Cultural, Molecular and Genetic Variability of Ustilaginoidea virens Causing Rice False Smut Disease

Abstract

Rice false smut disease is caused by Ustilaginoidea virens, an ascomycetous fungi. Thirty isolates of U. virens showed well defined colonies on potato sucrose medium (PSA). The maximum colony diameter was found to be 85.68 mm with a growth rate of 2.85 mm in the UV23 isolate and the minimum colony diameter was found to be 10.14 mm with a growth rate of 0.33 mm, which was observed in the UV15 isolate. However, thirty isolates exhibit various cultural and morphological characteristics like colony color, growth pattern, elevation, and chlamydospore formation. In cluster analysis, two major groups (I) and (II) were formed. The first major group (I) contains UV15 isolates and the second major group (II) contains 29UV isolates. Furthermore, the division of group II includes subgroup IIa, which contains 22 isolates, and subgroup IIb, with 7 isolates. The PCR amplification was done with a species-specific primer which yielded products of 380 bp and 230 bp, respectively. The results of the phylogenetic tree analysis revealed that cluster I contained 5 isolates and cluster II contained 28 isoates from China and Japan. The MAT1-1-1 primer yielded a product of 250 bp that contains 18 isolates. Whereas the MAT1-2-1 primer yielded a product of 220 bp with 12 isolates. The nucleotide divergence analysis results revealed 7 polymorphic sites (s), 10 mutations (Eta), 0.76515 nucleotide diversity (k) and -2.13885 for the tajimas test value. Likewise, haplotype analysis revealed 10 haplotype(h)groups, with a haplotype diversity (hd) of 0.4773. With 24 isolates, hap-1 was the most common. Similarly, clear nucleotide variation was observed between Indian and Chinese isolates as well as Japanese ones. The genetic similarity coefficient matrix revealed that thirty Indian isolates showed maximum similarity (0.9). whereas the UV32 isolate showed 0.6, the UV31 isolate exhibited 0.5, and the UVA33 isolate had 0.4,.These results indicate a genetic variability between the Indian UV isolates and the isolates from China.