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Cuevas-Zuviria B, Fraile A, García-Arenal F. An Agent-Based Model Shows How Mixed Infections Drive Multiyear Pathotype Dynamics in a Plant-Virus System. PHYTOPATHOLOGY 2024; 114:1276-1288. [PMID: 38330173 DOI: 10.1094/phyto-06-23-0214-r] [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: 02/10/2024]
Abstract
Mathematical models are widely used to understand the evolution and epidemiology of plant pathogens under a variety of scenarios. Here, we used this approach to analyze the effects of different traits intrinsic and extrinsic to plant-virus interactions on the dynamics of virus pathotypes in genetically heterogeneous plant-virus systems. For this, we propose an agent-based epidemiological model that includes epidemiologically significant pathogen life-history traits related to virulence, transmission, and survival in the environment and allows for integrating long- and short-distance transmission, primary and secondary infections, and within-host pathogen competition in mixed infections. The study focuses on the tobamovirus-pepper pathosystem. Model simulations allowed us to integrate pleiotropic effects of resistance-breaking mutations on different virus life-history traits into the net costs of resistance breaking, allowing for predictions on multiyear pathotype dynamics. We also explored the effects of two control measures, the use of host resistance and roguing of symptomatic plants, that modify epidemiological attributes of the pathogens to understand how their populations will respond to evolutionary pressures. One major conclusion points to the importance of pathogen competition within mixed-infected hosts as a component of the overall fitness of each pathogen that, thus, drives their multiyear dynamics.
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Affiliation(s)
- Bruno Cuevas-Zuviria
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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Wei S, Liu L, Chen G, Yang H, Huang L, Gong G, Luo P, Zhang M. Molecular evolution and phylogeographic analysis of wheat dwarf virus. Front Microbiol 2024; 15:1314526. [PMID: 38419641 PMCID: PMC10901289 DOI: 10.3389/fmicb.2024.1314526] [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: 10/10/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10-4 substitutions/site/year (95% credibility interval, 2.828 × 10-4-5.723 × 10-4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517-1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China.
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Affiliation(s)
- Shiqing Wei
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Linwen Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Guoliang Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Hui Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Liang Huang
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoshu Gong
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - PeiGao Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
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Poulicard N, Pagán I, González-Jara P, Mora MÁ, Hily JM, Fraile A, Piñero D, García-Arenal F. Repeated loss of the ability of a wild pepper disease resistance gene to function at high temperatures suggests that thermoresistance is a costly trait. THE NEW PHYTOLOGIST 2024; 241:845-860. [PMID: 37920100 DOI: 10.1111/nph.19371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023]
Abstract
Specificity in plant-pathogen gene-for-gene (GFG) interactions is determined by the recognition of pathogen proteins by the products of plant resistance (R) genes. The evolutionary dynamics of R genes in plant-virus systems is poorly understood. We analyse the evolution of the L resistance locus to tobamoviruses in the wild pepper Capsicum annuum var. glabriusculum (chiltepin), a crop relative undergoing incipient domestication. The frequency, and the genetic and phenotypic diversity, of the L locus was analysed in 41 chiltepin populations under different levels of human management over its distribution range in Mexico. The frequency of resistance was lower in Cultivated than in Wild populations. L-locus genetic diversity showed a strong spatial structure with no isolation-by-distance pattern, suggesting environment-specific selection, possibly associated with infection by the highly virulent tobamoviruses found in the surveyed regions. L alleles differed in recognition specificity and in the expression of resistance at different temperatures, broad-spectrum recognition of P0 + P1 pathotypes and expression above 32°C being ancestral traits that were repeatedly lost along L-locus evolution. Overall, loss of resistance co-occurs with incipient domestication and broad-spectrum resistance expressed at high temperatures has apparent fitness costs. These findings contribute to understand the role of fitness trade-offs in plant-virus coevolution.
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Affiliation(s)
- Nils Poulicard
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Pablo González-Jara
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Miguel Ángel Mora
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Jean-Michel Hily
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
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Spiegelman Z, Dinesh-Kumar SP. Breaking Boundaries: The Perpetual Interplay Between Tobamoviruses and Plant Immunity. Annu Rev Virol 2023; 10:455-476. [PMID: 37254097 DOI: 10.1146/annurev-virology-111821-122847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plant viruses of the genus Tobamovirus cause significant economic losses in various crops. The emergence of new tobamoviruses such as the tomato brown rugose fruit virus (ToBRFV) poses a major threat to global agriculture. Upon infection, plants mount a complex immune response to restrict virus replication and spread, involving a multilayered defense system that includes defense hormones, RNA silencing, and immune receptors. To counter these defenses, tobamoviruses have evolved various strategies to evade or suppress the different immune pathways. Understanding the interactions between tobamoviruses and the plant immune pathways is crucial for the development of effective control measures and genetic resistance to these viruses. In this review, we discuss past and current knowledge of the intricate relationship between tobamoviruses and host immunity. We use this knowledge to understand the emergence of ToBRFV and discuss potential approaches for the development of new resistance strategies to cope with emerging tobamoviruses.
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Affiliation(s)
- Ziv Spiegelman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel;
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and Genome Center, College of Biological Sciences, University of California, Davis, California, USA
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Billard E, Barro M, Sérémé D, Bangratz M, Wonni I, Koala M, Kassankogno AI, Hébrard E, Thébaud G, Brugidou C, Poulicard N, Tollenaere C. Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot. Virus Evol 2023; 9:vead049. [PMID: 37649958 PMCID: PMC10465090 DOI: 10.1093/ve/vead049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at a local scale remains scarce, in spite of potential implications for crop protection. Here, we describe a 5-year (2015-9) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon, and Karfiguela). It confirmed one irrigated site as a disease hotspot and also found one rainfed lowland (RL) site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a 5-m distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site scale (ca. 520 ha) and also within various specific fields (25 m side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20 per cent or less in 2015-6 to more than 65 per cent in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found, however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at the highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at a small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation under controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.
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Affiliation(s)
- Estelle Billard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Mariam Barro
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Martine Bangratz
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Moustapha Koala
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Eugénie Hébrard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Gaël Thébaud
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Charlotte Tollenaere
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
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Hak H, Raanan H, Schwarz S, Sherman Y, Dinesh‐Kumar SP, Spiegelman Z. Activation of Tm-2 2 resistance is mediated by a conserved cysteine essential for tobacco mosaic virus movement. MOLECULAR PLANT PATHOLOGY 2023; 24:838-848. [PMID: 37086003 PMCID: PMC10346382 DOI: 10.1111/mpp.13318] [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: 10/07/2022] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 05/03/2023]
Abstract
The tomato Tm-22 gene was considered to be one of the most durable resistance genes in agriculture, protecting against viruses of the Tobamovirus genus, such as tomato mosaic virus (ToMV) and tobacco mosaic virus (TMV). However, an emerging tobamovirus, tomato brown rugose fruit virus (ToBRFV), has overcome Tm-22 , damaging tomato production worldwide. Tm-22 encodes a nucleotide-binding leucine-rich repeat (NLR) class immune receptor that recognizes its effector, the tobamovirus movement protein (MP). Previously, we found that ToBRFV MP (MPToBRFV ) enabled the virus to overcome Tm-22 -mediated resistance. Yet, it was unknown how Tm-22 remained durable against other tobamoviruses, such as TMV and ToMV, for over 60 years. Here, we show that a conserved cysteine (C68) in the MP of TMV (MPTMV ) plays a dual role in Tm-22 activation and viral movement. Substitution of MPToBRFV amino acid H67 with the corresponding amino acid in MPTMV (C68) activated Tm-22 -mediated resistance. However, replacement of C68 in TMV and ToMV disabled the infectivity of both viruses. Phylogenetic and structural prediction analysis revealed that C68 is conserved among all Solanaceae-infecting tobamoviruses except ToBRFV and localizes to a predicted jelly-roll fold common to various MPs. Cell-to-cell and subcellular movement analysis showed that C68 is required for the movement of TMV by regulating the MP interaction with the endoplasmic reticulum and targeting it to plasmodesmata. The dual role of C68 in viral movement and Tm-22 immune activation could explain how TMV was unable to overcome this resistance for such a long period.
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Affiliation(s)
- Hagit Hak
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
| | - Hagai Raanan
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
- Gilat Research CenterAgricultural Research OrganizationNegevIsrael
| | - Shahar Schwarz
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
| | - Yifat Sherman
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
- The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Savithramma P. Dinesh‐Kumar
- Department of Plant Biology and Genome CenterCollege of Biological Sciences, University of CaliforniaDavisCaliforniaUSA
| | - Ziv Spiegelman
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
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Wei S, Chen G, Yang H, Huang L, Gong G, Luo P, Zhang M. Global molecular evolution and phylogeographic analysis of barley yellow dwarf virus based on the cp and mp genes. Virol J 2023; 20:130. [PMID: 37340422 DOI: 10.1186/s12985-023-02084-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/26/2023] [Indexed: 06/22/2023] Open
Abstract
Barley yellow dwarf virus (BYDV) has caused considerable losses in the global production of grain crops such as wheat, barley and maize. We investigated the phylodynamics of the virus by analysing 379 and 485 nucleotide sequences of the genes encoding the coat protein and movement protein, respectively. The maximum clade credibility tree indicated that BYDV-GAV and BYDV-MAV, BYDV-PAV and BYDV-PAS share the same evolutionary lineage, respectively. The diversification of BYDV arises from its adaptability to vector insects and geography. Bayesian phylogenetic analyses showed that the mean substitution rates of the coat and movement proteins of BYDV ranged from 8.327 × 10- 4 (4.700 × 10- 4-1.228 × 10- 3) and 8.671 × 10- 4 (6.143 × 10- 4-1.130 × 10- 3) substitutions/site/year, respectively. The time since the most recent common BYDV ancestor was 1434 (1040-1766) CE (Common Era). The Bayesian skyline plot (BSP) showed that the BYDV population experienced dramatic expansions approximately 8 years into the 21st century, followed by a dramatic decline in less than 15 years. Our phylogeographic analysis showed that the BYDV population originating in the United States was subsequently introduced to Europe, South America, Australia and Asia. The migration pathways of BYDV suggest that the global spread of BYDV is associated with human activities.
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Affiliation(s)
- Shiqing Wei
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoliang Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liang Huang
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guoshu Gong
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - PeiGao Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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Clin P, Grognard F, Andrivon D, Mailleret L, Hamelin FM. The proportion of resistant hosts in mixtures should be biased towards the resistance with the lowest breaking cost. PLoS Comput Biol 2023; 19:e1011146. [PMID: 37228168 DOI: 10.1371/journal.pcbi.1011146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Current agricultural practices facilitate emergence and spread of plant diseases through the wide use of monocultures. Host mixtures are a promising alternative for sustainable plant disease control. Their effectiveness can be partly explained by priming-induced cross-protection among plants. Priming occurs when plants are challenged with non-infective pathogen genotypes, resulting in increased resistance to subsequent infections by infective pathogen genotypes. We developed an epidemiological model to explore how mixing two distinct resistant varieties can reduce disease prevalence. We considered a pathogen population composed of three genotypes infecting either one or both varieties. We found that host mixtures should not contain an equal proportion of resistant plants, but a biased ratio (e.g. 80 : 20) to minimize disease prevalence. Counter-intuitively, the optimal ratio of resistant varieties should contain a lower proportion of the costliest resistance for the pathogen to break. This benefit is amplified by priming. This strategy also prevents the invasion of pathogens breaking all resistances.
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Affiliation(s)
- Pauline Clin
- Institut Agro, Univ Rennes, INRAE, IGEPP, Rennes, France
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia-Antipolis, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, Sophia-Antipolis, France
| | | | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia-Antipolis, France
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, Sophia-Antipolis, France
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Moreno‐Pérez MG, Bera S, McLeish M, Fraile A, García‐Arenal F. Reversion of a resistance-breaking mutation shows reversion costs and high virus diversity at necrotic local lesions. MOLECULAR PLANT PATHOLOGY 2023; 24:142-153. [PMID: 36435959 PMCID: PMC9831284 DOI: 10.1111/mpp.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/28/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
An instance of host range evolution relevant to plant virus disease control is resistance breaking. Resistance breaking can be hindered by across-host fitness trade-offs generated by negative effects of resistance-breaking mutations on the virus fitness in susceptible hosts. Different mutations in pepper mild mottle virus (PMMoV) coat protein result in the breaking in pepper plants of the resistance determined by the L3 resistance allele. Of these, mutation M138N is widespread in PMMoV populations, despite associated fitness penalties in within-host multiplication and survival. The stability of mutation M138N was analysed by serial passaging in L3 resistant plants. Appearance on passaging of necrotic local lesions (NLL), indicating an effective L3 resistance, showed reversion to nonresistance-breaking phenotypes was common. Most revertant genotypes had the mutation N138K, which affects the properties of the virus particle, introducing a penalty of reversion. Hence, the costs of reversion may determine the evolution of resistance-breaking in addition to resistance-breaking costs. The genetic diversity of the virus population in NLL was much higher than in systemically infected tissues, and included mutations reported to break L3 resistance other than M138N. Infectivity assays on pepper genotypes with different L alleles showed high phenotypic diversity in respect to L alleles in NLL, including phenotypes not reported in nature. Thus, high diversity at NLL may potentiate the appearance of genotypes that enable the colonization of new host genotypes or species. Collectively, the results of this study contribute to better understanding the evolutionary dynamics of resistance breaking and host-range expansions.
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Affiliation(s)
- Manuel G. Moreno‐Pérez
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
| | - Sayanta Bera
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
| | - Michael McLeish
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
| | - Fernando García‐Arenal
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
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10
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Comparative Analysis of Tomato Brown Rugose Fruit Virus Isolates Shows Limited Genetic Diversity. Viruses 2022; 14:v14122816. [PMID: 36560820 PMCID: PMC9784425 DOI: 10.3390/v14122816] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Tomato is an important vegetable in the United States and around the world. Recently, tomato brown rugose fruit virus (ToBRFV), an emerging tobamovirus, has impacted tomato crops worldwide and can result in fruit loss. ToBRFV causes severe symptoms, such as mosaic, puckering, and necrotic lesions on leaves; other symptoms include brown rugose and marbling on fruits. More importantly, ToBRFV can overcome resistance in tomato cultivars carrying the Tm-22 locus. In this study, we recovered ToBRFV sequences from tomato seeds, leaves, and fruits from the U.S., Mexico, and Peru. Samples were pre-screened using a real-time RT-PCR assay prior to high-throughput sequencing. Virus draft genomes from 22 samples were assembled and analyzed against more than 120 publicly available genomes. Overall, most sequenced isolates were similar to each other and did not form a distinct population. Phylogenetic analysis revealed three clades within the ToBRFV population. Most of the isolates (95%) clustered in clade 3. Genetic analysis revealed differentiation between the three clades indicating minor divergence occurring. Overall, pairwise identity showed limited genetic diversity among the isolates in this study with worldwide isolates, with a pairwise identity ranging from 99.36% and 99.97%. The overall population is undergoing high gene flow and population expansion with strong negative selection pressure at all ToBRFV genes. Based on the results of this study, it is likely that the limited ToBRFV diversity is associated with the rapid movement and eradication of ToBRFV-infected material between countries.
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Host Diversification May Split Epidemic Spread into Two Successive Fronts Advancing at Different Speeds. Bull Math Biol 2022; 84:68. [DOI: 10.1007/s11538-022-01023-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/13/2022] [Indexed: 11/02/2022]
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12
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Huang H, Zuo C, Zhao Y, Huang S, Wang T, Zhu M, Li J, Tao X. Determination of key residues in tospoviral NSm required for Sw-5b recognition, their potential ability to overcome resistance, and the effective resistance provided by improved Sw-5b mutants. MOLECULAR PLANT PATHOLOGY 2022; 23:622-633. [PMID: 34962031 PMCID: PMC8995064 DOI: 10.1111/mpp.13182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 05/03/2023]
Abstract
Sw-5b is an effective resistance gene used widely in tomato to control tomato spotted wilt virus (TSWV), which causes severe losses in crops worldwide. Sw-5b confers resistance by recognizing a 21-amino-acid peptide region of the viral movement protein NSm (NSm21, amino acids 115-135). However, C118Y or T120N mutation within this peptide region of NSm has given rise to field resistance-breaking (RB) TSWV isolates. To investigate the potential ability of TSWV to break Sw-5b-mediated resistance, we mutagenized each amino acid on NSm21 and determined which amino acid mutations would evade Sw-5b recognition. Among all alanine-scan mutants, NSmP119A , NSmW121A , NSmD122A , NSmR124A , and NSmQ126A failed to induce a hypersensitive response (HR) when coexpressed with Sw-5b in Nicotiana benthamiana leaves. TSWV with the NSmP119A , NSmW121A , or NSmQ126A mutation was defective in viral cell-to-cell movement and systemic infection, while TSWV carrying the NSmD122A or NSmR124A mutation was not only able to infect wild-type N. benthamiana plants systemically but also able to break Sw-5b-mediated resistance and establish systemic infection on Sw-5b-transgenic N. benthamiana plants. Two improved mutants, Sw-5bL33P/K319E/R927A and Sw-5bL33P/K319E/R927Q , which we recently engineered and which provide effective resistance against field RB isolates carrying NSmC118Y or NSmT120N mutations, recognized all NSm21 alanine-substitution mutants and conferred effective resistance against new experimental RB TSWV with the NSmD122A or NSmR124A mutation. Collectively, we determined the key residues of NSm for Sw-5b recognition, investigated their potential RB ability, and demonstrated that the improved Sw-5b mutants could provide effective resistance to both field and potential RB TSWV isolates.
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Affiliation(s)
- Haining Huang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Chongkun Zuo
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Yaqian Zhao
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Shen Huang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Tongkai Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Min Zhu
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Jia Li
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Xiaorong Tao
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
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Clin P, Grognard F, Andrivon D, Mailleret L, Hamelin FM. Host mixtures for plant disease control: benefits from pathogen selection and immune priming. Evol Appl 2022; 15:967-975. [PMID: 35782013 PMCID: PMC9234633 DOI: 10.1111/eva.13386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/28/2022] [Accepted: 04/05/2022] [Indexed: 11/29/2022] Open
Abstract
Multiline and cultivar mixtures are highly effective methods for agroecological plant disease control. Priming‐induced cross protection, occurring when plants are challenged by avirulent pathogen genotypes and resulting in increased resistance to subsequent infection by virulent ones, is one critical key to their lasting performance against polymorphic pathogen populations. Strikingly, this mechanism was until recently absent from mathematical models aiming at designing optimal host mixtures. We developed an epidemiological model to explore the effect of host mixtures composed of variable numbers of single‐resistance cultivars on the equilibrium prevalence of the disease caused by pathogen populations polymorphic for virulence complexity. This model shows that a relatively large amount of resistance genes must be deployed to achieve low disease prevalence, as pathogen competition in mixtures tends to select for intermediate virulence complexity. By contrast, priming significantly reduces the number of plant genotypes needed to drop disease prevalence below an acceptable threshold. Given the limited availability of resistance genes in cultivars, this mechanism of plant immunity should be assessed when designing host mixtures.
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Affiliation(s)
- Pauline Clin
- Institut Agro Univ Rennes INRAE IGEPP 35000 Rennes France
- Université Côte d’Azur INRAE CNRS, ISA France
| | - Frédéric Grognard
- Université Côte d’Azur Inria, INRAE CNRS Sorbonne Université Biocore France
| | | | - Ludovic Mailleret
- Université Côte d’Azur INRAE CNRS, ISA France
- Université Côte d’Azur Inria, INRAE CNRS Sorbonne Université Biocore France
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14
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Zhao W, Wu S, Du L, Li T, Cheng Z, Zhou Y, Ji Y. Development of a reverse-transcription loop-mediated isothermal amplification assay for the detection of Tobacco mild green mosaic virus (TMGMV). J Virol Methods 2021; 298:114277. [PMID: 34492235 DOI: 10.1016/j.jviromet.2021.114277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 08/02/2021] [Accepted: 09/02/2021] [Indexed: 11/22/2022]
Abstract
Tobacco mild green mosaic virus (TMGMV), a member species of the genus Tobamovirus, infects pepper (Capsicum annuum) and a number of other economically important species in the Solanaceae family. TMGMV infections had seriously impacted pepper production worldwide, including China. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect TMGMV in pepper field samples and seed. This assay was based on four primers that matched to six sequences in the C-terminal region of the TMGMV genome. RT-LAMP assay could detect the presence of the virus in 3.0 × 10-7 µg of total RNA extract from pepper leaves, which was ten times more sensitive than the corresponding reverse-transcription polymerase chain reaction (RT-PCR) assay. This method specifically detected TMGMV but not the closely related species of the same genus Pepper mild mottle virus, Cucumber green mottle mosaic virus and Tomato mosaic virus. In addition, the use of SYBR Green I facilitated the detection of the TMGMV RT-LAMP products by the naked eye. These results indicated that the RT-LAMP assay was a simple, sensitive, specific and affordable diagnostic tool that has the potential to detect and monitor TMGMV infection in field samples.
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Affiliation(s)
- Wenhao Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Shuhua Wu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Tingfang Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Zhaobang Cheng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Yinghua Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China.
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15
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Clin P, Grognard F, Mailleret L, Val F, Andrivon D, Hamelin FM. Taking Advantage of Pathogen Diversity and Immune Priming to Minimize Disease Prevalence in Host Mixtures: A Model. PHYTOPATHOLOGY 2021; 111:1219-1227. [PMID: 33297731 DOI: 10.1094/phyto-09-20-0429-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Host mixtures are a promising method for agroecological plant disease control. Plant immunity is key to the success of host mixtures against polymorphic pathogen populations. This immunity results from priming-induced cross-protection, whereby plants able to resist infection by specific pathogen genotypes become more resistant to other pathogen genotypes. Strikingly, this phenomenon was absent from mathematical models aiming at designing host mixtures. We developed a model to specifically explore how priming affects the coexistence of two pathogen genotypes in host mixtures composed of two host genotypes and how it affects disease prevalence. The main effect of priming is to reduce the coexistence region in the parameter space (due to the cross-protection) and to generate a singular mixture of resistant and susceptible hosts corresponding to the maximal reduction disease prevalence (in absence of priming, a resistant pure stand is optimal). The epidemiological advantage of host mixtures over a resistant pure stand thus appears as a direct consequence of immune priming. We also showed that there is indirect cross-protection between host genotypes in a mixture. Moreover, the optimal mix prevents the emergence of a resistance-breaking pathogen genotype. Our results highlight the importance of considering immune priming to design optimal and sustainable host mixtures.
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Affiliation(s)
- Pauline Clin
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
- Université Côte d'Azur, INRAE, CNRS, ISA, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, France
| | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISA, France
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, France
| | - Florence Val
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
| | - Didier Andrivon
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
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16
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McLeish MJ, Fraile A, García-Arenal F. Population Genomics of Plant Viruses: The Ecology and Evolution of Virus Emergence. PHYTOPATHOLOGY 2021; 111:32-39. [PMID: 33210987 DOI: 10.1094/phyto-08-20-0355-fi] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now being studied with high-throughput technologies, traditional genetics methods, and new computational tools for big-data. In this review, we discuss the utility of these approaches to monitor and detect changes in virus populations within cells and individuals, and over wider areas across species and communities of ecosystems. The advent of genomics in virology has fostered a multidisciplinary approach to tackling disease risk. The ability to make sense of the information now generated in this integrated setting is by far the most substantial obstacle to the ultimate goal of plant virology to minimize the threats to food security posed by disease. To achieve this goal, it is imperative to understand and forecast how populations respond to future changes in complex natural systems.
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Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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17
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Watkinson-Powell B, Gilligan CA, Cunniffe NJ. When Does Spatial Diversification Usefully Maximize the Durability of Crop Disease Resistance? PHYTOPATHOLOGY 2020; 110:1808-1820. [PMID: 32500812 DOI: 10.1094/phyto-07-19-0261-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Maximizing the durability of crop disease resistance genes in the face of pathogen evolution is a major challenge in modern agricultural epidemiology. Spatial diversification in the deployment of resistance genes, where susceptible and resistant fields are more closely intermixed, is predicted to drive lower epidemic intensities over evolutionary timescales. This is due to an increase in the strength of dilution effects, caused by pathogen inoculum challenging host tissue to which it is not well-specialized. The factors that interact with and determine the magnitude of this spatial suppressive effect are not currently well understood, however, leading to uncertainty over the pathosystems where such a strategy is most likely to be cost-effective. We model the effect on landscape scale disease dynamics of spatial heterogeneity in the arrangement of fields planted with either susceptible or resistant cultivars, and the way in which this effect depends on the parameters governing the pathosystem of interest. Our multiseason semidiscrete epidemiological model tracks spatial spread of wild-type and resistance-breaking pathogen strains, and incorporates a localized reservoir of inoculum, as well as the effects of within and between field transmission. The pathogen dispersal characteristics, any fitness cost(s) of the resistance-breaking trait, the efficacy of host resistance, and the length of the timeframe of interest all influence the strength of the spatial diversification effect. A key result is that spatial diversification has the strongest beneficial effect at intermediate fitness costs of the resistance-breaking trait, an effect driven by a complex set of nonlinear interactions. On the other hand, however, if the resistance-breaking strain is not fit enough to invade the landscape, then a partially effective resistance gene can result in spatial diversification actually worsening the epidemic. These results allow us to make general predictions of the types of system for which spatial diversification is most likely to be cost-effective, paving the way for potential economic modeling and pathosystem specific evaluation. These results highlight the importance of studying the effect of genetics on landscape scale spatial dynamics within host-pathogen disease systems.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Benjamin Watkinson-Powell
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
| | - Christopher A Gilligan
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
| | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
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18
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Weiland JJ, Bornemann K, Neubauer JD, Khan MFR, Bolton MD. Prevalence and Distribution of Beet Necrotic Yellow Vein Virus Strains in North Dakota and Minnesota. PLANT DISEASE 2019; 103:2083-2089. [PMID: 31210599 DOI: 10.1094/pdis-02-19-0360-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Beet necrotic yellow vein virus (BNYVV) is the causal agent of rhizomania, a disease of global importance to the sugar beet industry. The most widely implemented resistance gene to rhizomania to date is Rz1, but resistance has been circumvented by resistance-breaking (RB) isolates worldwide. In an effort to gain greater understanding of the distribution of BNYVV and the nature of RB isolates in Minnesota and eastern North Dakota, sugar beet plants were grown in 594 soil samples obtained from production fields and subsequently were analyzed for the presence of BNYVV as well as coding variability in the viral P25 gene, the gene previously implicated in the RB pathotype. Baiting of virus from the soil with sugar beet varieties possessing no known resistance to rhizomania resulted in a disease incidence level of 10.6% in the region examined. Parallel baiting analysis of sugar beet genotypes possessing Rz1, the more recently introgressed Rz2, and with the combination of Rz1 + Rz2 resulted in a disease incidence level of 4.2, 1.0, and 0.8%, respectively. Virus sequences recovered from sugar beet bait plants possessing resistance genes Rz1 and/or Rz2 exhibited reduced genetic diversity in the P25 gene relative to those recovered from the susceptible genotype while confirming the hypervariable nature of the coding for amino acids (AAs) at position 67 and 68 in the P25 protein. In contrast to previous reports, we did not find an association between any one specific AA signature at these positions and the ability to circumvent Rz1-mediated resistance. The data document ongoing virulence development in BNYVV populations to previously resistant varieties and provide a baseline for the analysis of genetic change in the virus population that may accompany the implementation of new resistance genes to manage rhizomania.
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Affiliation(s)
- John J Weiland
- 1United States Department of Agriculture - Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
| | - Kathrin Bornemann
- 1United States Department of Agriculture - Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
- 2Department of Plant Pathology, North Dakota State University, Fargo, ND
| | - Jonathan D Neubauer
- 1United States Department of Agriculture - Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
| | - Mohamed F R Khan
- 2Department of Plant Pathology, North Dakota State University, Fargo, ND
- 3Department of Plant Pathology, University of Minnesota, St. Paul, MN
| | - Melvin D Bolton
- 1United States Department of Agriculture - Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
- 2Department of Plant Pathology, North Dakota State University, Fargo, ND
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Numminen E, Vaumourin E, Parratt SR, Poulin L, Laine AL. Variation and correlations between sexual, asexual and natural enemy resistance life-history traits in a natural plant pathogen population. BMC Evol Biol 2019; 19:142. [PMID: 31299905 PMCID: PMC6624897 DOI: 10.1186/s12862-019-1468-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/26/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Understanding the mechanisms by which diversity is maintained in pathogen populations is critical for epidemiological predictions. Life-history trade-offs have been proposed as a hypothesis for explaining long-term maintenance of variation in pathogen populations, yet the empirical evidence supporting trade-offs has remained mixed. This is in part due to the challenges of documenting successive pathogen life-history stages in many pathosystems. Moreover, little is understood of the role of natural enemies of pathogens on their life-history evolution. RESULTS We characterize life-history-trait variation and possible trade-offs in fungal pathogen Podosphaera plantaginis infecting the host plant Plantago lanceolata. We measured the timing of both asexual and sexual stages, as well as resistance to a hyperparasite of seven pathogen strains that vary in their prevalence in nature. We find significant variation among the strains in their life-history traits that constitute the infection cycle, but no evidence for trade-offs among pathogen development stages, apart from fast pathogen growth coninciding with fast hyperparasite growth. Also, the seemingly least fit pathogen strain was the most prevalent in the nature. CONCLUSIONS We conclude that in the nature environmental variation, and interactions with the antagonists of pathogens themselves may maintain variation in pathogen populations.
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Affiliation(s)
- Elina Numminen
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland.
| | - Elise Vaumourin
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland
| | - Steven R Parratt
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland.,University of Liverpool, Institute of Integrative Biology, Liverpool, L69 3BX, UK
| | - Lucie Poulin
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland.,Université de Nantes, Faculté des Sciences et des Techniques, Laboratoire de Biologie et de Pathologie Végétales (LBPV), EA 1157, SFR 4207 QUASAV, 2, rue de la Houssinière, BP 92 208, F-44322, Nantes Cedex 3, France
| | - Anna-Liisa Laine
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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Bera S, Fraile A, García-Arenal F. Analysis of Fitness Trade-Offs in the Host Range Expansion of an RNA Virus, Tobacco Mild Green Mosaic Virus. J Virol 2018; 92:e01268-18. [PMID: 30257999 PMCID: PMC6258955 DOI: 10.1128/jvi.01268-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022] Open
Abstract
The acquisition of new hosts provides a virus with more opportunities for transmission and survival but may be limited by across-host fitness trade-offs. Major causes of across-host trade-offs are antagonistic pleiotropy, that is, host differential phenotypic effects of mutations, a Genotype x Environment interaction, and epistasis, a Genotype x Genotype interaction. Here, we analyze if there are trade-offs, and what are the causes, associated with the acquisition by tobacco mild green mosaic virus (TMGMV) of a new host. For this, the multiplication of sympatric field isolates of TMGMV from its wild reservoir host Nicotiana glauca and from pepper crops was quantified in the original and the heterologous hosts. TMGMV isolates from N. glauca were adapted to their host, but pepper isolates were not adapted to pepper, and the acquisition of this new host was associated with a fitness penalty in the original host. Analyses of the collection of field isolates and of mutant genotypes derived from biologically active cDNA clones showed a role of mutations in the coat protein and the 3' untranslated region in determining within-host virus fitness. Fitness depended on host-specific effects of these mutations, on the genetic background in which they occurred, and on higher-order interactions of the type Genotype x Genotype x Environment. These types of effects had been reported to generate across-host fitness trade-offs under experimental evolution. Our results show they may also operate in heterogeneous natural environments and could explain why pepper isolates were not adapted to pepper and their lower fitness in N. glaucaIMPORTANCE The acquisition of new hosts conditions virus epidemiology and emergence; hence it is important to understand the mechanisms behind host range expansion. Experimental evolution studies have identified antagonistic pleiotropy and epistasis as genetic mechanisms that limit host range expansion, but studies from virus field populations are few. Here, we compare the performance of isolates of tobacco mild green mosaic virus from its reservoir host, Nicotiana glauca, and its new host, pepper, showing that acquisition of a new host was not followed by adaptation to it but was associated with a fitness loss in the original host. Analysis of mutations determining host-specific virus multiplication identified antagonistic pleiotropy, epistasis, and host-specific epistasis as mechanisms generating across-host fitness trade-offs that may prevent adaptation to pepper and cause a loss of fitness in N. glauca Thus, mechanisms determining trade-offs, identified under experimental evolution, could also operate in the heterogeneous environment in which natural plant virus populations occur.
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Affiliation(s)
- Sayanta Bera
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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Laine AL, Mäkinen H. Life-history correlations change under coinfection leading to higher pathogen load. Evol Lett 2018; 2:126-133. [PMID: 30283670 PMCID: PMC6121793 DOI: 10.1002/evl3.48] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/21/2018] [Indexed: 12/12/2022] Open
Abstract
The ability of a parasite strain to establish and grow on its host may be drastically altered by simultaneous infection by other parasite strains. However, we still lack an understanding of how life-history allocations may change under coinfection, although life-history correlations are a critical mechanism restricting the evolutionary potential and epidemiological dynamics of pathogens. Here, we study how life-history stages and their correlations change in the obligate fungal pathogen Podosphaera plantaginis under single infection and coinfection scenarios. We find increased pathogen loads under coinfection, but this is not explained by an enhanced performance at any of the life-history stages that constitute infections. Instead, we show that under coinfection the correlation between timing of sporulation and final pathogen load becomes positive. The changes in pathogen life-history allocations leading to more severe infections under coinfection can have far-reaching epidemiological consequences, as well as implication for our understanding of the evolution of virulence.
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Affiliation(s)
- Anna-Liisa Laine
- Research Programme in Organismal & Evolutionary Biology University of Helsinki PO Box 65 (Viikinkaari 1) FI-00014 Finland
| | - Hannu Mäkinen
- Research Programme in Organismal & Evolutionary Biology University of Helsinki PO Box 65 (Viikinkaari 1) FI-00014 Finland
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22
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Guan X, Yang C, Fu J, Du Z, Ho SY, Gao F. Rapid evolutionary dynamics of pepper mild mottle virus. Virus Res 2018; 256:96-99. [DOI: 10.1016/j.virusres.2018.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/26/2018] [Accepted: 08/04/2018] [Indexed: 11/24/2022]
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Abstract
The study of tobacco mosaic virus and other tobamovirus species has greatly contributed to the development of all areas of virology, including virus evolution. Research with tobamoviruses has been pioneer, or particularly significant, in all major areas of research in this field, including: the characterization of the genetic diversity of virus populations, the mechanisms and rates of generation of genetic diversity, the analysis of the genetic structure of virus populations and of the factors that shape it, the adaptation of viruses to hosts and the evolution of host range, and the evolution of virus taxa and of virus-host interactions. Many of these continue to be hot topics in evolutionary biology, or have been identified recently as such, including (i) host-range evolution, (ii) predicting the overcoming of resistance in crops, (iii) trade-offs between virus life-history traits in virus evolution, and (iv) the codivergence of viruses and hosts at different taxonomical and spatial scales. Tobamoviruses may be particularly appropriate to address these topics with plant viruses, as they provide convenient experimental systems, and as the detailed knowledge on their molecular and structural biology allows the analysis of the mechanisms behind evolutionary processes. Also, the extensive information on parameters related to infection dynamics and population structure may facilitate the development of realistic models to predict virus evolution. Certainly, tobamoviruses will continue to be favorite system for the study of virus evolution.
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Affiliation(s)
- Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I., Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I., Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain.
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24
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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25
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McLeish MJ, Fraile A, García-Arenal F. Ecological Complexity in Plant Virus Host Range Evolution. Adv Virus Res 2018; 101:293-339. [PMID: 29908592 DOI: 10.1016/bs.aivir.2018.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution. Recent work shows that the distributions of pathogenic and resistant genotypes, vectors, and other resources supporting transmission vary widely in the environment, producing both expected and unanticipated patterns. The distributions of all of these factors are influenced further by competitive effects, natural enemies, anthropogenic disturbance, the abiotic environment, and herbivory to mention some. We suggest the need for further development of approaches that (i) explicitly consider resource use and the abiotic and biotic factors that affect the strategies by which viruses exploit resources; and (ii) are sensitive across scales. Host range and habitat specificity will largely determine which phyla are most likely to be new hosts, but predicting which host and when it is likely to be infected is enormously challenging because it is unclear how environmental heterogeneity affects the interactions of viruses and hosts.
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Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain.
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26
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Wininger K, Rank N. Evolutionary dynamics of interactions between plants and their enemies: comparison of herbivorous insects and pathogens. Ann N Y Acad Sci 2017; 1408:46-60. [PMID: 29125186 DOI: 10.1111/nyas.13541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 09/29/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023]
Abstract
Plants colonized land over 400 million years ago. Shortly thereafter, organisms began to consume terrestrial plant tissue as a nutritional resource. Most plant enemies are plant pathogens or herbivores, and they impose natural selection for plants to evolve defenses. These traits generate selection pressures on enemies. Coevolution between terrestrial plants and their enemies is an important element of the evolutionary history of both groups. However, coevolutionary studies of plant-pathogen interactions have tended to focus on different research topics than plant-herbivore interactions. Specifically, studies of plant-pathogen interactions often adopt a "gene-for-gene" conceptual framework. In contrast, studies of plants and herbivores often investigate escalation or elaboration of plant defense and herbivore adaptations to overcome it. The main exceptions to the general pattern are studies that focus on small, sessile herbivores that share many features with plant pathogens, studies that incorporate both herbivores and pathogens into a single investigation, and studies that test aspects of Thompson's geographic mosaic theory for coevolution. We discuss the implications of these findings for future research.
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Affiliation(s)
- Kerry Wininger
- Department of Biology, Sonoma State University, Rohnert Park, California
| | - Nathan Rank
- Department of Biology, Sonoma State University, Rohnert Park, California
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Djidjou-Demasse R, Moury B, Fabre F. Mosaics often outperform pyramids: insights from a model comparing strategies for the deployment of plant resistance genes against viruses in agricultural landscapes. THE NEW PHYTOLOGIST 2017; 216:239-253. [PMID: 28776688 DOI: 10.1111/nph.14701] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
The breakdown of plant virus resistance genes is a major issue in agriculture. We investigated whether a set of resistance genes would last longer when stacked into a single plant cultivar (pyramiding) or when deployed individually in regional mosaics (mosaic strategy). We modeled the genetic and epidemiological processes shaping the demogenetic dynamics of viruses under a multilocus gene-for-gene system, from the plant to landscape scales. The landscape consisted of many fields, was subject to seasonality, and of a reservoir hosting viruses year-round. Strategy performance depended principally on the fitness costs of adaptive mutations, epidemic intensity before resistance deployment and landscape connectivity. Mosaics were at least as good as pyramiding strategies in most production situations tested. Pyramiding strategies performed better only with slowly changing virus reservoir dynamics. Mosaics are more versatile than pyramiding strategies, and we found that deploying a mosaic of three to five resistance genes generally provided effective disease control, unless the epidemics were driven mostly by within-field infections. We considered the epidemiological and evolutionary mechanisms underlying the greater versatility of mosaics in our case study, with a view to providing breeders and growers with guidance as to the most appropriate deployment strategy.
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Affiliation(s)
| | - Benoît Moury
- UR 407, Pathologie Végétale, INRA, Montfavet, F-84140, France
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28
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Bera S, Moreno-Pérez MG, García-Figuera S, Pagán I, Fraile A, Pacios LF, García-Arenal F. Pleiotropic Effects of Resistance-Breaking Mutations on Particle Stability Provide Insight into Life History Evolution of a Plant RNA Virus. J Virol 2017; 91:e00435-17. [PMID: 28679755 PMCID: PMC5571237 DOI: 10.1128/jvi.00435-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022] Open
Abstract
In gene-for-gene host-virus interactions, virus evolution to infect and multiply in previously resistant host genotypes, i.e., resistance breaking, is a case of host range expansion, which is predicted to be associated with fitness penalties. Negative effects of resistance-breaking mutations on within-host virus multiplication have been documented for several plant viruses. However, understanding virus evolution requires analyses of potential trade-offs between different fitness components. Here we analyzed whether coat protein (CP) mutations in Pepper mild mottle virus that break L-gene resistance in pepper affect particle stability and, thus, survival in the environment. For this purpose, CP mutations determining the overcoming of L 3 and L 4 resistance alleles were introduced in biologically active cDNA clones. The kinetics of the in vitro disassembly of parental and mutant particles were compared under different conditions. Resistance-breaking mutations variously affected particle stability. Structural analyses identified the number and type of axial and side interactions of adjacent CP subunits in virions, which explained differences in particle stability and contribute to understanding of tobamovirus disassembly. Resistance-breaking mutations also affected virus multiplication and virulence in the susceptible host, as well as infectivity. The sense and magnitude of the effects of resistance-breaking mutations on particle stability, multiplication, virulence, or infectivity depended on the specific mutation rather than on the ability to overcome the different resistance alleles, and effects on different traits were not correlated. Thus, the results do not provide evidence of links or trade-offs between particle stability, i.e., survival, and other components of virus fitness or virulence.IMPORTANCE The effect of survival on virus evolution remains underexplored, despite the fact that life history trade-offs may constrain virus evolution. We approached this topic by analyzing whether breaking of L-gene resistance in pepper by Pepper mild mottle virus, determined by coat protein (CP) mutations, is associated with reduced particle stability and survival. Resistance-breaking mutations affected particle stability by altering the interactions between CP subunits. However, the sense and magnitude of these effects were unrelated to the capacity to overcome different resistance alleles. Thus, resistance breaking was not traded with survival. Resistance-breaking mutations also affected virus fitness within the infected host, virulence, and infectivity in a mutation-specific manner. Comparison of the effects of CP mutations on these various traits indicates that there are neither trade-offs nor positive links between survival and other life history traits. These results demonstrate that trade-offs between life history traits may not be a general constraint in virus evolution.
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Affiliation(s)
- Sayanta Bera
- Centro de Biotecnología y Genómica de Plantas and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Manuel G Moreno-Pérez
- Centro de Biotecnología y Genómica de Plantas and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Sara García-Figuera
- Centro de Biotecnología y Genómica de Plantas and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Luis F Pacios
- Centro de Biotecnología y Genómica de Plantas and Escuela Técnica Superior de Ingenieros de Montes, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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29
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Susi H, Laine AL. Host resistance and pathogen aggressiveness are key determinants of coinfection in the wild. Evolution 2017; 71:2110-2119. [PMID: 28608539 DOI: 10.1111/evo.13290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/23/2017] [Indexed: 12/24/2022]
Abstract
Coinfection, whereby the same host is infected by more than one pathogen strain, may favor faster host exploitation rates as strains compete for the same limited resources. Hence, coinfection is expected to have major consequences for pathogen evolution, virulence, and epidemiology. Theory predicts genetic variation in host resistance and pathogen infectivity to play a key role in how coinfections are formed. The limited number of studies available has demonstrated coinfection to be a common phenomenon, but little is known about how coinfection varies in space, and what its determinants are. Our aim is to understand how variation in host resistance and pathogen infectivity and aggressiveness contribute to how coinfections are formed in the interaction between fungal pathogen Podosphaera plantaginis and Plantago lanceolata. Our phenotyping study reveals that more aggressive strains are more likely to form coinfections than less aggressive strains in the natural populations. In the natural populations most of the variation in coinfection is found at the individual plant level, and results from a common garden study confirm the prevalence of coinfection to vary significantly among host genotypes. These results show that genetic variation in both the host and pathogen populations are key determinants of coinfection in the wild.
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Affiliation(s)
- Hanna Susi
- Metapopulation Research Centre, Department of Biosciences, PO Box 65 (Viikinkaari 1),, FI-00014, Finland
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, PO Box 65 (Viikinkaari 1),, FI-00014, Finland
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30
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Koh SH, Li H, Sivasithamparam K, Admiraal R, Jones MGK, Wylie SJ. Evolution of a wild-plant tobamovirus passaged through an exotic host: Fixation of mutations and increased replication. Virus Evol 2017; 3:vex001. [PMID: 28458912 PMCID: PMC5399921 DOI: 10.1093/ve/vex001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Tobamovirus is a group of viruses that have become serious pathogens of crop plants. As part of a study informing risk of wild plant virus spill over to crops, we investigated the capacity of a solanaceous-infecting tobamovirus from an isolated indigenous flora to adapt to new exotic hosts. Yellow tailflower mild mottle virus (YTMMV) (genus Tobamovirus, family Virgaviridae) was isolated from a wild plant of yellow tailflower (Anthocercis littoria, family Solanaceae) and initially passaged through a plant of Nicotiana benthamiana, then one of Nicotiana glutinosa where a single local lesion was used to inoculate a N. benthamiana plant. Sap from this plant was used as starting material for nine serial passages through three plant species. The virus titre was recorded periodically, and 85% of the virus genome was sequenced at each passage for each host. Six polymorphic sites were found in the YTMMV genome across all hosts and passages. At five of these, the alternate alleles became fixed in the viral genome until the end of the experiment. Of these five alleles, one was a non-synonymous mutation (U1499C) that occurred only when the virus replicated in tomato. The mutant isolate harbouring U1499C, designated YTMMV-δ, increased its titre over passages in tomato and outcompeted the wild-type isolate when both were co-inoculated to tomato. That YTMMV-δ had greater reproductive fitness in an exotic host than did the wild type isolate suggests YTMMV evolution is influenced by host changes.
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Affiliation(s)
- Shu Hui Koh
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Hua Li
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Krishnapillai Sivasithamparam
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Ryan Admiraal
- School of Engineering and Information Technology, Mathematics & Statistics, Murdoch University, Perth, WA 6150, Australia
| | - Michael G K Jones
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Stephen J Wylie
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia
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31
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Moreno-Pérez MG, García-Luque I, Fraile A, García-Arenal F. Mutations That Determine Resistance Breaking in a Plant RNA Virus Have Pleiotropic Effects on Its Fitness That Depend on the Host Environment and on the Type, Single or Mixed, of Infection. J Virol 2016; 90:9128-37. [PMID: 27489266 PMCID: PMC5044817 DOI: 10.1128/jvi.00737-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/25/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Overcoming host resistance in gene-for-gene host-virus interactions is an important instance of host range expansion, which can be hindered by across-host fitness trade-offs. Trade-offs are generated by negative effects of host range mutations on the virus fitness in the original host, i.e., by antagonistic pleiotropy. It has been reported that different mutations in Pepper mild mottle virus (PMMoV) coat protein result in overcoming L-gene resistance in pepper. To analyze if resistance-breaking mutations in PMMoV result in antagonistic pleiotropy, all reported mutations determining the overcoming of L(3) and L(4) alleles were introduced in biologically active cDNA clones. Then, the parental and mutant virus genotypes were assayed in susceptible pepper genotypes with an L(+), L(1), or L(2) allele, in single and in mixed infections. Resistance-breaking mutations had pleiotropic effects on the virus fitness that, according to the specific mutation, the host genotype, and the type of infection, single or mixed with other virus genotypes, were antagonistic or positive. Thus, resistance-breaking mutations can generate fitness trade-offs both across hosts and across types of infection, and the frequency of host range mutants will depend on the genetic structure of the host population and on the frequency of mixed infections by different virus genotypes. Also, resistance-breaking mutations variously affected virulence, which may further influence the evolution of host range expansion. IMPORTANCE A major cause of virus emergence is host range expansion, which may be hindered by across-host fitness trade-offs caused by negative pleiotropy of host range mutations. An important instance of host range expansion is overcoming host resistance in gene-for-gene plant-virus interactions. We analyze here if mutations in the coat protein of Pepper mild mottle virus determining L-gene resistance-breaking in pepper have associated fitness penalties in susceptible host genotypes. Results show that pleiotropic effects of resistance-breaking mutations on virus fitness depend on the specific mutation, the susceptible host genotype, and the type of infection, single or mixed, with other virus genotypes. Accordingly, resistance-breaking mutations can have negative, positive, or no pleiotropic effects on virus fitness. These results underscore the complexity of host range expansion evolution and, specifically, the difficulty of predicting the overcoming of resistance factors in crops.
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Affiliation(s)
- Manuel G Moreno-Pérez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | | | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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32
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The Influence of Crop Habitat and Control Strategies on Pepper Viruses in Andalusia (Spain). HORTICULTURAE 2016. [DOI: 10.3390/horticulturae2040015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wang Y, Hajimorad MR. Gain of virulence by Soybean mosaic virus on Rsv4-genotype soybeans is associated with a relative fitness loss in a susceptible host. MOLECULAR PLANT PATHOLOGY 2016; 17:1154-9. [PMID: 26662495 PMCID: PMC6638382 DOI: 10.1111/mpp.12354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
'Gene-for-gene' theory predicts that gain of virulence by an avirulent pathogen on plants expressing resistance (R) genes is associated with fitness loss in susceptible hosts. However, the validity of this prediction has been studied in only a few plant viral pathosystems. In this study, the Soybean mosaic virus (SMV)-Rsv4 pathosystem was exploited to test this prediction. In Rsv4-genotype soybeans, P3 of avirulent SMV strains provokes an as yet uncharacterized resistance mechanism that restricts the invading virus to the inoculated leaves. A single amino acid substitution in P3 functionally converts an avirulent to a virulent strain, suggesting that the genetic composition of P3 plays a crucial role in virulence on Rsv4-genotype soybeans. In this study, we examined the impact of gain of virulence mutation(s) on the fitness of virulent variants derived from three avirulent SMV strains in a soybean genotype lacking the Rsv4 gene. Our data demonstrate that gain of virulence mutation(s) by all avirulent viruses on Rsv4-genotype soybean is associated with a relative fitness loss in a susceptible host. The implications of this finding on the durable deployment of the Rsv4 gene in soybean are discussed.
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Affiliation(s)
- Y Wang
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - M R Hajimorad
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, 37996, USA
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34
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Atsumi G, Suzuki H, Miyashita Y, Choi SH, Hisa Y, Rihei S, Shimada R, Jeon EJ, Abe J, Nakahara KS, Uyeda I. P3N-PIPO, a Frameshift Product from the P3 Gene, Pleiotropically Determines the Virulence of Clover Yellow Vein Virus in both Resistant and Susceptible Peas. J Virol 2016; 90:7388-7404. [PMID: 27279605 PMCID: PMC4984661 DOI: 10.1128/jvi.00190-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/25/2016] [Indexed: 12/17/2022] Open
Abstract
UNLABELLED Peas carrying the cyv1 recessive resistance gene are resistant to clover yellow vein virus (ClYVV) isolates No.30 (Cl-No.30) and 90-1 (Cl-90-1) but can be infected by a derivative of Cl-90-1 (Cl-90-1 Br2). The main determinant for the breaking of cyv1 resistance by Cl-90-1 Br2 is P3N-PIPO produced from the P3 gene via transcriptional slippage, and the higher level of P3N-PIPO produced by Cl-90-1 Br2 than by Cl-No.30 contributes to the breaking of resistance. Here we show that P3N-PIPO is also a major virulence determinant in susceptible peas that possess another resistance gene, Cyn1, which does not inhibit systemic infection with ClYVV but causes hypersensitive reaction-like lethal systemic cell death. We previously assumed that the susceptible pea cultivar PI 226564 has a weak allele of Cyn1 Cl-No.30 did not induce cell death, but Cl-90-1 Br2 killed the plants. Our results suggest that P3N-PIPO is recognized by Cyn1 and induces cell death. Unexpectedly, heterologously strongly expressed P3N-PIPO of Cl-No.30 appears to be recognized by Cyn1 in PI 226564. The level of P3N-PIPO accumulation from the P3 gene of Cl-No.30 was significantly lower than that of Cl-90-1 Br2 in a Nicotiana benthamiana transient assay. Therefore, Cyn1-mediated cell death also appears to be determined by the level of P3N-PIPO. The more efficiently a ClYVV isolate broke cyv1 resistance, the more it induced cell death systemically (resulting in a loss of the environment for virus accumulation) in susceptible peas carrying Cyn1, suggesting that antagonistic pleiotropy of P3N-PIPO controls the resistance breaking of ClYVV. IMPORTANCE Control of plant viral disease has relied on the use of resistant cultivars; however, emerging mutant viruses have broken many types of resistance. Recently, we revealed that Cl-90-1 Br2 breaks the recessive resistance conferred by cyv1, mainly by accumulating a higher level of P3N-PIPO than that of the nonbreaking isolate Cl-No.30. Here we show that a susceptible pea line recognized the increased amount of P3N-PIPO produced by Cl-90-1 Br2 and activated the salicylic acid-mediated defense pathway, inducing lethal systemic cell death. We found a gradation of virulence among ClYVV isolates in a cyv1-carrying pea line and two susceptible pea lines. This study suggests a trade-off between breaking of recessive resistance (cyv1) and host viability; the latter is presumably regulated by the dominant Cyn1 gene, which may impose evolutionary constraints upon P3N-PIPO for overcoming resistance. We propose a working model of the host strategy to sustain the durability of resistance and control fast-evolving viruses.
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Affiliation(s)
- Go Atsumi
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- National Institute of Advanced Industrial Science and Technology, Sapporo, Hokkaido, Japan
| | - Haruka Suzuki
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yuri Miyashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Sun Hee Choi
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yusuke Hisa
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shunsuke Rihei
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ryoko Shimada
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Eun Jin Jeon
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Junya Abe
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kenji S Nakahara
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Ichiro Uyeda
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Fournet S, Eoche-Bosy D, Renault L, Hamelin FM, Montarry J. Adaptation to resistant hosts increases fitness on susceptible hosts in the plant parasitic nematode Globodera pallida. Ecol Evol 2016; 6:2559-68. [PMID: 27066239 PMCID: PMC4797161 DOI: 10.1002/ece3.2079] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/28/2016] [Accepted: 02/09/2016] [Indexed: 12/30/2022] Open
Abstract
Trade-offs between virulence (defined as the ability to infect a resistant host) and life-history traits are of particular interest in plant pathogens for durable management of plant resistances. Adaptation to plant resistances (i.e., virulence acquisition) is indeed expected to be associated with a fitness cost on susceptible hosts. Here, we investigated whether life-history traits involved in the fitness of the potato cyst nematode Globodera pallida are affected in a virulent lineage compared to an avirulent one. Both lineages were obtained from the same natural population through experimental evolution on resistant and susceptible hosts, respectively. Unexpectedly, we found that virulent lineages were more fit than avirulent lineages on susceptible hosts: they produced bigger cysts, containing more larvae and hatching faster. We thus discuss possible reasons explaining why virulence did not spread into natural G. pallida populations.
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Affiliation(s)
- Sylvain Fournet
- INRA UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection) F-35653 Le Rheu France
| | - Delphine Eoche-Bosy
- INRA UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection) F-35653 Le Rheu France
| | - Lionel Renault
- INRA UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection) F-35653 Le Rheu France
| | - Frédéric M Hamelin
- INRA UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection) F-35653 Le Rheu France
| | - Josselin Montarry
- INRA UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection) F-35653 Le Rheu France
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Fabre F, Rousseau E, Mailleret L, Moury B. Epidemiological and evolutionary management of plant resistance: optimizing the deployment of cultivar mixtures in time and space in agricultural landscapes. Evol Appl 2015; 8:919-32. [PMID: 26640518 PMCID: PMC4662345 DOI: 10.1111/eva.12304] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/05/2015] [Indexed: 12/11/2022] Open
Abstract
The management of genes conferring resistance to plant–pathogens should make it possible to control epidemics (epidemiological perspective) and preserve resistance durability (evolutionary perspective). Resistant and susceptible cultivars must be strategically associated according to the principles of cultivar mixture (within a season) and rotation (between seasons). We explored these questions by modeling the evolutionary and epidemiological processes shaping the dynamics of a pathogen population in a landscape composed of a seasonal cultivated compartment and a reservoir compartment hosting pathogen year-round. Optimal deployment strategies depended mostly on the molecular basis of plant–pathogen interactions and on the agro-ecological context before resistance deployment, particularly epidemic intensity and landscape connectivity. Mixtures were much more efficient in landscapes in which between-field infections and infections originating from the reservoir were more prevalent than within-field infections. Resistance genes requiring two mutations of the pathogen avirulence gene to be broken down, rather than one, were particularly useful when infections from the reservoir predominated. Combining mixture and rotation principles were better than the use of the same mixture each season as (i) they controlled epidemics more effectively in situations in which within-field infections or infections from the reservoir were frequent and (ii) they fulfilled the epidemiological and evolutionary perspectives.
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Affiliation(s)
- Frédéric Fabre
- UMR 1065 Unité Santé et Agroécologie du Vignoble, INRA Villenave d'Ornon Cedex, France
| | - Elsa Rousseau
- Biocore Team, INRIA Sophia Antipolis, France ; UMR 1355 Institut Sophia Agrobiotech, INRA Sophia Antipolis, France ; UMR 7254 Institut Sophia Agrobiotech, Université Nice Sophia Antipolis Sophia Antipolis, France ; UMR 7254 Institut Sophia Agrobiotech, CNRS Sophia Antipolis, France ; UR 407 Pathologie Végétale, INRA Montfavet, France
| | - Ludovic Mailleret
- Biocore Team, INRIA Sophia Antipolis, France ; UMR 1355 Institut Sophia Agrobiotech, INRA Sophia Antipolis, France ; UMR 7254 Institut Sophia Agrobiotech, Université Nice Sophia Antipolis Sophia Antipolis, France ; UMR 7254 Institut Sophia Agrobiotech, CNRS Sophia Antipolis, France
| | - Benoît Moury
- UR 407 Pathologie Végétale, INRA Montfavet, France
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Murray GGR, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A, Welch JJ. The effect of genetic structure on molecular dating and tests for temporal signal. Methods Ecol Evol 2015; 7:80-89. [PMID: 27110344 PMCID: PMC4832290 DOI: 10.1111/2041-210x.12466] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/23/2015] [Indexed: 12/23/2022]
Abstract
‘Dated‐tip’ methods of molecular dating use DNA sequences sampled at different times, to estimate the age of their most recent common ancestor. Several tests of ‘temporal signal’ are available to determine whether data sets are suitable for such analysis. However, it remains unclear whether these tests are reliable. We investigate the performance of several tests of temporal signal, including some recently suggested modifications. We use simulated data (where the true evolutionary history is known), and whole genomes of methicillin‐resistant Staphylococcus aureus (to show how particular problems arise with real‐world data sets). We show that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artefact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period. More positively, we show that a ‘clustered permutation’ approach introduced by Duchêne et al. (Molecular Biology and Evolution, 32, 2015, 1895) can successfully correct for this artefact in all cases and introduce techniques for implementing this method with real data sets. The confounding of temporal and genetic structures may be difficult to avoid in practice, particularly for outbreaks of infectious disease, or when using ancient DNA. Therefore, we recommend the use of ‘clustered permutation’ for all analyses. The failure of the standard tests may explain why different methods of dating pathogen origins have reached such wildly different conclusions.
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Affiliation(s)
- Gemma G R Murray
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
| | - Fang Wang
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
| | - Ewan M Harrison
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ES UK
| | - Gavin K Paterson
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ESUK; School of Biological, Biomedical and Environmental Sciences University of Hull Cottingham Road Hull HU6 7RX UK
| | - Alison E Mather
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ESUK; Wellcome Trust Sanger Institute Hinxton CB10 1SA UK
| | | | - Mark A Holmes
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ES UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology University of Edinburgh King's Buildings Edinburgh EH9 3FL UK
| | - John J Welch
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
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38
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Peiró A, Cañizares MC, Rubio L, López C, Moriones E, Aramburu J, Sánchez-Navarro J. The movement protein (NSm) of Tomato spotted wilt virus is the avirulence determinant in the tomato Sw-5 gene-based resistance. MOLECULAR PLANT PATHOLOGY 2014; 15:802-13. [PMID: 24690181 PMCID: PMC6638753 DOI: 10.1111/mpp.12142] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The avirulence determinant triggering the resistance conferred by the tomato gene Sw-5 against Tomato spotted wilt virus (TSWV) is still unresolved. Sequence comparison showed two substitutions (C118Y and T120N) in the movement protein NSm present only in TSWV resistance-breaking (RB) isolates. In this work, transient expression of NSm of three TSWV isolates [RB1 (T120N), RB2 (C118Y) and non-resistance-breaking (NRB)] in Nicotiana benthamiana expressing Sw-5 showed a hypersensitive response (HR) only with NRB. Exchange of the movement protein of Alfalfa mosaic virus (AMV) with NSm supported cell-to-cell and systemic transport of the chimeric AMV RNAs into N. tabacum with or without Sw-5, except for the constructs with NBR when Sw-5 was expressed, although RB2 showed reduced cell-to-cell transport. Mutational analysis revealed that N120 was sufficient to avoid the HR, but the substitution V130I was required for systemic transport. Finally, co-inoculation of RB and NRB AMV chimeric constructs showed different prevalence of RB or NBR depending on the presence or absence of Sw-5. These results indicate that NSm is the avirulence determinant for Sw-5 resistance, and mutations C118Y and T120N are responsible for resistance breakdown and have a fitness penalty in the context of the heterologous AMV system.
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Affiliation(s)
- Ana Peiró
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022, Valencia, Spain
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39
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Abstract
Viruses are common agents of plant infectious diseases. During last decades, worldwide agriculture production has been compromised by a series of epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that show new pathogenic and epidemiological properties. Virus emergence has been generally associated with ecological change or with intensive agronomical practices. However, the complete picture is much more complex since the viral populations constantly evolve and adapt to their new hosts and vectors. This chapter puts emergence of plant viruses into the framework of evolutionary ecology, genetics, and epidemiology. We will stress that viral emergence begins with the stochastic transmission of preexisting genetic variants from the reservoir to the new host, whose fate depends on their fitness on each hosts, followed by adaptation to new hosts or vectors, and finalizes with an efficient epidemiological spread.
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Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Campus UPV, València, Spain; The Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and ETSI Agrónomos, UPM, Campus de Montegancedo, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and ETSI Agrónomos, UPM, Campus de Montegancedo, Madrid, Spain.
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40
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Interaction patterns between potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae. J Virol 2014; 88:9799-807. [PMID: 24942572 DOI: 10.1128/jvi.00930-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The structural pattern of infectivity matrices, which contains infection data resulting from inoculations of a set of hosts by a set of parasites, is a key parameter for our understanding of biological interactions and their evolution. This pattern determines the evolution of parasite pathogenicity and host resistance, the spatiotemporal distribution of host and parasite genotypes, and the efficiency of disease control strategies. Two major patterns have been proposed for plant-virus genotype infectivity matrices. In the gene-for-gene model, infectivity matrices show a nested pattern, where the host ranges of specialist virus genotypes are subsets of the host ranges of less specialized viruses. In contrast, in the matching-allele (MA) model, each virus genotype is specialized to infect one (or a small set of) host genotype(s). The corresponding infectivity matrix shows a modular pattern where infection is frequent for plants and viruses belonging to the same module but rare for those belonging to different modules. We analyzed the structure of infectivity matrices between Potato virus Y (PVY) and plant genotypes in the family Solanaceae carrying different eukaryotic initiation factor 4E (eIF4E)-coding alleles conferring recessive resistance. Whereas this system corresponds mechanistically to an MA model, the expected modular pattern was rejected based on our experimental data. This was mostly because PVY mutations involved in adaptation to a particular plant genotype displayed frequent pleiotropic effects, conferring simultaneously an adaptation to additional plant genotypes with different eIF4E alleles. Such effects should be taken into account for the design of strategies of sustainable control of PVY through plant varietal mixtures or rotations. IMPORTANCE The interaction pattern between host and virus genotypes has important consequences on their respective evolution and on issues regarding the application of disease control strategies. We found that the structure of the interaction between Potato virus Y (PVY) variants and host plants in the family Solanaceae departs significantly from the current model of interaction considered for these organisms because of frequent pleiotropic effects of virus mutations. These mutational effects allow the virus to expand rapidly its range of host plant genotypes, make it very difficult to predict the effects of mutations in PVY infectivity factors, and raise concerns about strategies of sustainable management of plant genetic resistance to viruses.
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41
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Fraile A, Hily JM, Pagán I, Pacios LF, García-Arenal F. Host resistance selects for traits unrelated to resistance-breaking that affect fitness in a plant virus. Mol Biol Evol 2014; 31:928-39. [PMID: 24441034 DOI: 10.1093/molbev/msu045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The acquisition by parasites of the capacity to infect resistant host genotypes, that is, resistance-breaking, is predicted to be hindered by across-host fitness trade-offs. All analyses of costs of resistance-breaking in plant viruses have focused on within-host multiplication without considering other fitness components, which may limit understanding of virus evolution. We have reported that host range expansion of tobamoviruses on L-gene resistant pepper genotypes was associated with severe within-host multiplication penalties. Here, we analyze whether resistance-breaking costs might affect virus survival in the environment by comparing tobamovirus pathotypes differing in infectivity on L-gene resistance alleles. We predicted particle stability from structural models, analyzed particle stability in vitro, and quantified virus accumulation in different plant organs and virus survival in the soil. Survival in the soil differed among tobamovirus pathotypes and depended on differential stability of virus particles. Structure model analyses showed that amino acid changes in the virus coat protein (CP) responsible for resistance-breaking affected the strength of the axial interactions among CP subunits in the rod-shaped particle, thus determining its stability and survival. Pathotypes ranked differently for particle stability/survival and for within-host accumulation. Resistance-breaking costs in survival add to, or subtract from, costs in multiplication according to pathotype. Hence, differential pathotype survival should be considered along with differential multiplication to understand the evolution of the virus populations. Results also show that plant resistance, in addition to selecting for resistance-breaking and for decreased multiplication, also selects for changes in survival, a trait unrelated to the host-pathogen interaction that may condition host range expansion.
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Affiliation(s)
- Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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42
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Zhan J, McDonald BA. Experimental measures of pathogen competition and relative fitness. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:131-53. [PMID: 23767846 DOI: 10.1146/annurev-phyto-082712-102302] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Competition among pathogen strains for limited host resources can have a profound effect on pathogen evolution. A better understanding of the principles and consequences of competition can be useful in designing more sustainable disease management strategies. The competitive ability and relative fitness of a pathogen strain are determined by its intrinsic biological properties, the resistance and heterogeneity of the corresponding host population, the population density and genetic relatedness of the competing strains, and the physical environment. Competitive ability can be inferred indirectly from fitness components, such as basic reproduction rate or transmission rate. However, pathogen strains that exhibit higher fitness components when they infect a host alone may not exhibit a competitive advantage when they co-infect the same host. The most comprehensive measures of competitive ability and relative fitness come from calculating selection coefficients in a mixed infection in a field setting. Mark-release-recapture experiments can be used to estimate fitness costs associated with unnecessary virulence and fungicide resistance.
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Affiliation(s)
- Jiasui Zhan
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Ishibashi K, Mawatari N, Miyashita S, Kishino H, Meshi T, Ishikawa M. Coevolution and hierarchical interactions of Tomato mosaic virus and the resistance gene Tm-1. PLoS Pathog 2012; 8:e1002975. [PMID: 23093939 PMCID: PMC3475678 DOI: 10.1371/journal.ppat.1002975] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/31/2012] [Indexed: 01/16/2023] Open
Abstract
During antagonistic coevolution between viruses and their hosts, viruses have a major advantage by evolving more rapidly. Nevertheless, viruses and their hosts coexist and have coevolved, although the processes remain largely unknown. We previously identified Tm-1 that confers resistance to Tomato mosaic virus (ToMV), and revealed that it encodes a protein that binds ToMV replication proteins and inhibits RNA replication. Tm-1 was introgressed from a wild tomato species Solanum habrochaites into the cultivated tomato species Solanum lycopersicum. In this study, we analyzed Tm-1 alleles in S. habrochaites. Although most part of this gene was under purifying selection, a cluster of nonsynonymous substitutions in a small region important for inhibitory activity was identified, suggesting that the region is under positive selection. We then examined the resistance of S. habrochaites plants to ToMV. Approximately 60% of 149 individuals from 24 accessions were resistant to ToMV, while the others accumulated detectable levels of coat protein after inoculation. Unexpectedly, many S. habrochaites plants were observed in which even multiplication of the Tm-1-resistance-breaking ToMV mutant LT1 was inhibited. An amino acid change in the positively selected region of the Tm-1 protein was responsible for the inhibition of LT1 multiplication. This amino acid change allowed Tm-1 to bind LT1 replication proteins without losing the ability to bind replication proteins of wild-type ToMV. The antiviral spectra and biochemical properties suggest that Tm-1 has evolved by changing the strengths of its inhibitory activity rather than diversifying the recognition spectra. In the LT1-resistant S. habrochaites plants inoculated with LT1, mutant viruses emerged whose multiplication was not inhibited by the Tm-1 allele that confers resistance to LT1. However, the resistance-breaking mutants were less competitive than the parental strains in the absence of Tm-1. Based on these results, we discuss possible coevolutionary processes of ToMV and Tm-1. Viruses rapidly evolve and adapt to their host organisms, and the evolutionary processes can be reproduced in the laboratory (experimental evolution). In contrast, cellular organisms (that can be viral hosts) evolve much more slowly than viruses, but the fact that they have antiviral systems suggests that viruses and their hosts have coevolved. To explore the coevolutionary histories of viruses and their hosts, we focused on Tm-1, a Solanum habrochaites gene that confers resistance to Tomato mosaic virus (ToMV). Based on analyses of the Tm-1 gene sequences in S. habrochaites, we demonstrated that a part of the gene has been under positive selection. Biochemical studies suggested that Tm-1 has evolved to strengthen its inhibitory activity rather than to diversify recognition spectra. In addition, experimental evolution analyses suggested that overcoming the Tm-1-mediated resistance by ToMV is associated with fitness costs. Based on these results, we discuss how ToMV and the plant resistance gene have coevolved.
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Affiliation(s)
- Kazuhiro Ishibashi
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan.
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44
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Wargo AR, Kurath G. Viral fitness: definitions, measurement, and current insights. Curr Opin Virol 2012; 2:538-45. [PMID: 22986085 PMCID: PMC7102723 DOI: 10.1016/j.coviro.2012.07.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/24/2012] [Indexed: 11/03/2022]
Abstract
Viral fitness is an active area of research, with recent work involving an expanded number of human, non-human vertebrate, invertebrate, plant, and bacterial viruses. Many publications deal with RNA viruses associated with major disease emergence events, such as HIV-1, influenza virus, and Dengue virus. Study topics include drug resistance, immune escape, viral emergence, host jumps, mutation effects, quasispecies diversity, and mathematical models of viral fitness. Important recent trends include increasing use of in vivo systems to assess vertebrate virus fitness, and a broadening of research beyond replicative fitness to also investigate transmission fitness and epidemiologic fitness. This is essential for a more integrated understanding of overall viral fitness, with implications for disease management in the future.
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Affiliation(s)
- Andrew R Wargo
- US Geological Survey, Western Fisheries Research Center, 6505 NE 65th Street, Seattle, WA 98115, USA
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Zhan J, Yang L, Zhu W, Shang L, Newton AC. Pathogen populations evolve to greater race complexity in agricultural systems--evidence from analysis of Rhynchosporium secalis virulence data. PLoS One 2012; 7:e38611. [PMID: 22723870 PMCID: PMC3377678 DOI: 10.1371/journal.pone.0038611] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 05/08/2012] [Indexed: 11/19/2022] Open
Abstract
Fitness cost associated with pathogens carrying unnecessary virulence alleles is the fundamental assumption for preventing the emergence of complex races in plant pathogen populations but this hypothesis has rarely been tested empirically on a temporal and spatial scale which is sufficient to distinguish evolutionary signals from experimental error. We analyzed virulence characteristics of ≈ 1000 isolates of the barley pathogen Rhynchosporium secalis collected from different parts of the United Kingdom between 1984 and 2005. We found a gradual increase in race complexity over time with a significant correlation between sampling date and race complexity of the pathogen (r(20) = 0.71, p = 0.0002) and an average loss of 0.1 avirulence alleles (corresponding to an average gain of 0.1 virulence alleles) each year. We also found a positive and significant correlation between barley cultivar diversity and R. secalis virulence variation. The conditions assumed to favour complex races were not present in the United Kingdom and we hypothesize that the increase in race complexity is attributable to the combination of natural selection and genetic drift. Host resistance selects for corresponding virulence alleles to fixation or dominant frequency. Because of the weak fitness penalty of carrying the unnecessary virulence alleles, genetic drift associated with other evolutionary forces such as hitch-hiking maintains the frequency of the dominant virulence alleles even after the corresponding resistance factors cease to be used.
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Affiliation(s)
- Jiasui Zhan
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
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46
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Fabre F, Montarry J, Coville J, Senoussi R, Simon V, Moury B. Modelling the evolutionary dynamics of viruses within their hosts: a case study using high-throughput sequencing. PLoS Pathog 2012; 8:e1002654. [PMID: 22532800 PMCID: PMC3330117 DOI: 10.1371/journal.ppat.1002654] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 03/07/2012] [Indexed: 02/04/2023] Open
Abstract
Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients β(ij) exerted by variant j on variant i are equal to their fitness ratio, r(j)/r(i). Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = -0.45%) and high (s = -13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F(ST), were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts.
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Fabre F, Rousseau E, Mailleret L, Moury B. Durable strategies to deploy plant resistance in agricultural landscapes. THE NEW PHYTOLOGIST 2012; 193:1064-1075. [PMID: 22260272 DOI: 10.1111/j.1469-8137.2011.04019.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The deployment of resistant crops often leads to the emergence of resistance-breaking pathogens that suppress the yield benefit provided by the resistance. Here, we theoretically explored how farmers' main leverages (resistant cultivar choice, resistance deployment strategy, landscape planning and cultural practices) can be best combined to achieve resistance durability while minimizing yield losses as a result of plant viruses. Assuming a gene-for-gene type of interaction, virus epidemics are modelled in a landscape composed of a mosaic of resistant and susceptible fields, subjected to seasonality, and a reservoir hosting viruses year-round. The model links the genetic and the epidemiological processes, shaping at nested scales the demogenetic dynamics of viruses. The choice of the resistance gene (characterized by the equilibrium frequency of the resistance-breaking virus at mutation-selection balance in a susceptible plant) is the most influential leverage of action. Our results showed that optimal strategies of resistance deployment range from 'mixture' (where susceptible and resistant cultivars coexist) to 'pure' strategies (with only resistant cultivar) depending on the resistance characteristics and the epidemiological context (epidemic incidence and landscape connectivity). We demonstrate and discuss gaps concerning virus epidemiology across the agro-ecological interface that must be filled to achieve sustainable disease management.
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Affiliation(s)
- Frédéric Fabre
- INRA, UR 407 Unité De Pathologie Végétale, F-84140 Montfavet, France
| | - Elsa Rousseau
- INRA, UR 407 Unité De Pathologie Végétale, F-84140 Montfavet, France
- INRA, UR 880 URIH, 400 route des Chappes, BP 167, F-06903 Sophia Antipolis, France
| | - Ludovic Mailleret
- INRA, UR 880 URIH, 400 route des Chappes, BP 167, F-06903 Sophia Antipolis, France
- INRIA, Biocore Team, F-06902 Sophia Antipolis, France
| | - Benoit Moury
- INRA, UR 407 Unité De Pathologie Végétale, F-84140 Montfavet, France
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Tena F, Molina-Galdeano M, Serra MT, García-Luque I. A single amino acid in the helicase domain of PMMoV-S is responsible for its enhanced accumulation in C. chinense (L(3)L(3)) plants at 32°C. Virology 2012; 427:34-43. [PMID: 22377122 DOI: 10.1016/j.virol.2012.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 10/15/2011] [Accepted: 01/14/2012] [Indexed: 11/19/2022]
Abstract
In Capsicum chinense (L(3)L(3)) plants a higher accumulation of the tobamovirus Pepper mild mottle virus strain S (PMMoV-S) as compared to the Italian strain PMMoV-I is detected when plants are grown at 32°C. By using a reverse genetic approach, we have established that a single amino acid at position 898 in the helicase domain of the polymerase protein, outside of the conserved regions of the helicase, is critical for the higher accumulation of PMMoV-S observed. It also is necessary for both increased accumulation of viral RNA of both polarities in pepper protoplasts and enhanced cell-to-cell movement in C. chinense plants. The influence of thermoresistance of PMMoV-S, a P(1,2) pathotype, and its prevalence on pepper cultivars over PMMoV-I, a P(1,2,3), pathotype, is discussed.
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Affiliation(s)
- Fátima Tena
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu no 9, 28040 Madrid, Spain
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Abstract
Compared to other vegetable crops, the major viral constraints affecting pepper crops in the Mediterranean basin have been remarkably stable for the past 20 years. Among these viruses, the most prevalent ones are the seed-transmitted tobamoviruses; the aphid-transmitted Potato virus Y and Tobacco etch virus of the genus Potyvirus, and Cucumber mosaic virus member of the genus Cucumovirus; and thrips-transmitted tospoviruses. The last major viral emergence concerns the tospovirus Tomato spotted wilt virus (TSWV), which has undergone major outbreaks since the end of the 1980s and the worldwide dispersal of the thrips vector Frankliniella occidentalis from the western part of the USA. TSWV outbreaks in the Mediterranean area might have been the result of both viral introductions from Northern America and local reemergence of indigenous TSWV isolates. In addition to introductions of new viruses, resistance breakdowns constitute the second case of viral emergences. Notably, the pepper resistance gene Tsw toward TSWV has broken down a few years after its deployment in several Mediterranean countries while there has been an expansion of L³-resistance breaking pepper mild mottle tobamovirus isolates. Beyond the agronomical and economical concerns induced by the breakdowns of virus resistance genes in pepper, they also constitute original models to understand plant-virus interactions and (co)evolution.
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Affiliation(s)
- Benoît Moury
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, Montfavet, France
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50
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Tellier A, Brown JKM. Spatial heterogeneity, frequency-dependent selection and polymorphism in host-parasite interactions. BMC Evol Biol 2011; 11:319. [PMID: 22044632 PMCID: PMC3273489 DOI: 10.1186/1471-2148-11-319] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 11/01/2011] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Genomic and pathology analysis has revealed enormous diversity in genes involved in disease, including those encoding host resistance and parasite effectors (also known in plant pathology as avirulence genes). It has been proposed that such variation may persist when an organism exists in a spatially structured metapopulation, following the geographic mosaic of coevolution. Here, we study gene-for-gene relationships governing the outcome of plant-parasite interactions in a spatially structured system and, in particular, investigate the population genetic processes which maintain balanced polymorphism in both species. RESULTS Following previous theory on the effect of heterogeneous environments on maintenance of polymorphism, we analysed a model with two demes in which the demes have different environments and are coupled by gene flow. Environmental variation is manifested by different coefficients of natural selection, the costs to the host of resistance and to the parasite of virulence, the cost to the host of being diseased and the cost to an avirulent parasite of unsuccessfully attacking a resistant host. We show that migration generates negative direct frequency-dependent selection, a condition for maintenance of stable polymorphism in each deme. Balanced polymorphism occurs preferentially if there is heterogeneity for costs of resistance and virulence alleles among populations and to a lesser extent if there is variation in the cost to the host of being diseased. We show that the four fitness costs control the natural frequency of oscillation of host resistance and parasite avirulence alleles. If demes have different costs, their frequencies of oscillation differ and when coupled by gene flow, there is amplitude death of the oscillations in each deme. Numerical simulations show that for a multiple deme island model, costs of resistance and virulence need not to be present in each deme for stable polymorphism to occur. CONCLUSIONS Our theoretical results confirm the importance of empirical studies for measuring the environmental heterogeneity for genetic costs of resistance and virulence alleles. We suggest that such studies should be developed to investigate the generality of this mechanism for the long-term maintenance of genetic diversity at host and parasite genes.
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Affiliation(s)
- Aurélien Tellier
- Section of Evolutionary Biology, Biocenter, University of Munich, 82152 Planegg-Martinsried, Germany.
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