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Kimunye JN, Muzhinji N, Mostert D, Viljoen A, Bester-van der Merwe AE, Mahuku G. Genetic Diversity and Mating Type Distribution of Pseudocercospora fijiensis on Banana in Uganda and Tanzania. PHYTOPATHOLOGY 2021; 111:741-750. [PMID: 32931393 DOI: 10.1094/phyto-04-20-0138-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Black Sigatoka, caused by Pseudocercospora fijiensis, is a major foliar disease of banana and plantain worldwide. There are few available data regarding the genetic diversity and population structure of the pathogen in East Africa, which are needed to design effective and durable disease management strategies. We genotyped 319 single-spore isolates of P. fijiensis collected from seven regions in Uganda and Tanzania and five isolates from Nigeria using 16 simple sequence repeat markers and mating type-specific primers. Isolates from each country and region within the country were treated as populations and subpopulations, respectively. A total of 296 multilocus genotypes (MLGs) were recovered, representing a clonal fraction of 7%. Subpopulations had a moderate level of genetic diversity (Hexp = 0.12 to 0.31; mean, 0.29). Mating type distribution did not deviate from equilibrium (MAT1-1: MAT1-2, 1:1 ratio) in Uganda; however, in Tanzania the mating types were not in equilibrium (4:1 ratio). The index of association tests (IA and r̄d) showed that all populations were at linkage equilibrium (P > 0.05), thus supporting the hypothesis of random association of alleles. These findings are consistent with a pathogen that reproduces both clonally and sexually. Low and insignificant levels of population differentiation were detected, with 90% of the variation occurring among isolates within subpopulations. The high intrapopulation variation has implications in breeding for resistance to P. fijiensis because isolates differing in aggressiveness and virulence are likely to exist over small spatial scales. Diverse isolates will be required for resistance screening to ensure selection of banana cultivars with durable resistance to Sigatoka in East Africa.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Janet N Kimunye
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | - Norman Muzhinji
- Department of Applied and Natural Sciences, Namibia University of Science and Technology, Private Bag 13388, Windhoek, Namibia
| | - Diane Mostert
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | - Altus Viljoen
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | | | - George Mahuku
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- International Institute of Tropical Agriculture, P.O. Box, 34441, Dar es Salaam, Tanzania
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Arango Isaza RE, Diaz-Trujillo C, Dhillon B, Aerts A, Carlier J, Crane CF, V. de Jong T, de Vries I, Dietrich R, Farmer AD, Fortes Fereira C, Garcia S, Guzman M, Hamelin RC, Lindquist EA, Mehrabi R, Quiros O, Schmutz J, Shapiro H, Reynolds E, Scalliet G, Souza M, Stergiopoulos I, Van der Lee TAJ, De Wit PJGM, Zapater MF, Zwiers LH, Grigoriev IV, Goodwin SB, Kema GHJ. Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control. PLoS Genet 2016; 12:e1005876. [PMID: 27512984 PMCID: PMC4981457 DOI: 10.1371/journal.pgen.1005876] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 01/27/2016] [Indexed: 12/03/2022] Open
Abstract
Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules to combat this pathogen and in improving the efficiency of banana breeding programs.
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Affiliation(s)
- Rafael E. Arango Isaza
- Escuela de Biociencias, Universidad Nacional de Colombia, Medellín, Colombia
- Plant Biotechnology Unit, Corporación Para Investigaciones Biológicas, Medellín, Colombia
| | | | - Braham Dhillon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Andrea Aerts
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | | | - Charles F. Crane
- USDA-Agricultural Research Service, West Lafayette, Indiana, United States of America
| | - Tristan V. de Jong
- Plant Research International, Wageningen University and Research, Wageningen, The Netherlands
| | - Ineke de Vries
- Plant Research International, Wageningen University and Research, Wageningen, The Netherlands
| | - Robert Dietrich
- Syngenta Biotechnology Inc., Research Triangle Park, United States of America
| | - Andrew D. Farmer
- National Center for Genome Resources, Santa Fe, United States of America
| | | | | | - Mauricio Guzman
- National Banana Corporation of Costa Rica (CORBANA), La Rita de Pococí, Limón, Costa Rica
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Erika A. Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Rahim Mehrabi
- Department of Genetics, Seed and Plant Improvement Institute, Karaj, Iran
| | - Olman Quiros
- National Banana Corporation of Costa Rica (CORBANA), La Rita de Pococí, Limón, Costa Rica
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Harris Shapiro
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Elizabeth Reynolds
- General Bioinformatics at Syngenta Crop protection Jeallots Hill International Research Centre, Bracknell Berkshire, United Kingdom
| | | | - Manoel Souza
- Embrapa-LABEX Europe, Wageningen, The Netherlands
| | | | - Theo A. J. Van der Lee
- Plant Research International, Wageningen University and Research, Wageningen, The Netherlands
| | | | | | | | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Stephen B. Goodwin
- USDA-Agricultural Research Service, West Lafayette, Indiana, United States of America
| | - Gert H. J. Kema
- Plant Research International, Wageningen University and Research, Wageningen, The Netherlands
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
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