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A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

View ORCID ProfileVeena Devi Ganeshan, Stephen O. Opiyo, Samuel K. Mutiga, Felix Rotich, David M. Thuranira, Vincent M. Were, Ibrahima OuéDraogo, BO Zhou, Darren M. Soanes, James C. Correll, Guo-Liang Wang, Nicholas J. Talbot, Thomas K. Mitchell
doi: https://doi.org/10.1101/418509
Veena Devi Ganeshan
1Department of Plant Pathology, The Ohio State University-Columbus, USA.
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  • ORCID record for Veena Devi Ganeshan
Stephen O. Opiyo
1Department of Plant Pathology, The Ohio State University-Columbus, USA.
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Samuel K. Mutiga
2Department of Plant Pathology, University of Arkansas-Fayetteville, USA.
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Felix Rotich
2Department of Plant Pathology, University of Arkansas-Fayetteville, USA.
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David M. Thuranira
3Biosciences Department, Exeter University, UK.
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Vincent M. Were
3Biosciences Department, Exeter University, UK.
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Ibrahima OuéDraogo
4Institute of Environment and Agricultural Research, Bobo-Dioulasso, Burkina Faso.
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BO Zhou
5International Rice Research Institute (IRRI), Philippines.
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Darren M. Soanes
3Biosciences Department, Exeter University, UK.
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James C. Correll
2Department of Plant Pathology, University of Arkansas-Fayetteville, USA.
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Guo-Liang Wang
1Department of Plant Pathology, The Ohio State University-Columbus, USA.
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Nicholas J. Talbot
3Biosciences Department, Exeter University, UK.
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Thomas K. Mitchell
1Department of Plant Pathology, The Ohio State University-Columbus, USA.
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  • For correspondence: mitchell.815@osu.edu
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ABSTRACT

The fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.

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Posted September 14, 2018.
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A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa
Veena Devi Ganeshan, Stephen O. Opiyo, Samuel K. Mutiga, Felix Rotich, David M. Thuranira, Vincent M. Were, Ibrahima OuéDraogo, BO Zhou, Darren M. Soanes, James C. Correll, Guo-Liang Wang, Nicholas J. Talbot, Thomas K. Mitchell
bioRxiv 418509; doi: https://doi.org/10.1101/418509
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A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa
Veena Devi Ganeshan, Stephen O. Opiyo, Samuel K. Mutiga, Felix Rotich, David M. Thuranira, Vincent M. Were, Ibrahima OuéDraogo, BO Zhou, Darren M. Soanes, James C. Correll, Guo-Liang Wang, Nicholas J. Talbot, Thomas K. Mitchell
bioRxiv 418509; doi: https://doi.org/10.1101/418509

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