POPULATION STRUCTURE AND GENETIC DIVERSITY ASSESSMENT OF EASTERN AFRICA FINGER MILLET BLAST FUNGUS USING GENOME-WIDE SNPS

Abstract

Finger millet (Eleusine coracana) is a key staple crop in eastern Africa cultivated mainly by smallholder farmers. It can withstand high temperatures, salinity, drought stress and low soil fertility. The use of unimproved varieties that are regularly affected by the finger millet blast disease and other abiotic stresses causes high grain yield losses. Blast disease is caused by Magnaporthe oryzae, which is a host-specific complex fungus species that affects different grasses, including rice and wheat. While many efforts have been directed towards characterizing rice blast, finger millet blast genetic diversity, specificity and virulence remain poorly understood. To address this, 226 blast isolates from Kenya, Tanzania, Uganda and Ethiopia, were previously sequenced using Illumina technology. One of these isolates, E2, was sequenced using a combination of PacBio and Illumina technologies and used to generate a reference genome assembly for finger millet blast. The sequenced reads from the other 225 isolates were mapped to it. The study reported here investigated the genetic diversity of this collection and used the sequence data for variant calling, which identified 174,300 SNPs. Cluster analysis was then conducted using STRUCTURE, principal component analysis (PCA) and maximum-likelihood phylogenetic inference. The Fst statistic and AMOVA analysis were conducted to determine the genetic diversity of the finger millet blast pathogen. It was found that in eastern Africa, finger millet blast isolates grouped into two main populations with sub-population structures. The results further showed that the isolates did not cluster according to the countries they were collected from. Isolates from Ethiopia and Tanzania grouped together but formed a different cluster from the Ugandan and Kenyan isolates, which formed a separate group. There was a clear correlation between isolates’ clustering patterns and the latitude north or south of the equator from where they were collected. Further, more diversity was observed within Ugandan and Ethiopian isolates than in vi Kenyan and Tanzanian collections. The overall Fst value was 0.338. The lowest pairwise Fst value was detected between Kenyan isolates and Ugandan isolates (ranged from 0.05 to 0.12), while the highest value (0.52) was detected between Ethiopian and Ugandan isolates. Outliers of each of these two groups were sparsely spread between them and could have evolved from the migration of the pathogen between the collection points in the different countries. For example, between Kenya and Tanzania, through informal seed exchanges that could have transported the pathogen across borders. This new information will enhance the existing knowledge of the population structure and genetic diversity of the blast fungus and contribute to the development of effective control strategies against the pathogen, especially in finger millet.