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

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.

Genome-wide association studies reveal the complex genetic architecture of DMI fungicide resistance inCercospora beticola

“…For fungal crop pathogens, GWAS may have direct applications in managing disease through the discovery of key genes underlying virulence and fungicide resistance. Populations of filamentous fungi have previously been used in genome-wide association analyses to find genetic determinants of adaptive traits (Atwell et al 2018; Ganeshan et al 2018; Gao et al 2016; Hartmann et al 2017; Martin et al 2020; Palma-Guerrero et al 2013; Richards et al 2019; Zhong et al 2017), including several studies for DMI resistance (Mohd-Assaad et al 2016; Pereira et al 2020; Talas et al 2016).…”

Cucumber mosaic virus: Global genome comparison and beyond

“…The success in the search for the association between single nucleotide polymorphic markers, pathogenicity and virulence was observed in many plant viruses and pathogens such as the rice blast fungus, tomato virus, chestnut pathogen, cassava brown streak virus, mungbean yellow mosaic virus and sugarcane leaf virus (Yadav et al, 2015;Xu et al, 2017;Ganeshan et al, 2018;Oyesigye et al, 2018;Pimenta et al, 2021;Stauber et al, 2021). One of the most studied target is the rice blast fungus where many researchers have identified markers of virulence via genome-wide association studies.…”

“…One of the most studied target is the rice blast fungus where many researchers have identified markers of virulence via genome-wide association studies. This genome-wide approach has been proven powerful in the discovery of novel gene functions related to rice blast disease previously unachievable using conventional experimental analysis (Ganeshan et al, 2018). The identified SNP markers were very effective in indicating the vital pathogenicity and virulence loci associated with overcoming resistance found in isolates harvested from a particular country of origin and host species (Ganeshan et al, 2018).…”

“…This genome-wide approach has been proven powerful in the discovery of novel gene functions related to rice blast disease previously unachievable using conventional experimental analysis (Ganeshan et al, 2018). The identified SNP markers were very effective in indicating the vital pathogenicity and virulence loci associated with overcoming resistance found in isolates harvested from a particular country of origin and host species (Ganeshan et al, 2018). This research pipeline can be implemented on the cucumber mosaic virus to further enhance our comprehension on the CMV pathogenicity and virulence associated gene loci in the future.…”