, R6M 1Y5 Canada
| | - Owen Wally
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, Ontario, N0R 1G0 Canada
| | - Richard R Bélanger
- Centre de Recherche en Innovation des Végétaux, Université Laval, Québec, G1V 0A6 Canada
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The Histological, Effectoromic, and Transcriptomic Analyses of Solanum pinnatisectum Reveal an Upregulation of Multiple NBS-LRR Genes Suppressing Phytophthora infestans Infection. Int J Mol Sci 2020; 21:ijms21093211. [PMID: 32370102 PMCID: PMC7247345 DOI: 10.3390/ijms21093211] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Utilization of disease resistance components from wild potatoes is a promising and sustainable approach to control Phytophthora blight. Here, we combined avirulence (Avr) genes screen with RNA-seq analysis to discover the potential mechanism of resistance in Mexican wild potato species, Solanum pinnatisectum. Histological characterization displayed that hyphal expansion was significantly restricted in epidermal cells and mesophyll cell death was predominant, indicating that a typical defense response was initiated in S. pinnatisectum. Inoculation of S. pinnatisectum with diverse Phytophthora infestans isolates showed distinct resistance patterns, suggesting that S. pinnatisectum has complex genetic resistance to most of the prevalent races of P. infestans in northwestern China. Further analysis by Avr gene screens and comparative transcriptomic profiling revealed the presence and upregulation of multiple plant NBS-LRR genes corresponding to biotic stresses. Six NBS-LRR alleles of R1, R2, R3a, R3b, R4, and Rpi-smira2 were detected, and over 60% of the 112 detected NLR proteins were significantly induced in S. pinnatisectum. On the contrary, despite the expression of the Rpi-blb1, Rpi-vnt1, and Rpi-smira1 alleles, fewer NLR proteins were expressed in susceptible Solanum cardophyllum. Thus, the enriched NLR genes in S. pinnatisectum make it an ideal genetic resource for the discovery and deployment of resistance genes for potato breeding.
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