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Vy TTP, Inoue Y, Asuke S, Chuma I, Nakayashiki H, Tosa Y. The ACE1 secondary metabolite gene cluster is a pathogenicity factor of wheat blast fungus. Commun Biol 2024; 7:812. [PMID: 38965407 PMCID: PMC11224330 DOI: 10.1038/s42003-024-06517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Wheat blast caused by Pyricularia oryzae pathotype Triticum is now becoming a very serious threat to global food security. Here, we report an essential pathogenicity factor of the wheat blast fungus that is recognized and may be targeted by a rice resistance gene. Map-based cloning of Pwt2 showed that its functional allele is the ACE1 secondary metabolite gene cluster of the wheat blast fungus required for its efficient penetration of wheat cell walls. ACE1 is required for the strong aggressiveness of Triticum, Eleusine, and Lolium pathotypes on their respective hosts, but not for that of Oryza and Setaria pathotypes on rice and foxtail millet, respectively. All ACE1 alleles found in wheat blast population are recognized by a rice resistance gene, Pi33, when introduced into rice blast isolates. ACE1 mutations for evading the recognition by Pi33 do not affect the aggressiveness of the rice blast fungus on rice but inevitably impair the aggressiveness of the wheat blast fungus on wheat. These results suggest that a blast resistance gene already defeated in rice may be revived as a durable resistance gene in wheat by targeting an Achilles heel of the wheat blast fungus.
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Affiliation(s)
- Trinh T P Vy
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Yoshihiro Inoue
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Soichiro Asuke
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Izumi Chuma
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Hitoshi Nakayashiki
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan.
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Lin L, Sun T, Guo J, Lin L, Chen M, Wang Z, Bao J, Norvienyeku J, Zhang D, Han Y, Lu G, Rensing C, Zheng H, Zhong Z, Wang Z. Transposable elements impact the population divergence of rice blast fungus Magnaporthe oryzae. mBio 2024; 15:e0008624. [PMID: 38534157 PMCID: PMC11077969 DOI: 10.1128/mbio.00086-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Dynamic transposition of transposable elements (TEs) in fungal pathogens has significant impact on genome stability, gene expression, and virulence to the host. In Magnaporthe oryzae, genome plasticity resulting from TE insertion is a major driving force leading to the rapid evolution and diversification of this fungus. Despite their importance in M. oryzae population evolution and divergence, our understanding of TEs in this context remains limited. Here, we conducted a genome-wide analysis of TE transposition dynamics in the 11 most abundant TE families in M. oryzae populations. Our results show that these TEs have specifically expanded in recently isolated M. oryzae rice populations, with the presence/absence polymorphism of TE insertions highly concordant with population divergence on Geng/Japonica and Xian/Indica rice cultivars. Notably, the genes targeted by clade-specific TEs showed clade-specific expression patterns and are involved in the pathogenic process, suggesting a transcriptional regulation of TEs on targeted genes. Our study provides a comprehensive analysis of TEs in M. oryzae populations and demonstrates a crucial role of recent TE bursts in adaptive evolution and diversification of the M. oryzae rice-infecting lineage. IMPORTANCE Magnaporthe oryzae is the causal agent of the destructive blast disease, which caused massive loss of yield annually worldwide. The fungus diverged into distinct clades during adaptation toward the two rice subspecies, Xian/Indica and Geng/Japonica. Although the role of TEs in the adaptive evolution was well established, mechanisms underlying how TEs promote the population divergence of M. oryzae remain largely unknown. In this study, we reported that TEs shape the population divergence of M. oryzae by differentially regulating gene expression between Xian/Indica-infecting and Geng/Japonica-infecting populations. Our results revealed a TE insertion-mediated gene expression adaption that led to the divergence of M. oryzae population infecting different rice subspecies.
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Affiliation(s)
- Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meilian Chen
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Zhe Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiandong Bao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Justice Norvienyeku
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Dongmei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yijuan Han
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huakun Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
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3
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Zaffaroni M, Rimbaud L, Rey J, Papaïx J, Fabre F. Effects of pathogen reproduction system on the evolutionary and epidemiological control provided by deployment strategies for two major resistance genes in agricultural landscapes. Evol Appl 2024; 17:e13627. [PMID: 38283600 PMCID: PMC10810173 DOI: 10.1111/eva.13627] [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: 03/08/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 01/30/2024] Open
Abstract
Resistant cultivars are of value for protecting crops from disease, but can be rapidly overcome by pathogens. Several strategies have been proposed to delay pathogen adaptation (evolutionary control), while maintaining effective protection (epidemiological control). Resistance genes can be (i) combined in the same cultivar (pyramiding), (ii) deployed in different cultivars sown in the same field (mixtures) or in different fields (mosaics), or (iii) alternated over time (rotations). The outcomes of these strategies have been investigated principally in pathogens displaying pure clonal reproduction, but many pathogens have at least one sexual event in their annual life cycles. Sexual reproduction may promote the emergence of superpathogens adapted to all the resistance genes deployed. Here, we improved the spatially explicit stochastic model landsepi to include pathogen sexual reproduction, and we used the improved model to investigate the effect of sexual reproduction on evolutionary and epidemiological outcomes across deployment strategies for two major resistance genes. Sexual reproduction favours the establishment of a superpathogen when single mutant pathogens are present together at a sufficiently high frequency, as in mosaic and mixture strategies. However, sexual reproduction did not affect the strategy recommendations for a wide range of mutation probabilities, associated fitness costs, and landscape organisations.
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Affiliation(s)
- Marta Zaffaroni
- INRAE, Bordeaux Sciences Agro, SAVEVillenave d'OrnonFrance
- INRAE, BioSPAvignonFrance
| | | | | | | | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVEVillenave d'OrnonFrance
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Gautam RK, Singh PK, Sakthivel K, Venkatesan K, Rao SS, Srikumar M, Vijayan J, Rakesh B, Ray S, Akhtar J, Meena BR, Langyan S, Ali S, Krishnamurthy SL. Marker-assisted enhancement of bacterial blight ( Xanthomonas oryzae pv . oryzae) resistance in a salt-tolerant rice variety for sustaining rice production of tropical islands. FRONTIERS IN PLANT SCIENCE 2023; 14:1221537. [PMID: 37818314 PMCID: PMC10561094 DOI: 10.3389/fpls.2023.1221537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023]
Abstract
Introduction Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae is a major disease of rice, specially in the tropical regions of the world. Developing rice varieties with host resistance against the disease is the most effective and economical solution for managing the disease. Methods Pyramiding resistance genes (Xa4, xa5, xa13,and Xa21) in popular rice varieties using marker-assisted backcross breeding (MABB) has been demonstrated as a cost-effective and sustainable approach for establishing durable BB resistance. Here, we report our successful efforts in introgressing four resistance genes (Xa4, xa5, xa13, and Xa21) from IRBB60 to CARI Dhan 5, a popular salt-tolerant variety developed from a somaclonal variant of Pokkali rice, through functional MABB. Results and discussion Both BB and coastal salinity are among the major challenges for rice production in tropical island and coastal ecosystems. Plants with four, three, and two gene pyramids were generated, which displayed high levels of resistance to the BB pathogen at the BC3F2 stage. Under controlled salinity microplot environments, the line 131-2-175-1223 identified with the presence of three gene pyramid (Xa21+xa13+xa5) displayed notable resistance across locations and years as well as exhibited a salinity tolerance comparable to the recurrent parent, CARI Dhan 5. Among two BB gene combinations (Xa21+xa13), two lines, 17-1-69-334 and 46-3-95-659, demonstrated resistance across locations and years, as well as salt tolerance and grain production comparable to CARI Dhan 5. Besides salinity tolerance, five lines, 17-1-69-179, 46-3-95-655, 131-2-190-1197, 131-2-175-1209, and 131-2-175-1239, exhibited complete resistance to BB disease. Following multilocation testing, potential lines have been identified that can serve as a prospective candidate for producing varieties for the tropical Andaman and Nicobar Islands and other coastal locations, which are prone to BB and coastal salinity stresses.
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Affiliation(s)
- Raj Kumar Gautam
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Pankaj Kumar Singh
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Krishnan Sakthivel
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Oilseeds Research, Hyderabad, India
| | - K. Venkatesan
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources (NBPGR), Regional Research Station, Thrissur, Kerala, India
| | - Shyam S. Rao
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - M. Srikumar
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Joshitha Vijayan
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - B. Rakesh
- Indian Council of Agricultural Research (ICAR)-Central Island Agricultural Research Institute, Port Blair, India
| | - Soham Ray
- Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Jameel Akhtar
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Bharat Raj Meena
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sapna Langyan
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sharik Ali
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. L. Krishnamurthy
- Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, India
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Gogoi A, Rossmann SL, Lysøe E, Stensvand A, Brurberg MB. Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry. Front Microbiol 2023; 14:1214924. [PMID: 37465018 PMCID: PMC10351607 DOI: 10.3389/fmicb.2023.1214924] [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: 04/30/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Phytophthora cactorum has two distinct pathotypes that cause crown rot and leather rot in strawberry (Fragaria × ananassa). Strains of the crown rot pathotype can infect both the rhizome (crown) and fruit tissues, while strains of the leather rot pathotype can only infect the fruits of strawberry. The genome of a highly virulent crown rot strain, a low virulent crown rot strain, and three leather rot strains were sequenced using PacBio high fidelity (HiFi) long read sequencing. The reads were de novo assembled to 66.4-67.6 megabases genomes in 178-204 contigs, with N50 values ranging from 892 to 1,036 kilobases. The total number of predicted complete genes in the five P. cactorum genomes ranged from 17,286 to 17,398. Orthology analysis identified a core secretome of 8,238 genes. Comparative genomic analysis revealed differences in the composition of potential virulence effectors, such as putative RxLR and Crinklers, between the crown rot and the leather rot pathotypes. Insertions, deletions, and amino acid substitutions were detected in genes encoding putative elicitors such as beta elicitin and cellulose-binding domain proteins from the leather rot strains compared to the highly virulent crown rot strain, suggesting a potential mechanism for the crown rot strain to escape host recognition during compatible interaction with strawberry. The results presented here highlight several effectors that may facilitate the tissue-specific colonization of P. cactorum in strawberry.
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Affiliation(s)
- Anupam Gogoi
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Simeon L. Rossmann
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Erik Lysøe
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Arne Stensvand
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - May Bente Brurberg
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
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Gautier A, Laval V, Faure S, Rouxel T, Balesdent MH. Polymorphism of Avirulence Genes and Adaptation to Brassica Resistance Genes Is Gene-Dependent in the Phytopathogenic Fungus Leptosphaeria maculans. PHYTOPATHOLOGY 2023; 113:1222-1232. [PMID: 36802873 DOI: 10.1094/phyto-12-22-0466-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: 06/18/2023]
Abstract
The fungal phytopathogen Leptosphaeria maculans, which causes stem canker (blackleg) of rapeseed (Brassica napus), is mainly controlled worldwide by genetic resistance, which includes major resistance genes (Rlm). This model is one of those for which the highest number of avirulence genes (AvrLm) has been cloned. In many systems, including the L. maculans-B. napus interaction, intense use of resistance genes exerts strong selection pressure on the corresponding avirulent isolates, and the fungi may rapidly escape resistance through various molecular events which modify the avirulence genes. In the literature, the study of polymorphism at avirulence loci is often focused on single genes under selection pressure. In this study, we investigate allelic polymorphism at 11 avirulence loci in a French population of 89 L. maculans isolates collected on a trap cultivar in four geographic locations in the 2017-2018 cropping season. The corresponding Rlm genes have been (i) used for a long time, (ii) recently used, or (iii) unused in agricultural practice. The sequence data generated indicate an extreme diversity of situations. For example, genes submitted to an ancient selection may have either been deleted in populations (AvrLm1) or replaced by a single-nucleotide mutated virulent version (AvrLm2, AvrLm5-9). Genes that have never been under selection may either be nearly invariant (AvrLm6, AvrLm10A, AvrLm10B), exhibit rare deletions (AvrLm11, AvrLm14), or display a high diversity of alleles and isoforms (AvrLmS-Lep2). These data suggest that the evolutionary trajectory of avirulence/virulence alleles is gene-dependent and independent of selection pressure in L. maculans. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Angélique Gautier
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | - Valérie Laval
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | - Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
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Mutiga SK, Orwa P, Nganga EM, Kyallo MM, Rotich F, Gichuhi E, Kimani JM, Mwongera DT, Were VM, Yanoria MJ, Murori R, Mgonja E, Ziyomo C, Wasilwa L, Bachabi F, Ndjiondjop MN, Ouedraogo I, Correll JC, Talbot NJ. Characterization of Blast Resistance in a Diverse Rice Panel from Sub-Saharan Africa. PHYTOPATHOLOGY 2023; 113:1278-1288. [PMID: 36802875 DOI: 10.1094/phyto-10-22-0379-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: 06/18/2023]
Abstract
There is a recent unparalleled increase in demand for rice in sub-Saharan Africa, yet its production is affected by blast disease. Characterization of blast resistance in adapted African rice cultivars can provide important information to guide growers and rice breeders. We used molecular markers for known blast resistance genes (Pi genes; n = 21) to group African rice genotypes (n = 240) into similarity clusters. We then used greenhouse-based assays to challenge representative rice genotypes (n = 56) with African isolates (n = 8) of Magnaporthe oryzae which varied in virulence and genetic lineage. The markers grouped rice cultivars into five blast resistance clusters (BRC) which differed in foliar disease severity. Using stepwise regression, we found that the Pi genes associated with reduced blast severity were Pi50 and Pi65, whereas Pik-p, Piz-t, and Pik were associated with increased susceptibility. All rice genotypes in the most resistant cluster, BRC 4, possessed Pi50 and Pi65, the only genes that were significantly associated with reduced foliar blast severity. Cultivar IRAT109, which contains Piz-t, was resistant against seven African M. oryzae isolates, whereas ARICA 17 was susceptible to eight isolates. The popular Basmati 217 and Basmati 370 were among the most susceptible genotypes. These findings indicate that most tested genes were not effective against African blast pathogen collections. Pyramiding genes in the Pi2/9 multifamily blast resistance cluster on chromosome 6 and Pi65 on chromosome 11 could confer broad-spectrum resistance capabilities. To gain further insights into genomic regions associated with blast resistance, gene mapping could be conducted with resident blast pathogen collections. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Samuel K Mutiga
- Biosciences for Eastern and Central Africa-International Livestock Research Institute, Nairobi, Kenya
- The University of Arkansas System-Division of Agriculture, Fayetteville, AR, U.S.A
| | | | | | - Martina M Kyallo
- Biosciences for Eastern and Central Africa-International Livestock Research Institute, Nairobi, Kenya
| | | | - Emily Gichuhi
- Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
| | - John M Kimani
- Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
| | - David T Mwongera
- Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
| | | | - Mary Jeanie Yanoria
- International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | | | | | - Cathrine Ziyomo
- Biosciences for Eastern and Central Africa-International Livestock Research Institute, Nairobi, Kenya
| | - Lusike Wasilwa
- Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
| | - Famata Bachabi
- Africa Rice Center (AfricaRice), Station de M'bé, Bouaké, Côte d'Ivoire
| | | | - Ibrahima Ouedraogo
- Institute of Environment and Agricultural Research, Ouagadougou, Burkina Faso
| | - James C Correll
- The University of Arkansas System-Division of Agriculture, Fayetteville, AR, U.S.A
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Kloppe T, Whetten RB, Kim SB, Powell OR, Lück S, Douchkov D, Whetten RW, Hulse-Kemp AM, Balint-Kurti P, Cowger C. Two pathogen loci determine Blumeria graminis f. sp. tritici virulence to wheat resistance gene Pm1a. THE NEW PHYTOLOGIST 2023; 238:1546-1561. [PMID: 36772855 DOI: 10.1111/nph.18809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Blumeria graminis f. sp. tritici (Bgt) is a globally important fungal pathogen of wheat that can rapidly evolve to defeat wheat powdery mildew (Pm) resistance genes. Despite periodic regional deployment of the Pm1a resistance gene in US wheat production, Bgt strains that overcome Pm1a have been notably nonpersistent in the United States, while on other continents, they are more widely established. A genome-wide association study (GWAS) was conducted to map sequence variants associated with Pm1a virulence in 216 Bgt isolates from six countries, including the United States. A virulence variant apparently unique to Bgt isolates from the United States was detected in the previously mapped gene AvrPm1a (BgtE-5612) on Bgt chromosome 6; an in vitro growth assay suggested no fitness reduction associated with this variant. A gene on Bgt chromosome 8, Bgt-51526, was shown to function as a second determinant of Pm1a virulence, and despite < 30% amino acid identity, BGT-51526 and BGTE-5612 were predicted to share > 85% of their secondary structure. A co-expression study in Nicotiana benthamiana showed that BGTE-5612 and BGT-51526 each produce a PM1A-dependent hypersensitive response. More than one member of a B. graminis effector family can be recognized by a single wheat immune receptor, and a two-gene model is necessary to explain virulence to Pm1a.
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Affiliation(s)
- Tim Kloppe
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Rebecca B Whetten
- Plant Science Research Unit, USDA Agricultural Research Service, Raleigh, NC, 27695, USA
| | - Saet-Byul Kim
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Stefanie Lück
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, OT Gatersleben, Seeland, Germany
| | - Dimitar Douchkov
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, OT Gatersleben, Seeland, Germany
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA Agricultural Research Service, Raleigh, NC, 27695, USA
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
- Plant Science Research Unit, USDA Agricultural Research Service, Raleigh, NC, 27695, USA
| | - Christina Cowger
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
- Plant Science Research Unit, USDA Agricultural Research Service, Raleigh, NC, 27695, USA
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Saubin M, Louet C, Bousset L, Fabre F, Frey P, Fudal I, Grognard F, Hamelin F, Mailleret L, Stoeckel S, Touzeau S, Petre B, Halkett F. Improving sustainable crop protection using population genetics concepts. Mol Ecol 2022; 32:2461-2471. [PMID: 35906846 DOI: 10.1111/mec.16634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 10/16/2022]
Abstract
Growing genetically resistant plants allows pathogen populations to be controlled and reduces the use of pesticides. However, pathogens can quickly overcome such resistance. In this context, how can we achieve sustainable crop protection? This crucial question has remained largely unanswered despite decades of intense debate and research effort. In this study, we used a bibliographic analysis to show that the research field of resistance durability has evolved into three subfields: (i) 'plant breeding' (generating new genetic material), (ii) 'molecular interactions' (exploring the molecular dialogue governing plant-pathogen interactions) and (iii) 'epidemiology and evolution' (explaining and forecasting of pathogen population dynamics resulting from selection pressure(s) exerted by resistant plants). We argue that this triple split of the field impedes integrated research progress and ultimately compromises the sustainable management of genetic resistance. After identifying a gap among the three subfields, we argue that the theoretical framework of population genetics could bridge this gap. Indeed, population genetics formally explains the evolution of all heritable traits, and allows genetic changes to be tracked along with variation in population dynamics. This provides an integrated view of pathogen adaptation, in particular via evolutionary-epidemiological feedbacks. In this Opinion Note, we detail examples illustrating how such a framework can better inform best practices for developing and managing genetically resistant cultivars.
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Affiliation(s)
| | - Clémentine Louet
- Université de Lorraine, INRAE, IAM, Nancy, France.,Université Paris Saclay, INRAE, BIOGER, Thiverval-Grignon, France
| | - Lydia Bousset
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, F-33882 Villenave d'Ornon, France
| | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Isabelle Fudal
- Université Paris Saclay, INRAE, BIOGER, Thiverval-Grignon, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
| | - Frédéric Hamelin
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Ludovic Mailleret
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France.,Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Suzanne Touzeau
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
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10
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Zhao Y, Zhu X, Chen X, Zhou JM. From plant immunity to crop disease resistance. J Genet Genomics 2022; 49:693-703. [PMID: 35728759 DOI: 10.1016/j.jgg.2022.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Plant diseases caused by diverse pathogens lead to serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases. In the last decade, our understanding of plant immunity at both molecular and genomic levels has improved greatly. Combined with advances in biotechnologies, particularly CRISPR/Cas9-based genome editing, we can now rapidly identify new resistance genes and engineer disease resistance crop plants like never before. In this review, we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants. We also discuss existing challenges in this field and suggest directions for future studies.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaobo Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainai 572025, China.
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11
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Sakr N. Adaptation of Phytopathogenic Fungi to Quantitative Host Resistance: In Vitro Selection for Greater Aggressiveness in Fusarium Head Blight Species on Wheat. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722030112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Dinh HX, Singh D, Gomez de la Cruz D, Hensel G, Kumlehn J, Mascher M, Stein N, Perovic D, Ayliffe M, Moscou MJ, Park RF, Pourkheirandish M. The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei. Nat Commun 2022; 13:2386. [PMID: 35501307 PMCID: PMC9061838 DOI: 10.1038/s41467-022-29840-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 04/03/2022] [Indexed: 01/04/2023] Open
Abstract
Leaf rust, caused by Puccinia hordei, is an economically significant disease of barley, but only a few major resistance genes to P. hordei (Rph) have been cloned. In this study, gene Rph3 was isolated by positional cloning and confirmed by mutational analysis and transgenic complementation. The Rph3 gene, which originated from wild barley and was first introgressed into cultivated Egyptian germplasm, encodes a unique predicted transmembrane resistance protein that differs from all known plant disease resistance proteins at the amino acid sequence level. Genetic profiles of diverse accessions indicated limited genetic diversity in Rph3 in domesticated germplasm, and higher diversity in wild barley from the Eastern Mediterranean region. The Rph3 gene was expressed only in interactions with Rph3-avirulent P. hordei isolates, a phenomenon also observed for transcription activator-like effector-dependent genes known as executors conferring resistance to Xanthomonas spp. Like known transmembrane executors such as Bs3 and Xa7, heterologous expression of Rph3 in N. benthamiana induced a cell death response. The isolation of Rph3 highlights convergent evolutionary processes in diverse plant-pathogen interaction systems, where similar defence mechanisms evolved independently in monocots and dicots. Leaf rust is an economically significant disease of barley. Here the authors describe cloning of the barley Rph3 leaf rust resistance gene and reveal it encodes a predicted transmembrane protein that is expressed upon infection by Rph3-avirulent Puccinia hordei isolates.
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13
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Ac/Ds-Induced Receptor-like Kinase Genes Deletion Provides Broad-Spectrum Resistance to Bacterial Blight in Rice. Int J Mol Sci 2022; 23:ijms23094561. [PMID: 35562952 PMCID: PMC9103808 DOI: 10.3390/ijms23094561] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) seriously affects rice yield production. The discovery and application of broad-spectrum resistance genes are of great advance for disease resistance breeding. Previously, we identified that multiple receptor-like kinase (RLK) family gene deletions induced by the Ac/Ds system resulted in a lesion mimic symptom. In this study, the mutant #29 showed that this lesion mimic symptom was isolated. Further analysis identified that four RLK genes (RLK19-22) were deleted in the #29 mutant. The #29 mutant exhibited broad-spectrum resistance to Xoo and subsequent analyses identified that pathogenesis-related genes PR1a, PBZ1, and cellular H2O2 levels were significantly induced in the mutant compared to wild-type plants. A genetic analysis revealed that reconstruction of RLK20, RLK21, or RLK22 rescued the lesion mimic symptom of the #29 mutant, indicating that these three RLKs are responsible for broad-spectrum resistance in rice. Further yeast two hybrid and bimolecular fluorescence complementation assays demonstrated that RLK20 interacts with RBOHB, which is a ROS producer in plants. Compared to wild-type plants, the #29 mutant was more, while #29/RLK20ox was less, susceptible to MV (methyl-viologen), an ROS inducer. Co-expression of RLK20 and RBOHB reduced RBOHB-promoted H2O2 accumulation in the cells. Taken together, our research indicated that the RLKs may inhibit RBOHB activity to negatively regulate rice resistance to Xoo. These results provide the theoretical basis and valuable information about the target genes necessary for the successful breeding of rice cultivars resistant to bacterial blight.
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14
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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15
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Louet C, Saubin M, Andrieux A, Persoons A, Gorse M, Pétrowski J, Fabre B, De Mita S, Duplessis S, Frey P, Halkett F. A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown. Mol Ecol 2021; 32:2472-2483. [PMID: 34843142 DOI: 10.1111/mec.16294] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 01/29/2023]
Abstract
The deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R-mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici-populina is a damaging pathogen of poplars in Europe. It underwent a major adaptive event in 1994, with the breakdown of the poplar RMlp7 resistance gene. Population genomics studies identified a locus in the genome of M. larici-populina that probably corresponds to the candidate avirulence gene AvrMlp7. Here, to further characterize this effector, we used a population genetics approach on a comprehensive set of 281 individuals recovered throughout a 28-year period encompassing the resistance breakdown event. Using two dedicated molecular tools, genotyping at the candidate locus highlighted two different alterations of a predominant allele found mainly before the resistance breakdown: a nonsynonymous mutation and a complete deletion of this locus. This results in six diploid genotypes: three genotypes related to the avirulent phenotype and three related to the virulent phenotype. The temporal survey of the candidate locus revealed that both alterations were found in association during the resistance breakdown event. They pre-existed before the breakdown in a heterozygous state with the predominant allele cited above. Altogether, these results suggest that the association of both alterations at the candidate locus AvrMlp7 drove the poplar rust adaptation to RMlp7-mediated immunity. This study demonstrates for the first time a case of adaptation from standing genetic variation in rust fungi during a qualitative resistance breakdown.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
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16
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El-Baky NA, Amara AAAF. Recent Approaches towards Control of Fungal Diseases in Plants: An Updated Review. J Fungi (Basel) 2021; 7:jof7110900. [PMID: 34829188 PMCID: PMC8621679 DOI: 10.3390/jof7110900] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Recent research demonstrates that the number of virulent phytopathogenic fungi continually grows, which leads to significant economic losses worldwide. Various procedures are currently available for the rapid detection and control of phytopathogenic fungi. Since 1940, chemical and synthetic fungicides were typically used to control phytopathogenic fungi. However, the substantial increase in development of fungal resistance to these fungicides in addition to negative effects caused by synthetic fungicides on the health of animals, human beings, and the environment results in the exploration of various new approaches and green strategies of fungal control by scientists from all over the world. In this review, the development of new approaches for controlling fungal diseases in plants is discussed. We argue that an effort should be made to bring these recent technologies to the farmer level.
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17
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Pokhrel S, Ponniah SK, Jia Y, Yu O, Manoharan M. Transgenic Rice Expressing Isoflavone Synthase Gene from Soybean Shows Resistance Against Blast Fungus ( Magnaporthe oryzae). PLANT DISEASE 2021; 105:3141-3146. [PMID: 33616428 DOI: 10.1094/pdis-08-20-1777-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The isoflavones are a group of plant secondary metabolites primarily synthesized in legumes and are known for their role in improving human health and plant disease resistance. The isoflavones, especially genistein, act as precursors for the production of phytoalexins, which may induce broad-spectrum disease resistance in plants. In this study, we screened transgenic rice lines expressing the isoflavone synthase (GmIFS1) gene from soybean for rice blast (Magnaporthe oryzae) resistance. Two homozygous transgenic lines (I2 and I10), based on single copy gene integration, were identified. The expression of GmIFS1 in transgenic lines was confirmed by quantitative real-time PCR. Genistein was detected in the transgenic lines using liquid chromatography with tandem mass spectrometry. Subsequently, the transgenic lines were evaluated against the rice blast pathogen, isolate YJ54 (race IB-54). The results indicated that >60% of the plants in both the lines (I2 and I10) showed resistance against the blast pathogen. The progenies of one of the resistant transgenic lines (I10) also showed >65% resistance against rice blast. The resistance of these transgenic lines against rice blast may be attributed to the synthesis of isoflavone (genistein) in rice.
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Affiliation(s)
- Suresh Pokhrel
- Department of Agriculture, University of Arkansas at Pine Bluff, Pine Bluff, AR 71601
| | - Sathish K Ponniah
- Department of Agriculture, University of Arkansas at Pine Bluff, Pine Bluff, AR 71601
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture-Agricultural Research Service, Stuttgart, AR 72160
| | | | - Muthusamy Manoharan
- Department of Agriculture, University of Arkansas at Pine Bluff, Pine Bluff, AR 71601
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18
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Rimbaud L, Fabre F, Papaïx J, Moury B, Lannou C, Barrett LG, Thrall PH. Models of Plant Resistance Deployment. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:125-152. [PMID: 33929880 DOI: 10.1146/annurev-phyto-020620-122134] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Owing to their evolutionary potential, plant pathogens are able to rapidly adapt to genetically controlled plant resistance, often resulting in resistance breakdown and major epidemics in agricultural crops. Various deployment strategies have been proposed to improve resistance management. Globally, these rely on careful selection of resistance sources and their combination at various spatiotemporal scales (e.g., via gene pyramiding, crop rotations and mixtures, landscape mosaics). However, testing and optimizing these strategies using controlled experiments at large spatiotemporal scales are logistically challenging. Mathematical models provide an alternative investigative tool, and many have been developed to explore resistance deployment strategies under various contexts. This review analyzes 69 modeling studies in light of specific model structures (e.g., demographic or demogenetic, spatial or not), underlying assumptions (e.g., whether preadapted pathogens are present before resistance deployment), and evaluation criteria (e.g., resistance durability, disease control, cost-effectiveness). It highlights major research findings and discusses challenges for future modeling efforts.
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Affiliation(s)
- Loup Rimbaud
- INRAE, Pathologie Végétale, 84140 Montfavet, France; ,
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, 33882 Villenave d'Ornon, France;
| | | | - Benoît Moury
- INRAE, Pathologie Végétale, 84140 Montfavet, France; ,
| | | | - Luke G Barrett
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
| | - Peter H Thrall
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
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19
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Potnis N. Harnessing Eco-Evolutionary Dynamics of Xanthomonads on Tomato and Pepper to Tackle New Problems of an Old Disease. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:289-310. [PMID: 34030449 DOI: 10.1146/annurev-phyto-020620-101612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacterial spot is an endemic seedborne disease responsible for recurring outbreaks on tomato and pepper around the world. The disease is caused by four diverse species, Xanthomonas gardneri, Xanthomonas euvesicatoria, Xanthomonas perforans, and Xanthomonas vesicatoria. There are no commercially available disease-resistant tomato varieties, and the disease is managed by chemical/biological control options, although these have not reduced the incidence of outbreaks. The disease on peppers is managed by disease-resistant cultivars that are effective against X. euvesicatoria but not X. gardneri. A significant shift in composition and prevalence of different species and races of the pathogen has occurred over the past century. Here, I attempt to review ecological and evolutionary processes associated with the population dynamics leading to disease emergence and spread. The goal of this review is to integrate the knowledge on population genomics and molecular plant-microbe interactions for this pathosystem to tailor disease management strategies.
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Affiliation(s)
- Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama 36849, USA;
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20
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Wang W, Su J, Chen K, Yang J, Chen S, Wang C, Feng A, Wang Z, Wei X, Zhu X, Lu GD, Zhou B. Dynamics of the Rice Blast Fungal Population in the Field After Deployment of an Improved Rice Variety Containing Known Resistance Genes. PLANT DISEASE 2021; 105:919-928. [PMID: 32967563 DOI: 10.1094/pdis-06-20-1348-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most destructive diseases of rice worldwide. Management through the deployment of host resistance genes would be facilitated by understanding the dynamics of the pathogen's population in the field. Here, to investigate the mechanism underlying the breakdown of disease resistance, we conducted a six-year field experiment to monitor the evolution of M. oryzae populations in Qujiang from Guangdong. The new variety of Xin-Yin-Zhan (XYZ) carrying R genes Pi50 and Pib was developed using the susceptible elite variety, Ma-Ba-Yin-Zhan (MBYZ), as the recurrent line. Field trials of disease resistance assessment revealed that the disease indices of XYZ in 2012, 2013, 2016, and 2017 were 0.19, 0.39, 0.70, and 0.90, respectively, indicating that XYZ displayed a very rapid increase of disease severity in the field. To investigate the mechanism underlying the quick erosion of resistance of XYZ, we collected isolates from both XYZ and MBYZ for pathogenicity testing against six different isogenic lines. The isolates collected from XYZ showed a similar virulence spectrum across four different years whereas those from MBYZ showed increasing virulence to the Pi50 and Pib isogenic lines from 2012 to 2017. Molecular analysis of AvrPib in the isolates from MBYZ identified four different AvrPib haplotypes, i.e., AvrPib-AP1-1, AvrPib-AP1-2, avrPib-AP2, and avrPib-AP3, verified by sequencing. AvrPib-AP1-1 and AvrPib-AP1-2 are avirulent to Pib whereas avrPib-AP2 and avrPib-AP3 are virulent. Insertions of a Pot3 and an Mg-SINE were identified in avrPib-AP2 and avrPib-AP3, respectively. Two major lineages based on rep-PCR analysis were further deduced in the field population, implying that the field population is composed of genetically related isolates. Our data suggest that clonal propagation and quick dominance of virulent isolates against the previously resistant variety could be the major genetic events contributing to the loss of varietal resistance against rice blast in the field.
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Affiliation(s)
- Wenjuan Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jing Su
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Kailing Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jianyuan Yang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shen Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Congying Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Aiqing Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Ocean Science, Minjiang University, Fuzhou 350108, China
| | - Xiaoyan Wei
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaoyuan Zhu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Guo-Dong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bo Zhou
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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21
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Zanardo LG, Trindade TA, Mar TB, Barbosa TMC, Milanesi DF, Alves MS, Lima RRPN, Zerbini FM, Janssen A, Mizubuti ESG, Elliot SL, Carvalho CM. Experimental evolution of cowpea mild mottle virus reveals recombination-driven reduction in virulence accompanied by increases in diversity and viral fitness. Virus Res 2021; 303:198389. [PMID: 33716182 DOI: 10.1016/j.virusres.2021.198389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 12/22/2022]
Abstract
Major themes in pathogen evolution are emergence, evolution of virulence, host adaptation and the processes that underlie them. RNA viruses are of particular interest due to their rapid evolution. The in vivo molecular evolution of an RNA plant virus was demonstrated here using a necrotic isolate of cowpea mild mottle virus (CPMMV) and a susceptible soybean genotype submitted to serial inoculations. We show that the virus lost the capacity to cause necrosis after six passages through the host plant. When a severe bottleneck was imposed, virulence reduction occurred in the second passage. The change to milder symptoms had fitness benefits for the virus (higher RNA accumulation) and for its vector, the whitefly Bemisia tabaci. Genetic polymorphisms were highest in ORF1 (viral replicase) and were independent of the symptom pattern. Recombination was a major contributor to this diversity - even with the strong genetic bottleneck, recombination events and hot spots were detected within ORF1. Virulence reduction was associated with different sites in ORF1 associated to recombination events in both experiments. Overall, the results demonstrate that the reduction in virulence was a consequence of the emergence of new variants, driven by recombination. Besides providing details of the evolutionary mechanisms behind a reduction in virulence and its effect under viral and vector fitness, we propose that this recombination-driven switch in virulence allows the pathogen to rapidly adapt to a new host and, potentially, switch back.
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Affiliation(s)
- Larissa G Zanardo
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tiago A Trindade
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Talita B Mar
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tarsiane M C Barbosa
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Diogo F Milanesi
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Murilo S Alves
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Roberta R P N Lima
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Arne Janssen
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil; IBED, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Eduardo S G Mizubuti
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Simon L Elliot
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Claudine M Carvalho
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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22
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Abstract
Rice blast disease is both the most explosive and potentially damaging disease of the world's rice (Oryza sativa) crop and a model system for research on the molecular mechanisms that fungi use to cause plant disease. The blast fungus, Magnaporthe oryzae, is highly evolved to sense when it is on a leaf surface; to develop a pressurized cell, the appressorium, to punch through the leaf cuticle; and then to hijack living rice cells to assist it in causing disease. Host specificity, determining which plants particular fungal strains can infect, is also an important topic for research. The blast fungus is a moving target, quickly overcoming rice resistance genes we deploy to control it, and recently emerging to cause devastating disease on an entirely new cereal crop, wheat. M. oryzae is highly adaptable, with multiple examples of genetic instability at certain gene loci and in certain genomic regions. Understanding the biology of the fungus in the field, and its potential for genetic and genome variability, is key to keep it from adapting to life in the research laboratory and losing relevance to the significant impact it has on global food security.
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Affiliation(s)
- Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
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23
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Huerta AI, Delorean EE, Bossa‐Castro AM, Tonnessen BW, Raghavan C, Corral R, Pérez‐Quintero ÁL, Leung H, Verdier V, Leach JE. Resistance and susceptibility QTL identified in a rice MAGIC population by screening with a minor-effect virulence factor from Xanthomonas oryzae pv. oryzae. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:51-63. [PMID: 32594636 PMCID: PMC7769240 DOI: 10.1111/pbi.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/02/2020] [Accepted: 06/17/2020] [Indexed: 05/07/2023]
Abstract
Effective and durable disease resistance for bacterial blight (BB) of rice is a continuous challenge due to the evolution and adaptation of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), on cultivated rice varieties. Fundamental to this pathogens' virulence is transcription activator-like (TAL) effectors that activate transcription of host genes and contribute differently to pathogen virulence, fitness or both. Host plant resistance is predicted to be more durable if directed at strategic virulence factors that impact both pathogen virulence and fitness. We characterized Tal7b, a minor-effect virulence factor that contributes incrementally to pathogen virulence in rice, is a fitness factor to the pathogen and is widely present in geographically diverse strains of Xoo. To identify sources of resistance to this conserved effector, we used a highly virulent strain carrying a plasmid borne copy of Tal7b to screen an indica multi-parent advanced generation inter-cross (MAGIC) population. Of 18 QTL revealed by genome-wide association studies and interval mapping analysis, six were specific to Tal7b (qBB-tal7b). Overall, 150 predicted Tal7b gene targets overlapped with qBB-tal7b QTL. Of these, 21 showed polymorphisms in the predicted effector binding element (EBE) site and 23 lost the EBE sequence altogether. Inoculation and bioinformatics studies suggest that the Tal7b target in one of the Tal7b-specific QTL, qBB-tal7b-8, is a disease susceptibility gene and that the resistance mechanism for this locus may be through loss of susceptibility. Our work demonstrates that minor-effect virulence factors significantly contribute to disease and provide a potential new approach to identify effective disease resistance.
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Affiliation(s)
- Alejandra I. Huerta
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Emily E. Delorean
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Ana M. Bossa‐Castro
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Bradley W. Tonnessen
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Extension Plant SciencesNew Mexico State UniversityLas CrucesNM88003USA
| | - Chitra Raghavan
- Division Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
- Present address:
Queensland Department of Agriculture and FisheriesHorticulture and Forestry SciencesCairnsQLD4870Australia
| | - Rene Corral
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | | | - Hei Leung
- Division Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
| | | | - Jan E. Leach
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
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Nilusmas S, Mercat M, Perrot T, Djian‐Caporalino C, Castagnone‐Sereno P, Touzeau S, Calcagno V, Mailleret L. Multi-seasonal modelling of plant-nematode interactions reveals efficient plant resistance deployment strategies. Evol Appl 2020; 13:2206-2221. [PMID: 33005219 PMCID: PMC7513734 DOI: 10.1111/eva.12989] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023] Open
Abstract
Root-knot nematodes, Meloidogyne spp., are soil-borne polyphagous pests with major impact on crop yield worldwide. Resistant crops efficiently control avirulent root-knot nematodes, but favour the emergence of virulent forms. Since virulence is associated with fitness costs, susceptible crops counter-select virulent root-knot nematodes. In this study, we identify optimal rotation strategies between susceptible and resistant crops to control root-knot nematodes and maximize crop yield. We developed an epidemiological model describing the within-season dynamics of avirulent and virulent root-knot nematodes on susceptible or resistant plant root-systems, and their between-season survival. The model was fitted to experimental data and used to predict yield-maximizing rotation strategies, with special attention to the impact of epidemic severity and genetic parameters. Crop rotations were found to be efficient under realistic parameter ranges. They were characterized by low ratios of resistant plants and were robust to parameter uncertainty. Rotations provide significant gain over resistant-only strategies, especially under intermediate fitness costs and severe epidemic contexts. Switching from the current general deployment of resistant crops to custom rotation strategies could not only maintain or increase crop yield, but also preserve the few and valuable R-genes available.
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Affiliation(s)
- Samuel Nilusmas
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
| | - Mathilde Mercat
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
| | - Thomas Perrot
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
| | | | | | - Suzanne Touzeau
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
| | | | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
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Joshi JB, Arul L, Ramalingam J, Uthandi S. Advances in the Xoo-rice pathosystem interaction and its exploitation in disease management. J Biosci 2020. [DOI: 10.1007/s12038-020-00085-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Could Environment Affect the Mutation of H1N1 Influenza Virus? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17093092. [PMID: 32365515 PMCID: PMC7246512 DOI: 10.3390/ijerph17093092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 12/12/2022]
Abstract
H1N1 subtype influenza A viruses are the most common type of influenza A virus to infect humans. The two major outbreaks of the virus in 1918 and 2009 had a great impact both on human health and social development. Though data on their complete genome sequences have recently been obtained, the evolution and mutation of A/H1N1 viruses remain unknown to this day. Among many drivers, the impact of environmental factors on mutation is a novel hypothesis worth studying. Here, a geographically disaggregated method was used to explore the relationship between environmental factors and mutation of A/H1N1 viruses from 2000-2019. All of the 11,721 geo-located cases were examined and the data was analysed of six environmental elements according to the time and location (latitude and longitude) of those cases. The main mutation value was obtained by comparing the sequence of the influenza virus strain with the earliest reported sequence. It was found that environmental factors systematically affect the mutation of A/H1N1 viruses. Minimum temperature displayed a nonlinear, rising association with mutation, with a maximum ~15 °C. The effects of precipitation and social development index (nighttime light) were more complex, while population density was linearly and positively correlated with mutation of A/H1N1 viruses. Our results provide novel insight into understanding the complex relationships between mutation of A/H1N1 viruses and environmental factors.
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Li W, Deng Y, Ning Y, He Z, Wang GL. Exploiting Broad-Spectrum Disease Resistance in Crops: From Molecular Dissection to Breeding. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:575-603. [PMID: 32197052 DOI: 10.1146/annurev-arplant-010720-022215] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant diseases reduce crop yields and threaten global food security, making the selection of disease-resistant cultivars a major goal of crop breeding. Broad-spectrum resistance (BSR) is a desirable trait because it confers resistance against more than one pathogen species or against the majority of races or strains of the same pathogen. Many BSR genes have been cloned in plants and have been found to encode pattern recognition receptors, nucleotide-binding and leucine-rich repeat receptors, and defense-signaling and pathogenesis-related proteins. In addition, the BSR genes that underlie quantitative trait loci, loss of susceptibility and nonhost resistance have been characterized. Here, we comprehensively review the advances made in the identification and characterization of BSR genes in various species and examine their application in crop breeding. We also discuss the challenges and their solutions for the use of BSR genes in the breeding of disease-resistant crops.
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Affiliation(s)
- Wei Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio 43210, USA;
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Derbyshire MC. Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action. Front Microbiol 2020; 11:644. [PMID: 32328056 PMCID: PMC7160247 DOI: 10.3389/fmicb.2020.00644] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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Chabas H, Nicot A, Meaden S, Westra ER, Tremblay DM, Pradier L, Lion S, Moineau S, Gandon S. Variability in the durability of CRISPR-Cas immunity. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180097. [PMID: 30905283 DOI: 10.1098/rstb.2018.0097] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) alleles of the bacteria Streptococcus thermophilus against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be because of variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
- Hélène Chabas
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| | - Antoine Nicot
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| | - Sean Meaden
- 2 Environment and Sustainability Institute, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9FE , UK
| | - Edze R Westra
- 2 Environment and Sustainability Institute, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9FE , UK
| | - Denise M Tremblay
- 3 Département de Biochimie, Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval , 1045 Avenue de la Médecine, Québec City, Quebec , Canada G1V 0A6.,4 Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval , Québec City, Qubec , Canada G1V 0A6
| | - Léa Pradier
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| | - Sébastien Lion
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| | - Sylvain Moineau
- 3 Département de Biochimie, Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval , 1045 Avenue de la Médecine, Québec City, Quebec , Canada G1V 0A6.,4 Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval , Québec City, Qubec , Canada G1V 0A6
| | - Sylvain Gandon
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
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30
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Harris MO, Pitzschke A. Plants make galls to accommodate foreigners: some are friends, most are foes. THE NEW PHYTOLOGIST 2020; 225:1852-1872. [PMID: 31774564 DOI: 10.1111/nph.16340] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
At the colonization site of a foreign entity, plant cells alter their trajectory of growth and development. The resulting structure - a plant gall - accommodates various needs of the foreigner, which are phylogenetically diverse: viruses, bacteria, protozoa, oomycetes, true fungi, parasitic plants, and many types of animals, including rotifers, nematodes, insects, and mites. The plant species that make galls also are diverse. We assume gall production costs the plant. All is well if the foreigner provides a gift that makes up for the cost. Nitrogen-fixing nodule-inducing bacteria provide nutritional services. Gall wasps pollinate fig trees. Unfortunately for plants, most galls are made for foes, some of which are deeply studied pathogens and pests: Agrobacterium tumefaciens, Rhodococcus fascians, Xanthomonas citri, Pseudomonas savastanoi, Pantoea agglomerans, 'Candidatus' phytoplasma, rust fungi, Ustilago smuts, root knot and cyst nematodes, and gall midges. Galls are an understudied phenomenon in plant developmental biology. We propose gall inception for discovering unifying features of the galls that plants make for friends and foes, talk about molecules that plants and gall-inducers use to get what they want from each other, raise the question of whether plants colonized by arbuscular mycorrhizal fungi respond in a gall-like manner, and present a research agenda.
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Affiliation(s)
- Marion O Harris
- Department of Entomology, North Dakota State University, Fargo, ND, 58014, USA
| | - Andrea Pitzschke
- Department of Biosciences, Salzburg University, Hellbrunner Strasse 34, A-5020, Salzburg, Austria
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Jiang N, Yan J, Liang Y, Shi Y, He Z, Wu Y, Zeng Q, Liu X, Peng J. Resistance Genes and their Interactions with Bacterial Blight/Leaf Streak Pathogens (Xanthomonas oryzae) in Rice (Oryza sativa L.)-an Updated Review. RICE (NEW YORK, N.Y.) 2020; 13:3. [PMID: 31915945 PMCID: PMC6949332 DOI: 10.1186/s12284-019-0358-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/18/2019] [Indexed: 05/19/2023]
Abstract
Rice (Oryza sativa L.) is a staple food crop, feeding more than 50% of the world's population. Diseases caused by bacterial, fungal, and viral pathogens constantly threaten the rice production and lead to enormous yield losses. Bacterial blight (BB) and bacterial leaf streak (BLS), caused respectively by gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), are two important diseases affecting rice production worldwide. Due to the economic importance, extensive genetic and genomic studies have been conducted to elucidate the molecular mechanism of rice response to Xoo and Xoc in the last two decades. A series of resistance (R) genes and their cognate avirulence and virulence effector genes have been characterized. Here, we summarize the recent advances in studies on interactions between rice and the two pathogens through these R genes or their products and effectors. Breeding strategies to develop varieties with durable and broad-spectrum resistance to Xanthomonas oryzae based on the published studies are also discussed.
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Affiliation(s)
- Nan Jiang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agronomy, Hunan Agricultural University, Changsha, 410128 Hunan China
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture Rural Affairs, School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106 Sichuan China
| | - Yi Liang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agronomy, Hunan Agricultural University, Changsha, 410128 Hunan China
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Yanlong Shi
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Zhizhou He
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Yuntian Wu
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Qin Zeng
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Xionglun Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agronomy, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Junhua Peng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agronomy, Hunan Agricultural University, Changsha, 410128 Hunan China
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
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32
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Biotechnological potential of engineering pathogen effector proteins for use in plant disease management. Biotechnol Adv 2019; 37:107387. [DOI: 10.1016/j.biotechadv.2019.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 11/19/2022]
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Rimbaud L, Papaïx J, Barrett LG, Burdon JJ, Thrall PH. Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy to deploy major gene resistance? Evol Appl 2018; 11:1791-1810. [PMID: 30459830 PMCID: PMC6231482 DOI: 10.1111/eva.12681] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/14/2018] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
Once deployed uniformly in the field, genetically controlled plant resistance is often quickly overcome by pathogens, resulting in dramatic losses. Several strategies have been proposed to constrain the evolutionary potential of pathogens and thus increase resistance durability. These strategies can be classified into four categories, depending on whether resistance sources are varied across time (rotations) or combined in space in the same cultivar (pyramiding), in different cultivars within a field (cultivar mixtures) or among fields (mosaics). Despite their potential to differentially affect both pathogen epidemiology and evolution, to date the four categories of deployment strategies have never been directly compared together within a single theoretical or experimental framework, with regard to efficiency (ability to reduce disease impact) and durability (ability to limit pathogen evolution and delay resistance breakdown). Here, we used a spatially explicit stochastic demogenetic model, implemented in the R package landsepi, to assess the epidemiological and evolutionary outcomes of these deployment strategies when two major resistance genes are present. We varied parameters related to pathogen evolutionary potential (mutation probability and associated fitness costs) and landscape organization (mostly the relative proportion of each cultivar in the landscape and levels of spatial or temporal aggregation). Our results, broadly focused on qualitative resistance to rust fungi of cereal crops, show that evolutionary and epidemiological control are not necessarily correlated and that no deployment strategy is universally optimal. Pyramiding two major genes offered the highest durability, but at high mutation probabilities, mosaics, mixtures and rotations can perform better in delaying the establishment of a universally infective superpathogen. All strategies offered the same short-term epidemiological control, whereas rotations provided the best long-term option, after all sources of resistance had broken down. This study also highlights the significant impact of landscape organization and pathogen evolutionary ability in considering the optimal design of a deployment strategy.
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Affiliation(s)
- Loup Rimbaud
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | | | - Luke G. Barrett
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | - Jeremy J. Burdon
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | - Peter H. Thrall
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
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Abrahamian P, Timilsina S, Minsavage GV, Kc S, Goss EM, Jones JB, Vallad GE. The Type III Effector AvrBsT Enhances Xanthomonas perforans Fitness in Field-Grown Tomato. PHYTOPATHOLOGY 2018; 108:1355-1362. [PMID: 29905507 DOI: 10.1094/phyto-02-18-0052-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Type III secretion system effectors contribute to pathogenicity through various mechanisms. Recent surveys showed an increasing prevalence of the type III secretion effector avrBsT among Xanthomonas perforans strains. We hypothesized that the acquisition of avrBsT has a fitness advantage for the pathogen. The contribution of avrBsT to fitness on tomato was evaluated based on disease severity, in planta growth, competition, and recovery rates of wild-type (WT) and avrBsT mutant strains in greenhouse and field plants. GEV872 and GEV1001, representative strains of two phylogenomic groups of X. perforans, were selected for generating avrBsT mutants. Disease severity was higher for WT strains compared with the avrBsT mutant strains. X. perforans WT and avrBsT mutant strains did not differ following leaf infiltration of greenhouse plants in direct competition and in planta growth assays. The effect of avrBsT on pathogen fitness was noticeable under field conditions. Differences in strain recovery were significant, with WT being recovered two to eight times more than avrBsT mutant strains in the case of both strains GEV872 and GEV1001. WT strains were capable of spreading longer distances across field plots compared with avrBsT mutant strains. Findings suggest that the functional AvrBsT affects the fitness of X. perforans under field conditions, making it an ideal candidate for bacterial spot resistance breeding efforts in tomato.
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Affiliation(s)
- Peter Abrahamian
- First, second, fourth, and seventh authors; Gulf Coast and Research Education Center, Wimauma, FL; first, second, third, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; and fifth author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Sujan Timilsina
- First, second, fourth, and seventh authors; Gulf Coast and Research Education Center, Wimauma, FL; first, second, third, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; and fifth author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Gerald V Minsavage
- First, second, fourth, and seventh authors; Gulf Coast and Research Education Center, Wimauma, FL; first, second, third, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; and fifth author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Sushmita Kc
- First, second, fourth, and seventh authors; Gulf Coast and Research Education Center, Wimauma, FL; first, second, third, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; and fifth author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Erica M Goss
- First, second, fourth, and seventh authors; Gulf Coast and Research Education Center, Wimauma, FL; first, second, third, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; and fifth author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Jeffrey B Jones
- First, second, fourth, and seventh authors; Gulf Coast and Research Education Center, Wimauma, FL; first, second, third, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; and fifth author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Gary E Vallad
- First, second, fourth, and seventh authors; Gulf Coast and Research Education Center, Wimauma, FL; first, second, third, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; and fifth author: Emerging Pathogens Institute, University of Florida, Gainesville
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Bousset L, Sprague SJ, Thrall PH, Barrett LG. Spatio-temporal connectivity and host resistance influence evolutionary and epidemiological dynamics of the canola pathogen Leptosphaeria maculans. Evol Appl 2018; 11:1354-1370. [PMID: 30151045 PMCID: PMC6099830 DOI: 10.1111/eva.12630] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/07/2018] [Indexed: 11/27/2022] Open
Abstract
Genetic, physiological and physical homogenization of agricultural landscapes creates ideal environments for plant pathogens to proliferate and rapidly evolve. Thus, a critical challenge in plant pathology and epidemiology is to design durable and effective strategies to protect cropping systems from damage caused by pathogens. Theoretical studies suggest that spatio-temporal variation in the diversity and distribution of resistant hosts across agricultural landscapes may have strong effects on the epidemiology and evolutionary potential of crop pathogens. However, we lack empirical tests of spatio-temporal deployment of host resistance to pathogens can be best used to manage disease epidemics and disrupt pathogen evolutionary dynamics in real-world systems. In a field experiment, we simulated how differences in Brassica napus resistance deployment strategies and landscape connectivity influence epidemic severity and Leptosphaeria maculans pathogen population composition. Host plant resistance, spatio-temporal connectivity [stubble loads], and genetic connectivity of the inoculum source [composition of canola stubble mixtures] jointly impacted epidemiology (disease severity) and pathogen evolution (population composition). Changes in population composition were consistent with directional selection for the ability to infect the host (infectivity), leading to changes in pathotype (multilocus phenotypes) and infectivity frequencies. We repeatedly observed decreases in the frequency of unnecessary infectivity, suggesting that carrying multiple infectivity genes is costly for the pathogen. From an applied perspective, our results indicate that varying resistance genes in space and time can be used to help control disease, even when resistance has already been overcome. Furthermore, our approach extends our ability to test not only for the efficacy of host varieties in a given year, but also for durability over multiple cropping seasons, given variation in the combination of resistance genes deployed.
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Affiliation(s)
- Lydia Bousset
- CSIRO Agriculture & FoodCanberraACTAustralia
- UMR1349 IGEPPINRALe RheuFrance
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Abstract
Durable disease resistance is a key component of global food security, and combining resistance genes into "pyramids" is an important way to increase durability of resistance. The mechanisms by which pyramids impart durability are not well known. The traditional view of resistance pyramids considers the use of major resistance gene (R-gene) combinations deployed against pathogens that are primarily asexual. Interestingly, published examples of the successful use of pyramids in the traditional sense are rare. In contrast, most published descriptions of durable pyramids in practice are for cereal rusts, and tend to indicate an association between durability and cultivars combining major R-genes with incompletely expressed, adult plant resistance genes. Pyramids have been investigated experimentally for a diversity of pathogens, and many reduce disease levels below that of the single best gene. Resistance gene combinations have been identified through phenotypic reactions, molecular markers, and challenge against effector genes. As resistance genes do not express equally in all genetic backgrounds, however, a combination of genetic information and phenotypic analyses provide the ideal scenario for testing of putative pyramids. Not all resistance genes contribute equally to pyramids, and approaches have been suggested to identify the best genes and combinations of genes for inclusion. Combining multiple resistance genes into a single plant genotype quickly is a challenge that is being addressed through alternative breeding approaches, as well as through genomics tools such as resistance gene cassettes and gene editing. Experimental and modeling tests of pyramid durability are in their infancy, but have promise to help direct future studies of pyramids. Several areas for further work on resistance gene pyramids are suggested.
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Affiliation(s)
- Christopher C Mundt
- Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis 97331-2902
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Papaïx J, Rimbaud L, Burdon JJ, Zhan J, Thrall PH. Differential impact of landscape-scale strategies for crop cultivar deployment on disease dynamics, resistance durability and long-term evolutionary control. Evol Appl 2018; 11:705-717. [PMID: 29875812 PMCID: PMC5979631 DOI: 10.1111/eva.12570] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 10/23/2017] [Indexed: 01/28/2023] Open
Abstract
A multitude of resistance deployment strategies have been proposed to tackle the evolutionary potential of pathogens to overcome plant resistance. In particular, many landscape-based strategies rely on the deployment of resistant and susceptible cultivars in an agricultural landscape as a mosaic. However, the design of such strategies is not easy as strategies targeting epidemiological or evolutionary outcomes may not be the same. Using a stochastic spatially explicit model, we studied the impact of landscape organization (as defined by the proportion of fields cultivated with a resistant cultivar and their spatial aggregation) and key pathogen life-history traits on three measures of disease control. Our results show that short-term epidemiological dynamics are optimized when landscapes are planted with a high proportion of the resistant cultivar in low aggregation. Importantly, the exact opposite situation is optimal for resistance durability. Finally, well-mixed landscapes (balanced proportions with low aggregation) are optimal for long-term evolutionary equilibrium (defined here as the level of long-term pathogen adaptation). This work offers a perspective on the potential for contrasting effects of landscape organization on different goals of disease management and highlights the role of pathogen life history.
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Affiliation(s)
| | | | | | - Jiasui Zhan
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
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Rimbaud L, Papaïx J, Rey JF, Barrett LG, Thrall PH. Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens. PLoS Comput Biol 2018; 14:e1006067. [PMID: 29649208 PMCID: PMC5918245 DOI: 10.1371/journal.pcbi.1006067] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 04/24/2018] [Accepted: 02/27/2018] [Indexed: 11/18/2022] Open
Abstract
Genetically-controlled plant resistance can reduce the damage caused by pathogens. However, pathogens have the ability to evolve and overcome such resistance. This often occurs quickly after resistance is deployed, resulting in significant crop losses and a continuing need to develop new resistant cultivars. To tackle this issue, several strategies have been proposed to constrain the evolution of pathogen populations and thus increase genetic resistance durability. These strategies mainly rely on varying different combinations of resistance sources across time (crop rotations) and space. The spatial scale of deployment can vary from multiple resistance sources occurring in a single cultivar (pyramiding), in different cultivars within the same field (cultivar mixtures) or in different fields (mosaics). However, experimental comparison of the efficiency (i.e. ability to reduce disease impact) and durability (i.e. ability to limit pathogen evolution and delay resistance breakdown) of landscape-scale deployment strategies presents major logistical challenges. Therefore, we developed a spatially explicit stochastic model able to assess the epidemiological and evolutionary outcomes of the four major deployment options described above, including both qualitative resistance (i.e. major genes) and quantitative resistance traits against several components of pathogen aggressiveness: infection rate, latent period duration, propagule production rate, and infectious period duration. This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological and evolutionary parameters. This article describes the model and its parameterisation for rust diseases of cereal crops, caused by fungi of the genus Puccinia. To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance. The comparison of the four major deployment strategies described above will be the objective of future studies. There are many recent examples which demonstrate the evolutionary potential of plant pathogens to overcome the resistances deployed in agricultural landscapes to protect our crops. Increasingly, it is recognised that how resistance is deployed spatially and temporally can impact on rates of pathogen evolution and resistance breakdown. Such deployment strategies are mainly based on the combination of several sources of resistance at different spatiotemporal scales. However, comparison of these strategies in a predictive sense is not an easy task, owing to the logistical difficulties associated with experiments involving the spread of a pathogen at large spatio-temporal scales. Moreover, both the durability of a strategy and the epidemiological protection it provides to crops must be assessed since these evaluation criteria are not necessarily correlated. Surprisingly, no current simulation model allows a thorough comparison of the different options. Here we describe a spatio-temporal model able to simulate a wide range of deployment strategies and resistance sources. This model, implemented in the R package landsepi, facilitates assessment of both epidemiological and evolutionary outcomes across simulated scenarios. In this work, the model is used to investigate the combination of different sources of resistance against fungal diseases such as rusts of cereal crops.
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Affiliation(s)
- Loup Rimbaud
- CSIRO Agriculture and Food, Canberra, ACT, Australia
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Mideros SX, Chung CL, Wiesner-Hanks T, Poland JA, Wu D, Fialko AA, Turgeon BG, Nelson RJ. Determinants of Virulence and In Vitro Development Colocalize on a Genetic Map of Setosphaeria turcica. PHYTOPATHOLOGY 2018; 108:254-263. [PMID: 28952420 DOI: 10.1094/phyto-01-17-0021-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Generating effective and stable strategies for resistance breeding requires an understanding of the genetics of host-pathogen interactions and the implications for pathogen dynamics and evolution. Setosphaeria turcica causes northern leaf blight (NLB), an important disease of maize for which major resistance genes have been deployed. Little is known about the evolutionary dynamics of avirulence (AVR) genes in S. turcica. To test the hypothesis that there is a genetic association between avirulence and in vitro development traits, we (i) created a genetic map of S. turcica, (ii) located candidate AVRHt1 and AVRHt2 regions, and (iii) identified genetic regions associated with several in vitro development traits. A cross was generated between a race 1 and a race 23N strain, and 221 progeny were isolated. Genotyping by sequencing was used to score 2,078 single-nucleotide polymorphism markers. A genetic map spanning 1,981 centimorgans was constructed, consisting of 21 linkage groups. Genetic mapping extended prior evidence for the location and identity of the AVRHt1 gene and identified a region of interest for AVRHt2. The genetic location of AVRHt2 colocalized with loci influencing radial growth and mycelial abundance. Our data suggest a trade-off between virulence on Ht1 and Ht2 and the pathogen's vegetative growth rate. In addition, in-depth analysis of the genotypic data suggests the presence of significant duplication in the genome of S. turcica.
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Affiliation(s)
- Santiago X Mideros
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Chia-Lin Chung
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Tyr Wiesner-Hanks
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Jesse A Poland
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Dongliang Wu
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Ariel A Fialko
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - B Gillian Turgeon
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Rebecca J Nelson
- First author: University of Illinois at Urbana-Champaign, Urbana 61801; second author: National Taiwan University, Taipei, 10617, Taiwan; and third, fourth, fifth, sixth, seventh, and eighth authors: School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
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Nelson R, Wiesner-Hanks T, Wisser R, Balint-Kurti P. Navigating complexity to breed disease-resistant crops. Nat Rev Genet 2017; 19:21-33. [PMID: 29109524 DOI: 10.1038/nrg.2017.82] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plant diseases are responsible for substantial crop losses each year and pose a threat to global food security and agricultural sustainability. Improving crop resistance to pathogens through breeding is an environmentally sound method for managing disease and minimizing these losses. However, it is challenging to breed varieties with resistance that is effective, stable and broad-spectrum. Recent advances in genetic and genomic technologies have contributed to a better understanding of the complexity of host-pathogen interactions and have identified some of the genes and mechanisms that underlie resistance. This new knowledge is benefiting crop improvement through better-informed breeding strategies that utilize diverse forms of resistance at different scales, from the genome of a single plant to the plant varieties deployed across a region.
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Affiliation(s)
- Rebecca Nelson
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Tyr Wiesner-Hanks
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Randall Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716, USA
| | - Peter Balint-Kurti
- United States Department of Agriculture Agricultural Research Service (USDA-ARS), Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695-7616, USA
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Puri KD, Gurung S, Short DPG, Atallah ZK, Sandoya G, Davis RM, Hayes RJ, Subbarao KV. Short-Term Host Selection Pressure Has Little Effect on the Evolution of a Monoclonal Population of Verticillium dahliae Race 1. PHYTOPATHOLOGY 2017; 107:1417-1425. [PMID: 28653580 DOI: 10.1094/phyto-02-17-0071-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding pathogen evolution over time is vital for plant breeding and deployment of host resistance. In the context of a soilborne pathogen, the potential of host-directed evolution of a Verticillium dahliae race 1 isolate and genotypic variation of V. dahliae associated with two major hosts (lettuce and tomato) were determined. In total, 427 isolates were recovered over 6 years from a resistance screening nursery infested with a single V. dahliae race 1 isolate. In a separate study, an additional 206 isolates representing 163 and 43 isolates from commercial lettuce and tomato fields, respectively, were collected. Analyses of isolates recovered from the screening nursery over 6 years revealed no changes in the race and mating type composition but did uncover seven simple sequence repeat (SSR) variant genotypes. No significant genotypic variation in V. dahliae was observed between or within fields of either lettuce or tomato but pathogen populations were significantly differentiated between these two hosts. Replicated virulence assays of variant SSR genotypes on lettuce differential cultivars suggested no significant difference in virulence from the wild-type race 1 isolate introduced into the field. This suggests that deployed race 1 host resistance will be robust against the widespread race 1 populations in lettuce-growing regions at least for 6 years unless novel pathogen genotypes or races are introduced into the system.
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Affiliation(s)
- Krishna D Puri
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Suraj Gurung
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Dylan P G Short
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Z K Atallah
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - German Sandoya
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - R Michael Davis
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Ryan J Hayes
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Krishna V Subbarao
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
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Genome re-sequencing analysis uncovers pathogenecity-related genes undergoing positive selection in Magnaporthe oryzae. SCIENCE CHINA-LIFE SCIENCES 2017; 60:880-890. [PMID: 28755293 DOI: 10.1007/s11427-017-9076-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 04/05/2017] [Indexed: 10/19/2022]
Abstract
Rice blast caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of M. oryzae in nature, we re-sequenced the genomes of two field isolates, CH43 and Zhong-10-8-14, which showed distinct pathogenecity on most of the rice cultivars. Genome-wide genetic variation analysis reveals that ZHONG-10-8-14 exhibits higher sequence variations than CH43. Structural variations (SVs) detection shows that the sequence variations primarily occur in exons and intergenic regions. Bioinformatics analysis for gene variations reveals that many pathogenecity-related pathways are enriched. In addition, 193 candidate effectors with various DNA polymorphisms were identified, including two known effectors AVR-Pik and AVR-Pita1. Comparative polymorphism analysis of thirteen randomly selected effectors suggests that the genetic variations of effectors are under positive selection. The expression pattern analysis of several pathogenecity-related variant genes indicates that these genes are differentially regulated in two isolates, with much higher expression levels in Zhong-10-8-14 than CH43. Our data demonstrate that the genetic variations of effectors and pathogenecity-related genes are under positive selection, resulting in the distinct pathogenicities of CH43 and Zhong-10-8-14 on rice.
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Tock AJ, Fourie D, Walley PG, Holub EB, Soler A, Cichy KA, Pastor-Corrales MA, Song Q, Porch TG, Hart JP, Vasconcellos RCC, Vicente JG, Barker GC, Miklas PN. Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen. FRONTIERS IN PLANT SCIENCE 2017; 8:1170. [PMID: 28736566 PMCID: PMC5500643 DOI: 10.3389/fpls.2017.01170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/19/2017] [Indexed: 05/11/2023]
Abstract
Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).
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Affiliation(s)
- Andrew J. Tock
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
- Department of Plant Sciences, Faculty of Biology, University of CambridgeCambridge, United Kingdom
| | - Deidré Fourie
- ARC-Grain Crops InstitutePotchefstroom, South Africa
| | - Peter G. Walley
- Functional and Comparative Genomics, Institute of Integrative Biology, University of LiverpoolLiverpool, United Kingdom
| | - Eric B. Holub
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Alvaro Soler
- Grain Legume Genetics and Physiology Research Unit, Agricultural Research Service, US Department of AgricultureProsser, WA, United States
| | - Karen A. Cichy
- Sugarbeet and Bean Research Unit, Agricultural Research Service, US Department of AgricultureEast Lansing, MI, United States
| | - Marcial A. Pastor-Corrales
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, US Department of AgricultureBeltsville, MD, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, US Department of AgricultureBeltsville, MD, United States
| | - Timothy G. Porch
- Tropical Agriculture Research Station, Agricultural Research Service, US Department of AgricultureMayagüez, Puerto Rico
| | - John P. Hart
- Tropical Agriculture Research Station, Agricultural Research Service, US Department of AgricultureMayagüez, Puerto Rico
| | | | - Joana G. Vicente
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Guy C. Barker
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, Agricultural Research Service, US Department of AgricultureProsser, WA, United States
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Elisabeth Lof M, de Vallavieille-Pope C, van der Werf W. Achieving Durable Resistance Against Plant Diseases: Scenario Analyses with a National-Scale Spatially Explicit Model for a Wind-Dispersed Plant Pathogen. PHYTOPATHOLOGY 2017; 107:580-589. [PMID: 28095206 DOI: 10.1094/phyto-05-16-0207-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Genetic resistance in crops is a cornerstone of disease management in agriculture. Such genetic resistance is often rapidly broken due to selection for virulence in the pathogen population. Here, we ask whether there are strategies that can prolong the useful life of plant resistance genes. In a modeling study, we compared four deployment strategies: gene pyramiding, sequential use, simultaneous use, and a mixed strategy. We developed a spatially explicit model for France and parameterized it for the fungal pathogen Puccinia striiformis f. sp. tritici (causing wheat yellow rust) to test management strategies in a realistic spatial setting. We found that pyramiding two new resistance genes in one variety was the most durable solution only when the virulent genotype had to emerge by mutation. Deploying single-gene-resistant varieties concurrently with the pyramided variety eroded the durability of the gene pyramid. We found that continuation of deployment of varieties with broken-down resistance prolonged the useful life of simultaneous deployment of four single-gene-resistant varieties versus sequential use. However, when virulence was already present in the pathogen population, durability was low and none of the deployment strategies had effect. These results provide guidance on effective strategies for using resistance genes in crop protection practice.
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Affiliation(s)
- Marjolein Elisabeth Lof
- First and third authors: Wageningen University, Centre for Crop Systems Analysis, P.O. Box 430, 6700 AK Wageningen, The Netherlands; and second author: INRA UMR 1290 BIOGER, BP01, 78850 Thiverval-Grignon, France
| | - Claude de Vallavieille-Pope
- First and third authors: Wageningen University, Centre for Crop Systems Analysis, P.O. Box 430, 6700 AK Wageningen, The Netherlands; and second author: INRA UMR 1290 BIOGER, BP01, 78850 Thiverval-Grignon, France
| | - Wopke van der Werf
- First and third authors: Wageningen University, Centre for Crop Systems Analysis, P.O. Box 430, 6700 AK Wageningen, The Netherlands; and second author: INRA UMR 1290 BIOGER, BP01, 78850 Thiverval-Grignon, France
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Blanvillain‐Baufumé S, Reschke M, Solé M, Auguy F, Doucoure H, Szurek B, Meynard D, Portefaix M, Cunnac S, Guiderdoni E, Boch J, Koebnik R. Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:306-317. [PMID: 27539813 PMCID: PMC5316920 DOI: 10.1111/pbi.12613] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 05/04/2023]
Abstract
As a key virulence strategy to cause bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo) injects into the plant cell DNA-binding proteins called transcription activator-like effectors (TALEs) that bind to effector-binding elements (EBEs) in a sequence-specific manner, resulting in host gene induction. TALEs AvrXa7, PthXo3, TalC and Tal5, found in geographically distant Xoo strains, all target OsSWEET14, thus considered as a pivotal TALE target acting as major susceptibility factor during rice-Xoo interactions. Here, we report the generation of an allele library of the OsSWEET14 promoter through stable expression of TALE-nuclease (TALEN) constructs in rice. The susceptibility level of lines carrying mutations in AvrXa7, Tal5 or TalC EBEs was assessed. Plants edited in AvrXa7 or Tal5 EBEs were resistant to bacterial strains relying on the corresponding TALE. Surprisingly, although indels within TalC EBE prevented OsSWEET14 induction in response to BAI3 wild-type bacteria relying on TalC, loss of TalC responsiveness failed to confer resistance to this strain. The TalC EBE mutant line was, however, resistant to a strain expressing an artificial SWEET14-inducing TALE whose EBE was also edited in this line. This work offers the first set of alleles edited in TalC EBE and uncovers a distinct, broader range of activities for TalC compared to AvrXa7 or Tal5. We propose the existence of additional targets for TalC beyond SWEET14, suggesting that TALE-mediated plant susceptibility may result from induction of several, genetically redundant, host susceptibility genes by a single effector.
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Affiliation(s)
- Servane Blanvillain‐Baufumé
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
- Present address: LabEx CeMEBUniversité de MontpellierMontpellierFrance
| | - Maik Reschke
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Montserrat Solé
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Sustainable Agro Solutions S.A.Almacelles (Lleida)Spain
| | - Florence Auguy
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Hinda Doucoure
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Boris Szurek
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Donaldo Meynard
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Murielle Portefaix
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Sébastien Cunnac
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Emmanuel Guiderdoni
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Jens Boch
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Ralf Koebnik
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
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46
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Hu K, Cao J, Zhang J, Xia F, Ke Y, Zhang H, Xie W, Liu H, Cui Y, Cao Y, Sun X, Xiao J, Li X, Zhang Q, Wang S. Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement. NATURE PLANTS 2017; 3:17009. [PMID: 28211849 DOI: 10.1038/nplants.2017.9] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 01/21/2017] [Indexed: 05/03/2023]
Abstract
The major disease resistance gene Xa4 confers race-specific durable resistance against Xanthomonas oryzae pv. oryzae, which causes the most damaging bacterial disease in rice worldwide. Although Xa4 has been one of the most widely exploited resistance genes in rice production worldwide, its molecular nature remains unknown. Here we show that Xa4, encoding a cell wall-associated kinase, improves multiple traits of agronomic importance without compromising grain yield by strengthening the cell wall via promoting cellulose synthesis and suppressing cell wall loosening. Strengthening of the cell wall by Xa4 enhances resistance to bacterial infection, and also increases mechanical strength of the culm with slightly reduced plant height, which may improve lodging resistance of the rice plant. The simultaneous improvement of multiple agronomic traits conferred by Xa4 may account for its widespread and lasting utilization in rice breeding programmes globally.
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Affiliation(s)
- Keming Hu
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbo Cao
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Zhang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Xia
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yinggen Ke
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Haitao Zhang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenya Xie
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Cui
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yinglong Cao
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xinli Sun
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations. Appl Environ Microbiol 2017; 83:AEM.03095-16. [PMID: 28003195 DOI: 10.1128/aem.03095-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/13/2016] [Indexed: 12/31/2022] Open
Abstract
Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is considered one of the most harmful plant diseases in the world. Special attention should be paid to R. pseudosolanacearum phylotype I due to its large host range, its worldwide distribution, and its high evolutionary potential. So far, the molecular epidemiology and population genetics of this bacterium are poorly understood. Until now, the genetic structure of the RSSC has been analyzed on the worldwide and regional scales. Emerging questions regarding evolutionary forces in RSSC adaptation to hosts now require genetic markers that are able to monitor RSSC field populations. In this study, we aimed to evaluate the multilocus variable-number tandem-repeat analysis (MLVA) approach for its ability to discriminate genetically close phylotype I strains and for population genetics studies. We developed a new MLVA scheme (MLVA-7) allowing us to genotype 580 R. pseudosolanacearum phylotype I strains extracted from susceptible and resistant hosts and from different habitats (stem, soil, and rhizosphere). Based on specificity, polymorphism, and the amplification success rate, we selected seven fast-evolving variable-number tandem-repeat (VNTR) markers. The newly developed MLVA-7 scheme showed higher discriminatory power than the previously published MLVA-13 scheme when applied to collections sampled from the same location on different dates and to collections from different locations on very small scales. Our study provides a valuable tool for fine-scale monitoring and microevolution-related study of R. pseudosolanacearum phylotype I populations.IMPORTANCE Understanding the evolutionary dynamics of adaptation of plant pathogens to new hosts or ecological niches has become a key point for the development of innovative disease management strategies, including durable resistance. Whereas the molecular mechanisms underlying virulence or pathogenicity changes have been studied thoroughly, the population genetics of plant pathogen adaptation remains an open, unexplored field, especially for plant-pathogenic bacteria. MLVA has become increasingly popular for epidemiosurveillance and molecular epidemiology studies of plant pathogens. However, this method has been used mostly for genotyping and identification on a regional or global scale. In this study, we developed a new MLVA scheme, targeting phylotype I of the soilborne Ralstonia solanacearum species complex (RSSC), specifically to address the bacterial population genetics on the field scale. Such a MLVA scheme, based on fast-evolving loci, may be a tool of choice for field experimental evolution and spatial genetics studies.
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Plissonneau C, Benevenuto J, Mohd-Assaad N, Fouché S, Hartmann FE, Croll D. Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:119. [PMID: 28217138 PMCID: PMC5289978 DOI: 10.3389/fpls.2017.00119] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/20/2017] [Indexed: 05/20/2023]
Abstract
Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.
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Affiliation(s)
- Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
- UMR, BIOGER, INRA, AgroParisTech, Université Paris-SaclayThiverval-Grignon, France
| | - Juliana Benevenuto
- College of Agriculture “Luiz de Queiroz”, University of São PauloSão Paulo, Brazil
| | - Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaSelangor, Malaysia
| | - Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
| | - Fanny E. Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchatelNeuchatel, Switzerland
- *Correspondence: Daniel Croll,
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49
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Sundin GW, Castiblanco LF, Yuan X, Zeng Q, Yang C. Bacterial disease management: challenges, experience, innovation and future prospects: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2016; 17:1506-1518. [PMID: 27238249 PMCID: PMC6638406 DOI: 10.1111/mpp.12436] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plant diseases caused by bacterial pathogens place major constraints on crop production and cause significant annual losses on a global scale. The attainment of consistent effective management of these diseases can be extremely difficult, and management potential is often affected by grower reliance on highly disease-susceptible cultivars because of consumer preferences, and by environmental conditions favouring pathogen development. New and emerging bacterial disease problems (e.g. zebra chip of potato) and established problems in new geographical regions (e.g. bacterial canker of kiwifruit in New Zealand) grab the headlines, but the list of bacterial disease problems with few effective management options is long. The ever-increasing global human population requires the continued stable production of a safe food supply with greater yields because of the shrinking areas of arable land. One major facet in the maintenance of the sustainability of crop production systems with predictable yields involves the identification and deployment of sustainable disease management solutions for bacterial diseases. In addition, the identification of novel management tactics has also come to the fore because of the increasing evolution of resistance to existing bactericides. A number of central research foci, involving basic research to identify critical pathogen targets for control, novel methodologies and methods of delivery, are emerging that will provide a strong basis for bacterial disease management into the future. Near-term solutions are desperately needed. Are there replacement materials for existing bactericides that can provide effective disease management under field conditions? Experience should inform the future. With prior knowledge of bactericide resistance issues evolving in pathogens, how will this affect the deployment of newer compounds and biological controls? Knowledge is critical. A comprehensive understanding of bacterial pathosystems is required to not only identify optimal targets in the pathogens, but also optimal seasonal timings for deployment. Host resistance to effectors must be exploited, carefully and correctly. Are there other candidate genes that could be targeted in transgenic approaches? How can new technologies (CRISPR, TALEN, etc.) be most effectively used to add sustainable disease resistance to existing commercially desirable plant cultivars? We need an insider's perspective on the management of systemic pathogens. In addition to host resistance or reduced sensitivity, are there other methods that can be used to target these pathogen groups? Biological systems are variable. Can biological control strategies be improved for bacterial disease management and be made more predictable in function? The answers to the research foci outlined above are not all available, as will become apparent in this article, but we are heading in the right direction. In this article, we summarize the contributions from past experiences in bacterial disease management, and also describe how advances in bacterial genetics, genomics and host-pathogen interactions are informing novel strategies in virulence inhibition and in host resistance. We also outline potential innovations that could be exploited as the pressures to maximize a safe and productive food supply continue to become more numerous and more complex.
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Affiliation(s)
- George W. Sundin
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMI48824USA
| | - Luisa F. Castiblanco
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMI48824USA
| | - Xiaochen Yuan
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWI53211USA
| | - Quan Zeng
- Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment StationNew HavenCT06504USA
| | - Ching‐Hong Yang
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWI53211USA
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50
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Burdon JJ, Zhan J, Barrett LG, Papaïx J, Thrall PH. Addressing the Challenges of Pathogen Evolution on the World's Arable Crops. PHYTOPATHOLOGY 2016; 106:1117-1127. [PMID: 27584868 DOI: 10.1094/phyto-01-16-0036-fi] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Advances in genomic and molecular technologies coupled with an increasing understanding of the fine structure of many resistance and infectivity genes, have opened up a new era of hope in controlling the many plant pathogens that continue to be a major source of loss in arable crops. Some new approaches are under consideration including the use of nonhost resistance and the targeting of critical developmental constraints. However, the major thrust of these genomic and molecular approaches is to enhance the identification of resistance genes, to increase their ease of manipulation through marker and gene editing technologies and to lock a range of resistance genes together in simply manipulable resistance gene cassettes. All these approaches essentially continue a strategy that assumes the ability to construct genetic-based resistance barriers that are insurmountable to target pathogens. Here we show how the recent advances in knowledge and marker technologies can be used to generate more durable disease resistance strategies that are based on broad evolutionary principles aimed at presenting pathogens with a shifting, landscape of fluctuating directional selection.
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Affiliation(s)
- Jeremy J Burdon
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
| | - Jiasui Zhan
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
| | - Luke G Barrett
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
| | - Julien Papaïx
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
| | - Peter H Thrall
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
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