1
|
Prom LK, Ahn EJS, Perumal R, Isakeit TS, Odvody GN, Magill CW. Genetic and Pathogenic Variability among Isolates of Sporisorium reilianum Causing Sorghum Head Smut. J Fungi (Basel) 2024; 10:62. [PMID: 38248970 PMCID: PMC10820674 DOI: 10.3390/jof10010062] [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: 11/14/2023] [Revised: 12/31/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
Sporisorium reilianum, the causal agent of sorghum (Sorghum bicolor (L.) Moench) head smut, is present in most sorghum-producing regions. This seed replacement fungal disease can reduce yield by up to 80% in severely infected fields. Management of this disease can be challenging due to the appearance of different pathotypes within the pathogenic population. In this research, the genetic variability and pathogenicity of isolates collected from five Texas Counties was conducted. Due to the lack of available space, 21 out of 32 sequenced isolates were selected and evaluated for virulence patterns on the six sorghum differentials, Tx7078, BTx635, SC170-6-17 (TAM2571), SA281 (Early Hegari), Tx414, and BTx643. The results reveal the occurrence of a new pathotype, 1A, and four previously documented US pathotypes when the 21 isolates were evaluated for virulence patterns on the differentials. The most prevalent was pathotype 5, which was recovered from Brazos, Hidalgo, Nueces, and Willacy Counties, Texas. This pathotype was followed by 1A and 6 in frequency of recovery. Pathotype 4 was identified only from isolates collected from Hidalgo County, while pathotype 1 was from Burleson County, Texas. It appeared that the previous US head smut pathotypes (2 and 3) are no longer common, and the new pathotypes, 1A, 5, and 6, are now predominant. The phylogenetic tree constructed from the single-nucleotide polymorphism (SNP) data through the neighbor-joining method showed high genetic diversity among the tested isolates. Some of the diverse clades among the tested isolates were independent of their sampled locations. Notably, HS37, HS49, and HS65 formed a clade and were classified as 1A in the virulence study, while HS 61 and HS 66, which were collected from Nueces County, were grouped and identified as pathotype 5.
Collapse
Affiliation(s)
- Louis K. Prom
- USDA-ARS, Plains Area Agricultural Research Center, College Station, TX 77845, USA
| | | | - Ramasamy Perumal
- Department of Agronomy, Agricultural Research Center, Kansas State University, Hays, KS 67601, USA;
| | - Thomas S. Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA; (T.S.I.); (C.W.M.)
| | - Gary N. Odvody
- Department of Plant Pathology and Microbiology, Texas AgriLife Research Station, Corpus Christi, TX 78406, USA;
| | - Clint W. Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA; (T.S.I.); (C.W.M.)
| |
Collapse
|
2
|
Newman TE, Kim H, Khentry Y, Sohn KH, Derbyshire MC, Kamphuis LG. The broad host range pathogen Sclerotinia sclerotiorum produces multiple effector proteins that induce host cell death intracellularly. MOLECULAR PLANT PATHOLOGY 2023; 24:866-881. [PMID: 37038612 PMCID: PMC10346375 DOI: 10.1111/mpp.13333] [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: 10/18/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Sclerotinia sclerotiorum is a broad host range necrotrophic fungal pathogen, which causes disease on many economically important crop species. S. sclerotiorum has been shown to secrete small effector proteins to kill host cells and acquire nutrients. We set out to discover novel necrosis-inducing effectors and characterize their activity using transient expression in Nicotiana benthamiana leaves. Five intracellular necrosis-inducing effectors were identified with differing host subcellular localization patterns, which were named intracellular necrosis-inducing effector 1-5 (SsINE1-5). We show for the first time a broad host range pathogen effector, SsINE1, that uses an RxLR-like motif to enter host cells. Furthermore, we provide preliminary evidence that SsINE5 induces necrosis via an NLR protein. All five of the identified effectors are highly conserved in globally sourced S. sclerotiorum isolates. Taken together, these results advance our understanding of the virulence mechanisms employed by S. sclerotiorum and reveal potential avenues for enhancing genetic resistance to this damaging fungal pathogen.
Collapse
Affiliation(s)
- Toby E. Newman
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Haseong Kim
- Plant Immunity Research CenterSeoul National UniversitySeoul08826Republic of Korea
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kee Hoon Sohn
- Plant Immunity Research CenterSeoul National UniversitySeoul08826Republic of Korea
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Republic of Korea
- Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoul08826Republic of Korea
| | - Mark C. Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Lars G. Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| |
Collapse
|
3
|
The use of evolutionary analyses to predict functionally relevant traits in filamentous plant pathogens. Curr Opin Microbiol 2023; 73:102244. [PMID: 36889024 DOI: 10.1016/j.mib.2022.102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 03/08/2023]
Abstract
Identifying traits involved in plant-pathogen interactions is one of the major objectives in molecular plant pathology. Evolutionary analyses may assist in the identification of genes encoding traits that are involved in virulence and local adaptation, including adaptation to agricultural intervention strategies. In the past decades, the number of available genome sequences of fungal plant pathogens has rapidly increased, providing a rich source for the discovery of functionally important genes as well as inference of species histories. Positive selection in the form of diversifying or directional selection leaves particular signatures in genome alignments and can be identified with statistical genetics methods. This review summarises the concepts and approaches used in evolutionary genomics and lists major discoveries related to plant-pathogen adaptative evolution. We underline the significant contribution of evolutionary genomics in discovering virulence-related traits and the study of plant-pathogen ecology and adaptive evolution.
Collapse
|
4
|
Rogério F, Baroncelli R, Cuevas-Fernández FB, Becerra S, Crouch J, Bettiol W, Azcárate-Peril MA, Malapi-Wight M, Ortega V, Betran J, Tenuta A, Dambolena JS, Esker PD, Revilla P, Jackson-Ziems TA, Hiltbrunner J, Munkvold G, Buhiniček I, Vicente-Villardón JL, Sukno SA, Thon MR. Population Genomics Provide Insights into the Global Genetic Structure of Colletotrichum graminicola, the Causal Agent of Maize Anthracnose. mBio 2023; 14:e0287822. [PMID: 36533926 PMCID: PMC9973043 DOI: 10.1128/mbio.02878-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.
Collapse
Affiliation(s)
- Flávia Rogério
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Riccardo Baroncelli
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Francisco Borja Cuevas-Fernández
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Sioly Becerra
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - JoAnne Crouch
- Foreign Disease and Weed Science Unit, United States Department of Agriculture, Fort Detrick, Maryland, USA
| | | | - M. Andrea Azcárate-Peril
- Center for Gastrointestinal Biology and Disease, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- UNC Microbiome Core, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Martha Malapi-Wight
- USDA Animal and Plant Health Inspection Services, Biotechnology Regulatory Services, Riverdale, Maryland, USA
| | | | | | - Albert Tenuta
- Ontario Ministry of Agriculture, Food, and Rural Affairs, University of Guelph-Ridgetown, Ridgetown, Ontario, Canada
| | - José S. Dambolena
- Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, IMBIV-CONICET-ICTA, Córdoba, Argentina
| | - Paul D. Esker
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, Pennsylvania, USA
| | - Pedro Revilla
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Pontevedra, Spain
| | | | | | - Gary Munkvold
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Ivica Buhiniček
- BC Institute for Breeding and Production of Field Crops, Dugo Selo, Croatia
| | | | - Serenella A. Sukno
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Michael R. Thon
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| |
Collapse
|
5
|
Quintanilha-Peixoto G, Marone MP, Raya FT, José J, Oliveira A, Fonseca PLC, Tomé LMR, Bortolini DE, Kato RB, Araújo DS, De-Paula RB, Cuesta-Astroz Y, Duarte EAA, Badotti F, de Carvalho Azevedo VA, Brenig B, Soares ACF, Carazzolle MF, Pereira GAG, Aguiar ERGR, Góes-Neto A. Phylogenomics and gene selection in Aspergillus welwitschiae: Possible implications in the pathogenicity in Agave sisalana. Genomics 2022; 114:110517. [PMID: 36306958 DOI: 10.1016/j.ygeno.2022.110517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
Abstract
Aspergillus welwitschiae causes bole rot disease in sisal (Agave sisalana and related species) which affects the production of natural fibers in Brazil, the main worldwide producer of sisal fibers. This fungus is a saprotroph with a broad host range. Previous research established A. welwitschiae as the only causative agent of bole rot in the field, but little is known about the evolution of this species and its strains. In this work, we performed a comparative genomics analysis of 40 Aspergillus strains. We show the conflicting molecular identity of this species, with one sisal-infecting strain sharing its last common ancestor with Aspergillus niger, having diverged only 833 thousand years ago. Furthermore, our analysis of positive selection reveals sites under selection in genes coding for siderophore transporters, Sodium‑calcium exchangers, and Phosphatidylethanolamine-binding proteins (PEBPs). Herein, we discuss the possible impacts of these gene functions on the pathogenicity in sisal.
Collapse
Affiliation(s)
| | - Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Fábio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Juliana José
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Adriele Oliveira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Dener Eduardo Bortolini
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, United States
| | - Ruth B De-Paula
- Department of Neurology, Baylor College of Medicine, Houston, United States
| | - Yesid Cuesta-Astroz
- Instituto Colombiano de Medicina Tropical, Universidad CES, Medellín, Colombia
| | - Elizabeth A A Duarte
- Centro Universitário Maria Milza, Cruz das Almas, Brazil; Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Federal Center of Technological Education of Minas Gerais, Belo Horizonte, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Eric Roberto Guimarães Rocha Aguiar
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| |
Collapse
|
6
|
Snyder AB. The role of heat resistance in yeast spoilage of thermally processed foods: highlighting the need for a probabilistic, systems-based approach to microbial quality. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Transcriptional response to host chemical cues underpins the expansion of host range in a fungal plant pathogen lineage. THE ISME JOURNAL 2022; 16:138-148. [PMID: 34282282 PMCID: PMC8692328 DOI: 10.1038/s41396-021-01058-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 06/26/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
The host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic. The fungus Sclerotinia sclerotiorum has been reported to parasitize more than 400 plant species from diverse eudicot families while its close relative, S. trifoliorum, is restricted to plants from the Fabaceae family. We analyzed S. sclerotiorum global transcriptome reprogramming on hosts from six botanical families and reveal a flexible, host-specific transcriptional program. We generated a chromosome-level genome assembly for S. trifoliorum and found near-complete gene space conservation in two representative strains of broad and narrow host range Sclerotinia species. However, S. trifoliorum showed increased sensitivity to the Brassicaceae defense compound camalexin. Comparative analyses revealed a lack of transcriptional response to camalexin in the S. trifoliorum strain and suggest that regulatory variation in detoxification and effector genes at the population level may associate with the genetic accommodation of Brassicaceae in the Sclerotinia host range. Our work proposes transcriptional plasticity and the co-existence of signatures for generalist and polyspecialist adaptive strategies in the genome of a plant pathogen.
Collapse
|
8
|
Mercier A, Simon A, Lapalu N, Giraud T, Bardin M, Walker AS, Viaud M, Gladieux P. Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal Pathogen Botrytis cinerea in France. PHYTOPATHOLOGY 2021; 111:2355-2366. [PMID: 33829853 DOI: 10.1094/phyto-07-20-0302-fi] [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: 06/12/2023]
Abstract
Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help to prevent the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the gray mold pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host of origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and nonsynonymous sites, and analyses of presence and absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.
Collapse
Affiliation(s)
- Alex Mercier
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
- Université Paris-Saclay, Orsay, France
| | - Adeline Simon
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Marc Bardin
- UR0407 Pathologie Végétale, INRAE, 84143 Montfavet, France
| | - Anne-Sophie Walker
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Muriel Viaud
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| |
Collapse
|
9
|
Dumartinet T, Ravel S, Roussel V, Perez-Vicente L, Aguayo J, Abadie C, Carlier J. Complex adaptive architecture underlies adaptation to quantitative host resistance in a fungal plant pathogen. Mol Ecol 2021; 31:1160-1179. [PMID: 34845779 DOI: 10.1111/mec.16297] [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: 08/31/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022]
Abstract
Plant pathogens often adapt to plant genetic resistance so characterization of the architecture underlying such an adaptation is required to understand the adaptive potential of pathogen populations. Erosion of banana quantitative resistance to a major leaf disease caused by polygenic adaptation of the causal agent, the fungus Pseudocercospora fijiensis, was recently identified in the northern Caribbean region. Genome scan and quantitative genetics approaches were combined to investigate the adaptive architecture underlying this adaptation. Thirty-two genomic regions showing host selection footprints were identified by pool sequencing of isolates collected from seven plantation pairs of two cultivars with different levels of quantitative resistance. Individual sequencing and phenotyping of isolates from one pair revealed significant and variable levels of correlation between haplotypes in 17 of these regions with a quantitative trait of pathogenicity (the diseased leaf area). The multilocus pattern of haplotypes detected in the 17 regions was found to be highly variable across all the population pairs studied. These results suggest complex adaptive architecture underlying plant pathogen adaptation to quantitative resistance with a polygenic basis, redundancy, and a low level of parallel evolution between pathogen populations. Candidate genes involved in quantitative pathogenicity and host adaptation of P. fijiensis were identified in genomic regions by combining annotation analysis with available biological data.
Collapse
Affiliation(s)
- Thomas Dumartinet
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, INRAe, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Sébastien Ravel
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, INRAe, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Véronique Roussel
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, INRAe, CIRAD, Montpellier SupAgro, Montpellier, France
| | | | - Jaime Aguayo
- ANSES, Laboratoire de la Santé des Végétaux (LSV), Unité de Mycologie, Malzéville, France
| | - Catherine Abadie
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, INRAe, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Jean Carlier
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, INRAe, CIRAD, Montpellier SupAgro, Montpellier, France
| |
Collapse
|
10
|
Derbyshire MC, Khentry Y, Severn-Ellis A, Mwape V, Saad NSM, Newman TE, Taiwo A, Regmi R, Buchwaldt L, Denton-Giles M, Batley J, Kamphuis LG. Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola. THE PLANT GENOME 2021; 14:e20088. [PMID: 33629543 DOI: 10.1002/tpg2.20088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
The fungus Sclerotinia sclerotiorum infects hundreds of plant species including many crops. Resistance to this pathogen in canola (Brassica napus L. subsp. napus) is controlled by numerous quantitative trait loci (QTL). For such polygenic traits, genomic prediction may be useful for breeding as it can capture many QTL at once while also considering nonadditive genetic effects. Here, we test application of common regression models to genomic prediction of S. sclerotiorum resistance in canola in a diverse panel of 218 plants genotyped at 24,634 loci. Disease resistance was scored by infection with an aggressive isolate and monitoring over 3 wk. We found that including first-order additive × additive epistasis in linear mixed models (LMMs) improved accuracy of breeding value estimation between 3 and 40%, depending on method of assessment, and correlation between phenotypes and predicted total genetic values by 14%. Bayesian models performed similarly to or worse than genomic relationship matrix-based models for estimating breeding values or overall phenotypes from genetic values. Bayesian ridge regression, which is most similar to the genomic relationship matrix-based approach in the amount of shrinkage it applies to marker effects, was the most accurate of this family of models. This confirms several studies indicating the highly polygenic nature of sclerotinia stem rot resistance. Overall, our results highlight the use of simple epistasis terms for prediction of breeding values and total genetic values for a complex disease resistance phenotype in canola.
Collapse
Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Anita Severn-Ellis
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Virginia Mwape
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Nur Shuhadah Mohd Saad
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Akeem Taiwo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Roshan Regmi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Lone Buchwaldt
- Agriculture and Agri-Food, Saskatoon, Saskatchewan, Canada
| | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| |
Collapse
|
11
|
Michael PJ, Lui KY, Thomson LL, Lamichhane AR, Bennett SJ. Impact of Preconditioning Temperature and Duration Period on Carpogenic Germination of Diverse Sclerotinia sclerotiorum Populations in Southwestern Australia. PLANT DISEASE 2021; 105:1798-1805. [PMID: 33206012 DOI: 10.1094/pdis-09-20-1957-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The soilborne pathogen Sclerotinia sclerotiorum (Lib.) de Bary is the causal agent of Sclerotinia stem rot, a severe disease of broad-leaf crops including canola/rapeseed (Brassica napus) that can result in significant yield losses. Sclerotia, the hard melanized resting structure of the pathogen, requires preconditioning before carpogenic germination can occur. We investigated the effect of preconditioning temperature (4, 20, 35, 50°C, and field conditions) and duration (0, 30, 60, 120, 179, 240, and 301 days) on germination of S. sclerotiorum sclerotia collected from five canola fields in the southwestern Australia grain belt. The ecological diversity of each population was characterized using mycelial compatibility group (MCG) typing. No response was observed for isolates conditioned at 4°C at any time period, indicating that chilling is not a preconditioning requirement for these isolates. Sclerotia required preconditioning for a minimum of 60 days before any significant increase in germination occurred, with no further increases in germination recorded in response to longer conditioning after 60 days. The highest germination was observed in sclerotia conditioned at 50°C. The MCG results indicated significant diversity within and between populations, suggesting local adaptation to different environments as well as ensuring the ability to respond to seasonal variation between years.
Collapse
Affiliation(s)
- Pippa J Michael
- Centre for Crop and Disease Management, Curtin University, Bentley, Western Australia 6845, Australia
| | - King Yin Lui
- Centre for Crop and Disease Management, Curtin University, Bentley, Western Australia 6845, Australia
| | - Linda L Thomson
- Centre for Crop and Disease Management, Curtin University, Bentley, Western Australia 6845, Australia
| | - Ashmita Rijal Lamichhane
- Centre for Crop and Disease Management, Curtin University, Bentley, Western Australia 6845, Australia
| | - Sarita J Bennett
- Centre for Crop and Disease Management, Curtin University, Bentley, Western Australia 6845, Australia
| |
Collapse
|
12
|
Duan G, Bao J, Chen X, Xie J, Liu Y, Chen H, Zheng H, Tang W, Wang Z. Large-Scale Genome Scanning within Exonic Regions Revealed the Contributions of Selective Sweep Prone Genes to Host Divergence and Adaptation in Magnaporthe oryzae Species Complex. Microorganisms 2021; 9:562. [PMID: 33803140 PMCID: PMC8000120 DOI: 10.3390/microorganisms9030562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 11/30/2022] Open
Abstract
Magnaporthe oryzae, one of the most notorious plant pathogens in the agronomic ecosystem, causes a destructive rice blast disease around the world. The blast fungus infects wide arrays of cultivated and non-cultivated plants within the Poaceae. Studies have shown that host speciation exerts selection pressure that drives the evolution and divergence of the M. oryzae population. Population genetic relationship deducted by genome-wide single nucleotide polymorphisms showed that M. oryzae differentiation is highly consistent with the host speciation process. In particular, the rice-infecting population of M. oryzae is distinct from populations from other hosts. However, how genome regions prone to host-mediated selection pressures associated with speciation in M. oryzae, especially at a large-scale population level, has not been extensively characterized. Here, we detected strong evidence of sweep selection throughout the genomes of rice and non-rice pathotypes of M. oryzae population using integrated haplotype score (iHS), cross population extended haplotype homozygosity (XPEHH), and cross population composite likelihood ratio (XPCLR) tests. Functional annotation analyses of the genes associated with host-mediated selection pressure showed that 14 pathogenicity-related genes are under positive selection pressure. Additionally, we showed that 17 candidate effector proteins are under positive and divergent selection among the blast fungus population through sweep selection analysis. Specifically, we find that a divergent selective gene, MGG_13871, is experiencing host-directed mutation in two amino acid residues in rice and non-rice infecting populations. These results provide a crucial insight into the impact of selective sweeping on the differentiation of M. oryzae populations and the dynamic influences of genomic regions in promoting host adaptation and speciation among M. oryzae species.
Collapse
Affiliation(s)
- Guohua Duan
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiandong Bao
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Xiaomin Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiahui Xie
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuchan Liu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Huiquan Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Huakun Zheng
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Tang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| |
Collapse
|
13
|
Michael PJ, Lui KY, Thomson LL, Stefanova K, Bennett SJ. Carpogenic Germinability of Diverse Sclerotinia sclerotiorum Populations Within the Southwestern Australian Grain Belt. PLANT DISEASE 2020; 104:2891-2897. [PMID: 32924875 DOI: 10.1094/pdis-12-19-2575-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sclerotinia stem rot, caused by the necrotrophic plant pathogen Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease of canola and pulses in Australia. Current disease management relies greatly on cultural and chemical means of control. Timing of fungicide applications remains a challenge, because efficacy is dependent on accurate prediction of ascospore release and presence on the plant. The aims of this study were to determine the optimal temperature for carpogenic germination of S. sclerotiorum populations sampled from canola and lupin fields in southwestern Australia and characterize diversity using mycelial compatibility groupings (MCGs). Sclerotia were collected from four diseased canola and one diseased lupin field from across southwestern Australia. Forty sclerotia from each population were incubated at four alternating temperatures of 30/15, 20/15, 20/4, and 15/4°C (12-h/12-h light/dark cycle) and assessed every 2 to 3 days for a 180-day period. MCG groupings for populations were characterized using 12 reference isolates. Results indicated the time to initial carpogenic germination decreased as diurnal temperature fluctuations decreased, with a fluctuation of 5°C (20/15°C) having the most rapid initial germination followed by 11°C (15/4°C) followed by 16°C (20/4°C). Optimal germination temperature for all five populations was 20/15°C; however, population responses to other diurnal temperature regimes varied considerably. No germination was observed at 30/15°C. MCG results indicate extensive diversity within and between populations, with at least 40% of sclerotia within each population unable to be characterized. We suggest that this diversity has enabled S. sclerotiorum populations to adapt to varying environmental conditions within southwestern Australia.
Collapse
Affiliation(s)
- Pippa J Michael
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6845, Australia
| | - King Yin Lui
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6845, Australia
| | - Linda L Thomson
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6845, Australia
| | | | - Sarita J Bennett
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6845, Australia
| |
Collapse
|
14
|
Derbyshire MC. Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action. Front Microbiol 2020; 11:644. [PMID: 32328056 PMCID: PMC7160247 DOI: 10.3389/fmicb.2020.00644] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.
Collapse
Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| |
Collapse
|
15
|
Graham-Taylor C, Kamphuis LG, Derbyshire MC. A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum. BMC Genomics 2020; 21:7. [PMID: 31898475 PMCID: PMC6941272 DOI: 10.1186/s12864-019-6424-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/23/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes. RESULTS We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes. CONCLUSIONS These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.
Collapse
Affiliation(s)
- Carolyn Graham-Taylor
- 0000 0004 0375 4078grid.1032.0Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, Western Australia Australia
| | - Lars G. Kamphuis
- 0000 0004 0375 4078grid.1032.0Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, Western Australia Australia
| | - Mark C. Derbyshire
- 0000 0004 0375 4078grid.1032.0Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, Western Australia Australia
| |
Collapse
|
16
|
Xia S, Xu Y, Hoy R, Zhang J, Qin L, Li X. The Notorious Soilborne Pathogenic Fungus Sclerotinia sclerotiorum: An Update on Genes Studied with Mutant Analysis. Pathogens 2019; 9:pathogens9010027. [PMID: 31892134 PMCID: PMC7168625 DOI: 10.3390/pathogens9010027] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 01/06/2023] Open
Abstract
Ascomycete Sclerotinia sclerotiorum (Lib.) de Bary is one of the most damaging soilborne fungal pathogens affecting hundreds of plant hosts, including many economically important crops. Its genomic sequence has been available for less than a decade, and it was recently updated with higher completion and better gene annotation. Here, we review key molecular findings on the unique biology and pathogenesis process of S. sclerotiorum, focusing on genes that have been studied in depth using mutant analysis. Analyses of these genes have revealed critical players in the basic biological processes of this unique pathogen, including mycelial growth, appressorium establishment, sclerotial formation, apothecial and ascospore development, and virulence. Additionally, the synthesis has uncovered gaps in the current knowledge regarding this fungus. We hope that this review will serve to build a better current understanding of the biology of this under-studied notorious soilborne pathogenic fungus.
Collapse
Affiliation(s)
- Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China;
- Correspondence: (S.X.); (X.L.)
| | - Yan Xu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (Y.X.); (R.H.)
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ryan Hoy
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (Y.X.); (R.H.)
| | - Julia Zhang
- School of Kinesiology, University of British Columbia, Vancouver, BC V6T 1Z1, Canada;
| | - Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China;
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (Y.X.); (R.H.)
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Correspondence: (S.X.); (X.L.)
| |
Collapse
|
17
|
Derbyshire M, Mbengue M, Barascud M, Navaud O, Raffaele S. Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance. MOLECULAR PLANT PATHOLOGY 2019; 20:1279-1297. [PMID: 31361080 PMCID: PMC6715603 DOI: 10.1111/mpp.12841] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Fungal plant pathogens secrete effector proteins and metabolites to cause disease. Additionally, some species transfer small RNAs (sRNAs) into plant cells to silence host mRNAs through complementary base pairing and suppress plant immunity. The fungus Sclerotinia sclerotiorum infects over 600 plant species, but little is known about the molecular processes that govern interactions with its many hosts. In particular, evidence for the production of sRNAs by S. sclerotiorum during infection is lacking. We sequenced sRNAs produced by S. sclerotiorum in vitro and during infection of two host species, Arabidopsis thaliana and Phaseolus vulgaris. We found that S. sclerotiorum produces at least 374 distinct highly abundant sRNAs during infection, mostly originating from repeat-rich plastic genomic regions. We predicted the targets of these sRNAs in A. thaliana and found that these genes were significantly more down-regulated during infection than the rest of the genome. Predicted targets of S. sclerotiorum sRNAs in A. thaliana were enriched for functional domains associated with plant immunity and were more strongly associated with quantitative disease resistance in a genome-wide association study (GWAS) than the rest of the genome. Mutants in A. thaliana predicted sRNA target genes SERK2 and SNAK2 were more susceptible to S. sclerotiorum than wild-type, suggesting that S. sclerotiorum sRNAs may contribute to the silencing of immune components in plants. The prediction of fungal sRNA targets in plant genomes can be combined with other global approaches, such as GWAS, to assist in the identification of plant genes involved in quantitative disease resistance.
Collapse
Affiliation(s)
- Mark Derbyshire
- Centre for Crop and Disease ManagementCurtin UniversityPerthWestern AustraliaAustralia
| | - Malick Mbengue
- Laboratoire des Interactions Plantes Micro‐organismesINRA, CNRS, Université de ToulouseCastanet TolosanFrance
| | - Marielle Barascud
- Laboratoire des Interactions Plantes Micro‐organismesINRA, CNRS, Université de ToulouseCastanet TolosanFrance
| | - Olivier Navaud
- Laboratoire des Interactions Plantes Micro‐organismesINRA, CNRS, Université de ToulouseCastanet TolosanFrance
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes Micro‐organismesINRA, CNRS, Université de ToulouseCastanet TolosanFrance
| |
Collapse
|