1
|
Adams TM, Olsson TSG, Ramírez-González RH, Bryant R, Bryson R, Campos PE, Fenwick P, Feuerhelm D, Hayes C, Henriksson T, Hubbard A, Jevtić R, Judge C, Kerton M, Lage J, Lewis CM, Lilly C, Meidan U, Novoselović D, Patrick C, Wanyera R, Saunders DGO. Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP. BMC Genomics 2021; 22:166. [PMID: 33750297 PMCID: PMC7941908 DOI: 10.1186/s12864-021-07488-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/26/2021] [Indexed: 01/05/2023] Open
Abstract
Background Transcriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen (Puccinia striiformis f. sp. tritici, Pst) RNA-based sequencing (RNA-Seq) has proved particularly valuable, overcoming the barriers associated with its obligate biotrophic nature. This includes the application of RNA-Seq approaches to study Pst and wheat gene expression dynamics over time and the Pst population composition through the use of a novel RNA-Seq based surveillance approach called “field pathogenomics”. As a dual RNA-Seq approach, the field pathogenomics technique also provides gene expression data from the host, giving new insight into host responses. However, this has created a wealth of data for interrogation. Results Here, we used the field pathogenomics approach to generate 538 new RNA-Seq datasets from Pst-infected field wheat samples, doubling the amount of transcriptomics data available for this important pathosystem. We then analysed these datasets alongside 66 RNA-Seq datasets from four Pst infection time-courses and 420 Pst-infected plant field and laboratory samples that were publicly available. A database of gene expression values for Pst and wheat was generated for each of these 1024 RNA-Seq datasets and incorporated into the development of the rust expression browser (http://www.rust-expression.com). This enables for the first time simultaneous ‘point-and-click’ access to gene expression profiles for Pst and its wheat host and represents the largest database of processed RNA-Seq datasets available for any of the three Puccinia wheat rust pathogens. We also demonstrated the utility of the browser through investigation of expression of putative Pst virulence genes over time and examined the host plants response to Pst infection. Conclusions The rust expression browser offers immense value to the wider community, facilitating data sharing and transparency and the underlying database can be continually expanded as more datasets become publicly available. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07488-3.
Collapse
Affiliation(s)
- Thomas M Adams
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Ruth Bryant
- RAGT Seeds Ltd, Grange Road, Ickleton, Essex, CB10 1TA, UK
| | - Rosie Bryson
- BASF SE, Agricultural Centre, Limburgerhof, Germany
| | | | | | - David Feuerhelm
- Syngenta Seeds Ltd, Hill Farm Road, Cambridgeshire, CB22 4QT, UK
| | | | | | | | | | | | - Matthew Kerton
- DSV United Kingdom Ltd, Banbury, Oxfordshire, OX17 1FE, UK
| | - Jacob Lage
- KWS UK Limited, Hertfordshire, SG8 7RE, UK
| | - Clare M Lewis
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Christine Lilly
- Frontier Agriculture, Witham St Hughs, Lincolnshire, LN6 9TN, UK
| | - Udi Meidan
- Hazera Seeds Ltd., Berurim M.P Shikmim, 7983700, Tel Aviv-Yafo, Israel
| | | | - Colin Patrick
- Masstock Arable (UK) Ltd. (trading as Agrii), Andoversford, Gloucestershire, GL54 4LZ, UK
| | - Ruth Wanyera
- Kenya Agricultural and Livestock Research Organization, Njoro, Nakuru, Kenya
| | | |
Collapse
|
2
|
Ghimire B, Sapkota S, Bahri BA, Martinez-Espinoza AD, Buck JW, Mergoum M. Fusarium Head Blight and Rust Diseases in Soft Red Winter Wheat in the Southeast United States: State of the Art, Challenges and Future Perspective for Breeding. FRONTIERS IN PLANT SCIENCE 2020; 11:1080. [PMID: 32765563 PMCID: PMC7378807 DOI: 10.3389/fpls.2020.01080] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/30/2020] [Indexed: 05/21/2023]
Abstract
Among the biotic constraints to wheat (Triticum aestivum L.) production, fusarium head blight (FHB), caused by Fusarium graminearum, leaf rust (LR), caused by Puccinia triticina, and stripe rust (SR) caused by Puccinia striiformis are problematic fungal diseases worldwide. Each can significantly reduce grain yield while FHB causes additional food and feed safety concerns due to mycotoxin contamination of grain. Genetic resistance is the most effective and sustainable approach for managing wheat diseases. In the past 20 years, over 500 quantitative trait loci (QTLs) conferring small to moderate effects for the different FHB resistance types have been reported in wheat. Similarly, 79 Lr-genes and more than 200 QTLs and 82 Yr-genes and 140 QTLs have been reported for seedling and adult plant LR and SR resistance, respectively. Most QTLs conferring rust resistance are race-specific generally conforming to a classical gene-for-gene interaction while resistance to FHB exhibits complex polygenic inheritance with several genetic loci contributing to one resistance type. Identification and deployment of additional genes/QTLs associated with FHB and rust resistance can expedite wheat breeding through marker-assisted and/or genomic selection to combine small-effect QTL in the gene pool. LR disease has been present in the southeast United States for decades while SR and FHB have become increasingly problematic in the past 20 years, with FHB arguably due to increased corn acreage in the region. Currently, QTLs on chromosome 1B from Jamestown, 1A, 1B, 2A, 2B, 2D, 4A, 5A, and 6A from W14, Ning7840, Ernie, Bess, Massey, NC-Neuse, and Truman, and 3B (Fhb1) from Sumai 3 for FHB resistance, Lr9, Lr10, Lr18, Lr24, Lr37, LrA2K, and Lr2K38 genes for LR resistance, and Yr17 and YrR61 for SR resistance have been extensively deployed in southeast wheat breeding programs. This review aims to disclose the current status of FHB, LR, and SR diseases, summarize the genetics of resistance and breeding efforts for the deployment of FHB and rust resistance QTL on soft red winter wheat cultivars, and present breeding strategies to achieve sustainable management of these diseases in the southeast US.
Collapse
Affiliation(s)
- Bikash Ghimire
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Suraj Sapkota
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Bochra A. Bahri
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | | | - James W. Buck
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, United States
| |
Collapse
|
3
|
Figlan S, Ntushelo K, Mwadzingeni L, Terefe T, Tsilo TJ, Shimelis H. Breeding Wheat for Durable Leaf Rust Resistance in Southern Africa: Variability, Distribution, Current Control Strategies, Challenges and Future Prospects. FRONTIERS IN PLANT SCIENCE 2020; 11:549. [PMID: 32499800 PMCID: PMC7242648 DOI: 10.3389/fpls.2020.00549] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/09/2020] [Indexed: 05/30/2023]
Abstract
Leaf or brown rust of wheat caused by Puccinia triticina (Pt) is one of the most damaging diseases globally. Considerable progress has been made to control leaf rust through crop protection chemicals and host plant resistance breeding in southern Africa. However, frequent changes in the pathogen population still present a major challenge to achieve durable resistance. Disease surveillance and monitoring of the pathogen have revealed the occurrence of similar races across the region, justifying the need for concerted efforts by countries in southern Africa to develop and deploy more efficient and sustainable strategies to manage the disease. Understanding the genetic variability and composition of Pt is a pre-requisite for cultivar release with appropriate resistance gene combinations for sustainable disease management. This review highlights the variability and distribution of the Pt population, and the current control strategies, challenges and future prospects of breeding wheat varieties with durable leaf rust resistance in southern Africa. The importance of regular, collaborative and efficient surveillance of the pathogen and germplasm development across southern Africa is discussed, coupled with the potential of using modern breeding technologies to produce wheat cultivars with durable resistance.
Collapse
Affiliation(s)
- Sandiswa Figlan
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Agricultural Research Council-Small Grain, Bethlehem, South Africa
- Department of Agriculture and Animal Health, University of South Africa, Florida, South Africa
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa, Florida, South Africa
| | - Learnmore Mwadzingeni
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Agricultural Research Council-Small Grain, Bethlehem, South Africa
| | - Tarekegn Terefe
- Agricultural Research Council-Small Grain, Bethlehem, South Africa
| | - Toi J. Tsilo
- Agricultural Research Council-Small Grain, Bethlehem, South Africa
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| |
Collapse
|
4
|
Prasad P, Savadi S, Bhardwaj SC, Gupta PK. The progress of leaf rust research in wheat. Fungal Biol 2020; 124:537-550. [PMID: 32448445 DOI: 10.1016/j.funbio.2020.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/25/2023]
Abstract
Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.
Collapse
Affiliation(s)
- Pramod Prasad
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Siddanna Savadi
- ICAR-Directorate of Cashew Research, Puttur, Karnataka, 574202, India
| | - S C Bhardwaj
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
| |
Collapse
|
5
|
Bueno-Sancho V, Persoons A, Hubbard A, Cabrera-Quio LE, Lewis CM, Corredor-Moreno P, Bunting DCE, Ali S, Chng S, Hodson DP, Madariaga Burrows R, Bryson R, Thomas J, Holdgate S, Saunders DGO. Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variation and Host Specificity. Genome Biol Evol 2017; 9:3282-3296. [PMID: 29177504 PMCID: PMC5730935 DOI: 10.1093/gbe/evx241] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/27/2022] Open
Abstract
Recent disease outbreaks caused by (re-)emerging plant pathogens have been associated with expansions in pathogen geographic distribution and increased virulence. For example, in the past two decades' wheat yellow (stripe) rust, Puccinia striiformis f. sp. tritici, has seen the emergence of new races that are adapted to warmer temperatures, have expanded virulence profiles, and are more aggressive than previous races, leading to wide-scale epidemics. Here, we used field-based genotyping to generate high-resolution data on P. striiformis genetics and carried out global population analysis. We also undertook comparative analysis of the 2014 and 2013 UK populations and assessed the temporal dynamics and host specificity of distinct pathogen genotypes. Our analysis revealed that P. striiformis lineages recently detected in Europe are extremely diverse and in fact similar to globally dispersed populations. In addition, we identified a considerable shift in the UK P. striiformis population structure including the first identification of one infamous race known as Kranich. Next, by establishing the genotype of both the pathogen and host within a single infected field sample, we uncovered evidence for varietal specificity for genetic groups of P. striiformis. Finally, we found potential seasonal specificity for certain genotypes of the pathogen with several lineages identified only in samples collected in late spring and into the summer, whereas one lineage was identified throughout the wheat growing season. Our discovery of which wheat varieties are susceptible to which specific P. striiformis isolates, and when those isolates are prevalent throughout the year, represents a powerful tool for disease management.
Collapse
Affiliation(s)
| | - Antoine Persoons
- Crop Genetics, John Innes Centre, Norwich Research Park, United Kingdom
| | - Amelia Hubbard
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Luis Enrique Cabrera-Quio
- Earlham Institute, Norwich Research Park, United Kingdom
- The Sainsbury Laboratory, Norwich Research Park, United Kingdom
| | - Clare M Lewis
- Crop Genetics, John Innes Centre, Norwich Research Park, United Kingdom
| | | | | | - Sajid Ali
- The University of Agriculture, Peshawar, Pakistan
| | - Soonie Chng
- The New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
| | | | | | - Rosie Bryson
- BASF SE, Agricultural Centre, Limburgerhof, Germany
| | - Jane Thomas
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Sarah Holdgate
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
| | | |
Collapse
|
6
|
Rutter WB, Salcedo A, Akhunova A, He F, Wang S, Liang H, Bowden RL, Akhunov E. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses. BMC Genomics 2017; 18:291. [PMID: 28403814 PMCID: PMC5389088 DOI: 10.1186/s12864-017-3678-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). RESULTS The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. CONCLUSIONS Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen's ability to infect the host.
Collapse
Affiliation(s)
- William B. Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
- USDA-ARS, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414 USA
| | - Andres Salcedo
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Alina Akhunova
- Integrated Genomics Facility, Kansas State University, Manhattan, KS 66506 USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
- TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, 101 Gateway, Suite A, College Station, TX 77845 USA
| | - Hanquan Liang
- Integrated Genomics Facility, Kansas State University, Manhattan, KS 66506 USA
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, 510006 China
| | - Robert L. Bowden
- USDA ARS, Hard Winter Wheat Genetics Research Unit, Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| |
Collapse
|
7
|
Bueno-Sancho V, Bunting DCE, Yanes LJ, Yoshida K, Saunders DGO. Field Pathogenomics: An Advanced Tool for Wheat Rust Surveillance. Methods Mol Biol 2017; 1659:13-28. [PMID: 28856637 DOI: 10.1007/978-1-4939-7249-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Traditionally, diagnostic tools for plant pathogens were limited to the analysis of purified pathogen isolates subjected to phenotypic characterization and/or PCR-based genotypic analysis. However, these approaches detect only already known pathogenic agents, may not always recognize novel races, and can introduce bias in the results. Recent advances in next-generation sequencing technologies have provided new opportunities to integrate high-resolution genotype data into pathogen surveillance programs. Here, we describe some of the key bioinformatics analysis used in the newly developed "Field Pathogenomics" pathogen surveillance technique. This technique is based on RNA-seq data generated directly form pathogen-infected plant leaf samples collected in the field, providing a unique opportunity to characterize the pathogen population and its host directly in their natural environment. We describe two main analyses: (1) a phylogenetic analysis of the pathogen isolates that have been collected to understand how they are related to each other, and (2) a population structure analysis to provide insight into the genetic substructure within the pathogen population. This provides a high-resolution representation of pathogen population dynamics directly in the field, providing new insights into pathogen biology, population structure, and pathogenesis.
Collapse
Affiliation(s)
- Vanessa Bueno-Sancho
- Earlham Institute, Norwich Research Park, Norwich, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Daniel C E Bunting
- Earlham Institute, Norwich Research Park, Norwich, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Luis J Yanes
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Diane G O Saunders
- Earlham Institute, Norwich Research Park, Norwich, UK.
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| |
Collapse
|
8
|
Derevnina L, Petre B, Kellner R, Dagdas YF, Sarowar MN, Giannakopoulou A, De la Concepcion JC, Chaparro-Garcia A, Pennington HG, van West P, Kamoun S. Emerging oomycete threats to plants and animals. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150459. [PMID: 28080985 PMCID: PMC5095538 DOI: 10.1098/rstb.2015.0459] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2016] [Indexed: 12/31/2022] Open
Abstract
Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans, Phytophthora palmivora, Phytophthora ramorum, Plasmopara obducens, and the animal pathogens Aphanomyces invadans, Saprolegnia parasitica and Halioticida noduliformans For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
Collapse
Affiliation(s)
- Lida Derevnina
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ronny Kellner
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Yasin F Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mohammad Nasif Sarowar
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | | | | | | | | | - Pieter van West
- International Centre for Aquaculture Research and Development, Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| |
Collapse
|
9
|
Islam MT, Croll D, Gladieux P, Soanes DM, Persoons A, Bhattacharjee P, Hossain MS, Gupta DR, Rahman MM, Mahboob MG, Cook N, Salam MU, Surovy MZ, Sancho VB, Maciel JLN, NhaniJúnior A, Castroagudín VL, Reges JTDA, Ceresini PC, Ravel S, Kellner R, Fournier E, Tharreau D, Lebrun MH, McDonald BA, Stitt T, Swan D, Talbot NJ, Saunders DGO, Win J, Kamoun S. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biol 2016; 14:84. [PMID: 27716181 PMCID: PMC5047043 DOI: 10.1186/s12915-016-0309-7] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields. RESULTS Reinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae. CONCLUSION Our findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.
Collapse
Affiliation(s)
- M Tofazzal Islam
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Pierre Gladieux
- INRA, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, Montpellier, France
| | - Darren M Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | | | - Pallab Bhattacharjee
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Shaid Hossain
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Dipali Rani Gupta
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Mahbubur Rahman
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - M Golam Mahboob
- Argo-Environmental Remote Sensing and Modeling Lab, Bangladesh Agricultural Research Institute, Joydebpur 1701, Gazipur, Bangladesh
| | - Nicola Cook
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Moin U Salam
- Directorate of Grains Industry, Department of Agriculture and Food Western Australia (DAFWA), 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Musrat Zahan Surovy
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | | | - João Leodato Nunes Maciel
- Brazilian Agricultural Research Enterprise - EMBRAPA Wheat/Trigo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Antonio NhaniJúnior
- Brazilian Agricultural Research Enterprise - EMBRAPA Wheat/Trigo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Vanina Lilián Castroagudín
- Department of Crop Protection, Rural Engineering, and Soil Science, University of São Paulo State - UNESP, IlhaSolteira Campus, São Paulo, Brazil
| | - Juliana T de Assis Reges
- Department of Crop Protection, Rural Engineering, and Soil Science, University of São Paulo State - UNESP, IlhaSolteira Campus, São Paulo, Brazil
| | - Paulo Cezar Ceresini
- Department of Crop Protection, Rural Engineering, and Soil Science, University of São Paulo State - UNESP, IlhaSolteira Campus, São Paulo, Brazil
| | - Sebastien Ravel
- CIRAD, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, Montpellier, France
| | - Ronny Kellner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Elisabeth Fournier
- INRA, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, Montpellier, France
| | - Didier Tharreau
- CIRAD, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, Montpellier, France
| | - Marc-Henri Lebrun
- INRA, UMR 1290 Biologie et Gestion des Risques en agriculture BIOGER, Thiverval-Grignon, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Timothy Stitt
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Daniel Swan
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nicholas J Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Diane G O Saunders
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| |
Collapse
|
10
|
Matson MEH, Small IM, Fry WE, Judelson HS. Metalaxyl Resistance in Phytophthora infestans: Assessing Role of RPA190 Gene and Diversity Within Clonal Lineages. PHYTOPATHOLOGY 2015; 105:1594-600. [PMID: 26551315 DOI: 10.1094/phyto-05-15-0129-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Prior work has shown that the inheritance of resistance to metalaxyl, an oomycete-specific fungicide, is complex and may involve multiple genes. Recent research indicated that a single nucleotide polymorphism (SNP) in the gene encoding RPA190, the largest subunit of RNA polymerase I, confers resistance to metalaxyl (or mefenoxam) in some isolates of the potato late blight pathogen Phytophthora infestans. Using both DNA sequencing and high resolution melt assays for distinguishing RPA190 alleles, we show here that the SNP is absent from certain resistant isolates of P. infestans from North America, Europe, and Mexico. The SNP is present in some members of the US-23 and US-24 clonal lineages, but these tend to be fairly sensitive to the fungicide based on artificial media and field test data. Diversity in the level of sensitivity, RPA190 genotype, and RPA190 copy number was observed in these lineages but were uncorrelated. Controlled laboratory crosses demonstrated that RPA190 did not cosegregate with metalaxyl resistance from a Mexican and British isolate. We conclude that while metalaxyl may be used to control many contemporary strains of P. infestans, an assay based on RPA190 will not be sufficient to diagnose the sensitivity levels of isolates.
Collapse
Affiliation(s)
- Michael E H Matson
- First and fourth authors: Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521; and second and third authors: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| | - Ian M Small
- First and fourth authors: Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521; and second and third authors: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| | - William E Fry
- First and fourth authors: Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521; and second and third authors: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| | - Howard S Judelson
- First and fourth authors: Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521; and second and third authors: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| |
Collapse
|