Population genetic structure of <Emphasis Type="Italic">Rhizoctonia solani</Emphasis> AG1IA from rice field in North India

Rhizoctonia solani AG1IA is an important fungal pathogen causing significant yield and quality losses in rice production. However, little is known about the levels of genetic diversity and structure of this pathogen in North India. Out of 240 samples collected from different rice-growing regions of North India, 112 isolates were identified as R. solani AG1IA subgroups using species-specific primers. All 112 isolates were organized into four groups on the basis of percent disease index (PDI). The majority of the isolates were weakly virulent. Population genetic analysis was performed within and between populations using inter simple sequence repeat (ISSR) markers. A total of 8249 alleles were identified from the 112 isolates of R. solani AG1IA through analysis of the ten inter simple sequence repeat markers. All the ten ISSR markers were polymorphic. The average number of bands per primer was 7.3 which ranged in size from 250 to 1500 bp. Genetic structure of the isolates using inter simple sequence repeat primers showed high degree of polymorphism (PIC ≥0.81). The analysis of molecular variance (AMOVA) indicated that most of the genetic diversity occurred within populations (60%), while the variability among populations and among regions contributed 25 and 15%, respectively. Overall, the present study reveals that a large variation exists among rice-infecting isolates of R. solani AG1IA in North India. Fingerprinting of the isolates using ISSRs along with phenotypic characterization and virulence analysis will help epidemiological studies that can provide new insights into pathogen biology and disease spread.