PHYLOGENETIC EVOLUTION AND GEOGRAPHIC TRANSMISSION PATTERNS OF THE RICE BLAST PATHOGEN MAGNAPORTHE ORYZAE IN AFRICA

Abstract

Rice blast disease, caused by the fungal pathogen Magnaporthe oryzae, is the most disastrous disease in rice, and adversely constrains the growth and productivity of the crop worldwide. Outbreaks of the disease reoccur in all rice-growing areas, resulting in major losses to rice production and consequently threatening the global food security. Although global phylogenetic studies have been conducted previously to determine the global population dynamics of M. oryzae, there has been no study focusing on the genetic diversity and the phylogeography of M. oryzae within Africa alone, using whole genome data. Previous global phylogenetic studies using whole genome data included only a few isolates from a limited number of African countries. As a result, this has provided insufficient clues about patterns of introduction and migration routes of the pathogen in and within Africa. This study therefore analysed the phylogenetic evolution and geographic transmission patterns of the rice blast pathogen M. oryzae in Africa. The study focused on 49 isolates of this rice-infecting pathogen, 43 collected from various African countries and 6 from outside Africa. The latter 6 isolates were added to enhance comparability. Genome-wide single-nucleotide polymorphisms (SNPs) were extracted and used to explore the genetic diversity, population structure and phylogenetic evolution as explained by our 49 isolates. The distribution patterns of 178 known effector genes found in the genome of M. oryzae between the isolates from within Africa and outside were also compared. Three well-defined subpopulations of M. oryzae were found within our 49 isolates. These clusters were found to be consistent with the phylogenetic analysis and principal component analysis (PCA). Results from the admixture analysis showed evidence of genetic mixes within the majority of the isolates. Further, dissection of our isolates into two groups, those from Africa and outside Africa, and assessing the distribution patterns of the effector genes, revealed that isolates from outside Africa generally have a higher distribution of effector genes compared to the African isolates. The results showed that the African M. oryzae have higher diversity than was earlier perceived. It was postulated that the pathogen may have been introduced to Africa through multiple routes. Future studies can include more isolates from different regions within Africa, such as the northern and southern regions of Africa, in order to capture the true picture of diversity within Africa. Effector genes and the M. oryzae genome as a whole, continues to evolve as the pathogen spreads to different geographical areas as a means of adaptation. Findings from this study can help inform and shape existing control measures to help alleviate rice blast disease in the region. Keywords: Genetic diversity, Genome-wide SNPs, Magnaporthe oryzae,