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Your search keyword '"Martha Malapi-Wight"' showing total 4 results
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1. Population Genomics Provide Insights into the Global Genetic Structure of Colletotrichum graminicola, the Causal Agent of Maize Anthracnose

Author

Flávia Rogério, Riccardo Baroncelli, Francisco Borja Cuevas-Fernández, Sioly Becerra, JoAnne Crouch, Wagner Bettiol, M. Andrea Azcárate-Peril, Martha Malapi-Wight, Veronique Ortega, Javier Betran, Albert Tenuta, José S. Dambolena, Paul D. Esker, Pedro Revilla, Tamra A. Jackson-Ziems, Jürg Hiltbrunner, Gary Munkvold, Ivica Buhiniček, José L. Vicente-Villardón, Serenella A. Sukno, and Michael R. Thon

Subjects
fungal plant pathogen, population genetics, phylogeography, phytopathology, recombination, migration, Microbiology, QR1-502
Abstract

ABSTRACT Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.

Published
2023
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2. Genetic Diversity, Evolution, and Diagnosis of Sugarcane Yellow Leaf Virus from 19 Sugarcane-Producing Locations Worldwide

Author

Philippe C. Rott, Samuel Grinstead, Sylvie Dallot, Zachary S. L. Foster, Jean-Heinrich Daugrois, Emmanuel Fernandez, Claudia Jill Kaye, Leticia Hendrickson, Xiaojun Hu, Bishwo Adhikari, Martha Malapi-Wight, Niklaus J. Grünwald, Philippe Roumagnac, and Dimitre Mollov

Subjects
Plant Science, Agronomy and Crop Science
Abstract

Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf, has been reported in an increasing number of sugarcane growing locations since its first report in the 1990s in Brazil, Florida, and Hawaii. In this study, the genetic diversity of SCYLV was investigated using the genome coding sequence (5561-5612 nt) of 109 virus isolates from 19 geographical locations, including 65 new isolates from 16 geographical regions worldwide. These isolates were distributed in three major phylogenetic lineages (BRA, CUB, and REU), with the exception of one isolate from Guatemala. Twenty-two recombination events were identified among the 109 isolates of SCYLV, thus confirming that recombination was a significant driving force in the genetic diversity and evolution of this virus. No temporal signal was found in the genomic sequence data set, most likely because of the short temporal window of the 109 SCYLV isolates (1998-2020). Among 27 primers reported in the literature for the detection of the virus by RT-PCR, none matched 100% with all the 109 SCYLV sequences, suggesting that the use of some primer pairs may not result in the detection of all virus isolates. Primers YLS111/YLS462, which were the first primer pair used by numerous research organizations to detect the virus by RT-PCR, failed to detect isolates belonging to the CUB lineage. In contrast, primer pair ScYLVf1/ScYLVr1 efficiently detected isolates of all three lineages. Continuous pursuit of knowledge of SCYLV genetic variability is therefore critical for effective diagnosis of yellow leaf, especially in virus-infected and mainly asymptomatic sugarcane plants.

Published
2023
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3. Population Genomics Provide Insights into the Global Genetic Structure of

Author

Flávia, Rogério, Riccardo, Baroncelli, Francisco Borja, Cuevas-Fernández, Sioly, Becerra, JoAnne, Crouch, Wagner, Bettiol, M Andrea, Azcárate-Peril, Martha, Malapi-Wight, Veronique, Ortega, Javier, Betran, Albert, Tenuta, José S, Dambolena, Paul D, Esker, Pedro, Revilla, Tamra A, Jackson-Ziems, Jürg, Hiltbrunner, Gary, Munkvold, Ivica, Buhiniček, José L, Vicente-Villardón, Serenella A, Sukno, and Michael R, Thon

Abstract

Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes)

Published
2022

4. Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories : A step-by-step description

Author

Benedicte Lebas, Ian Adams, Maher Al Rwahnih, Steve Baeyen, Guillaume J. Bilodeau, Arnaud G. Blouin, Neil Boonham, Thierry Candresse, Anne Chandelier, Kris De Jonghe, Adrian Fox, Yahya Z. A. Gaafar, Pascal Gentit, Annelies Haegeman, Wellcome Ho, Oscar Hurtado‐Gonzales, Wilfried Jonkers, Jan Kreuze, Denis Kutjnak, Blanca Landa, Mingxin Liu, François Maclot, Martha Malapi‐Wight, Hano J. Maree, Francesco Martoni, Natasha Mehle, Angelantonio Minafra, Dimitre Mollov, Adriana Moreira, Mark Nakhla, Françoise Petter, Alexander M. Piper, Julien Ponchart, Robbie Rae, Benoit Remenant, Yazmin Rivera, Brendan Rodoni, Johanna W. Roenhorst, Johan Rollin, Pasquale Saldarelli, Johanna Santala, Rose Souza‐Richards, Davide Spadaro, David J. Studholme, Stefanie Sultmanis, René van der Vlugt, Lucie Tamisier, Charlotte Trontin, Ines Vazquez‐Iglesias, Claudia S. L. Vicente, Bart T. L. H. Vossenberg, Thierry Wetzel, Heiko Ziebell, Sebastien Massart, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Fera Science Ltd, University of California [Davis] (UC Davis), University of California (UC), Research Institute for Agricultural, Fisheries and Food (ILVO), Canadian Food Inspection Agency (CFIA), Newcastle University [Newcastle], Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 1Walloon Agricultural Research Centre, Gembloux, Belgium 2The Research Institute of Organic Agriculture (FIBL), Frick, Switzerland, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants, Laboratoire de santé des végétaux (LSV Angers), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Ministry for Primary Industries, Animal Plant Health Inspection Service, APHIS-USDA, Humble, Texas, 77338, USA., World Agroforestry Center [CGIAR, Pérou] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), National Institute of Biology [Ljubljana] (NIB), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Tasmania [Hobart, Australia] (UTAS), Stellenbosch University, Citrus Research International, Partenaires INRAE, Agriculture Victoria (AgriBio), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Horticultural Crops Research Unit, USDA-ARS : Agricultural Research Service, International Plant Protection Convention, European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes (EPPO), Liverpool John Moores University (LJMU), Netherlands Food and Consumer Product Safety Authority (NVWA), Finnish Food Authority, International Seed Federation (ISF), Università degli studi di Torino = University of Turin (UNITO), University of Exeter, Wageningen University and Research [Wageningen] (WUR), Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal] (INIAV), Dienstleistungszentrum Ländlicher Raum DLR Rheinpfalz (DLR Rheinpfalz), Julius Kühn-Institute, Federal Research Centre for Cultivated Plants-Institute for Biological Control, European Project: 773139,VALITEST, and European Commission

Subjects
plant pest diagnostic test, Biointeractions and Plant Health, [SDV]Life Sciences [q-bio], Life Science, high-throughput sequencing, Plant Science, Horticulture, PE&RC, Agronomy and Crop Science, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

High-throughput sequencing (HTS) is a powerful tool that enables the simultaneous detection and potential identification of any organisms present in a sample. The growing interest in the application of HTS technologies for routine diagnostics in plant health laboratories is triggering the development of guidelines on how to prepare laboratories for performing HTS testing. This paper describes general and technical recommendations to guide laboratories through the complex process of preparing a laboratory for HTS tests within existing quality assurance systems. From nucleic acid extractions to data analysis and interpretation, all of the steps are covered to ensure reliable and reproducible results. These guidelines are relevant for the detection and identification of any plant pest (e.g. arthropods, bacteria, fungi, nematodes, invasive plants or weeds, protozoa, viroids, viruses), and from any type of matrix (e.g. pure microbial culture, plant tissue, soil, water), regardless of the HTS technology (e.g. amplicon sequencing, shotgun sequencing) and of the application (e.g. surveillance programme, phytosanitary certification, quarantine, import control). These guidelines are written in general terms to facilitate the adoption of HTS technologies in plant pest routine diagnostics and enable broader application in all plant health fields, including research. A glossary of relevant terms is provided among the Supplementary Material., This article is based upon work from the work package 2 of the project VALITEST (https://www.valitest.eu/), supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 773139.

Published
2022
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