Molecular diversity of internal transcribed spacer among the monoconidial isolates of Magnaporthe oryzae isolated from rice in Southern Karnataka, India

Abstract

Blast disease of rice plant is caused by Magnaporthe oryzae (anamorph Pyricularia oryzae). This disease is recognized to be one of the most serious diseases of rice crop around the world. A total of 72 monoconidial isolates of M. oryzae obtained from blast disease samples collected around Southern Karnataka were characterized using internal transcribed spacers of the ribosomal DNA sequences. These were analyzed by comparing with already deposited sequences in GenBank database. It helped in diagnosing the invasive pathogen in all locations. Variability of rDNA sequences was found to be highly polymorphic with 0.068962 nucleotide diversity showing 6 distinct clades. 33 haplotype groups were identified with haplotype diversity of 0.8881 and Tajima's neutrality test with a D value of -1.96827 with P < 0.05 showing the presence of variations among the sequences of pathogen isolates. The Tajima's D value of less than one indicates the presence of a high number of rare alleles. Our study indicates that the pathogen might have undergone recent selection pressure because of the exposure to a large number of cultivars resulting in the evolution of rare alleles. This shows the importance of characterizing internal transcribed spacer (ITS) to know pathogen diversity and its fitness which has potential to contribute to the field of breeding for blast disease resistance.

Keywords: Haplotype diversity; ITS; Magnaporthe oryzae; Rice blast disease.

Fig. 1

Locations of rice blast disease samples collected from different Districts (dark red color) of Karnataka in India map (Inset shows the location of Karnataka in India). The number within the circle represents taluk number as given in Table 1.

Fig. 2

Gel electrophoresis of the amplified rDNA internal transcribed spacers region of 12 Magnaporthe oryzae isolates using 2% of agarose. First lane from left side is 100 bp DNA ladder.

Fig. 3

A Circular Dendrogram of 72 Magnaporthe oryzae Internal Transcribed Spacer (ITS1/ITS4) genotypes based on UPGMA using MEGA 7.

Fig. 4

Location of Haplotype distribution of 72 Magnaporthe oryzaeisolates in 11 districts of Karnataka State (Inset shows location of different districts of sample collection in Karnataka state). Colour code represents Haplotype number and number within the colorbox indicates collection number of isolates.