Assessment of genetic diversity and population structure of Magnaporthe oryzae causing rice blast disease using SSR markers

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice in the world. The blast fungus shows a high degree of variability in the field and limited information is available on its genetic diversity and population structure in India. Twenty five polymorphic SSR markers were used to investigate the genetic diversity and population structure of 96 blast isolates collected from Odisha and Chhattisgarh region. The markers yielded a total of 110 alleles and number of alleles per locus varied from 2 to 8. The gene diversity ranged from 0.02 to 0.49 whereas, major allele frequency varied from 0.50 to 0.98. The PIC value varied from 0.02 to 0.37 with a mean value of 0.29. Cluster analysis grouped the blast isolates into four distinct major clusters. The high level of genetic diversity was observed with ninety one haplotypes and nucleotide diversity of 0.293. The principal coordinate and structure analysis identified two genetic clusters of M. oryzae isolates with some degree of distinctness according to affected plant parts. Analysis of molecular variance revealed more genetic variation within populations and less among populations. The outcome of this study would help to understand the genetic diversity of M. oryzae from eastern India that would guide in the development of more effective control strategies and improving rice blast resistance through development of new resistant varieties through marker-assisted breeding.