REP-PCR DISTINGUISHES RICE BACTERIAL BLIGHT PATHOGEN (XANTHOMONAS ORYZAE pv. ORYZAE) STRAINS OF INDIAN MAINLAND AND BAY ISLANDS

Abstract

Thirty-two strains of Xanthomonas oryzae pv. oryzae (Xoo) representing 12 pathotypes from major rice growing Indian mainland states and Andaman Islands were analyzed using RepPCR and IS1112-based PCR approaches. All four PCR primers (BOX, REP, ERIC and JEL primers) confirmed the presence of high genetic variability among the Xoo strains studied. The REP primers generated more PCR fragments than other set of primers and the amplification pattern of BOX, REP, ERIC and JEL primers were 277, 171, 147 and 149 respectively with the band size varying from 200 to 3000 base pairs. Cluster analysis of 32 Xoo strains revealed that the combined dendrogram constructed using Rep–PCR analysis was effective in distinguishing Islands Xoo strains from Indian mainland strains with the similarity index of Islands clusters of about 53%. In case of IS1112 repeat element based PCR approach, the two of the mainland strains (DX_027 and DX_143) were grouped with one mainland isolate ANBB_4 in one sub cluster whereas remaining three mainland isolates grouped separately in a main cluster. This indicated that Islands strains were genetically distinct from mainland strains. Also, the Rep-PCR approach was found to be more precise and thus suitable for discriminating the variability among Xoo strains emanating from geographically diverse locations.