Molecular diversity of Bipolaris oryzae infecting Oryza sativa in India

Thirty-six strains of Bipolaris oryzae collected from infected seed from different geographical locations in India were used for the analysis of genetic variability by using molecular markers. The molecular characterization using three marker systems, i.e., universal rice primers (URPs), inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) was carried out, which revealed differences in strains from different geographical origins as well as by clustering of various B. oryzae strains which otherwise could not be revealed through conventional characterization. Out of 13 URPs, 20 ISSR and 30 RAPD primers screened, seven URPs, eight ISSR and 14 RAPD markers gave very good reproducibility banding patterns. Polymorphic bands ranging between 86.3% and 100% in URP, 81.8% and 100% in ISSR, and 91.6% and 100% were recorded in the case of RAPD markers. The total number of bands recorded was 1791 with an average of 255.86 in URP, 2541 with an average of 317.63 in ISSR, and 3226 with an average of 230.42 in RAPD markers. Maximum heterozygosity ( Hn ) was revealed by URP 30F (0.26), ISSR 6 (0.36) and RAPD marker OPB-1 (0.31). The polymorphism information content (PIC) values ranged between 0.69 and 6.43 in URP, 3.86 and 8.03 in ISS, and 2.58 and 8.55 in RAPD marker profiles. Maximum cophenetic correlation was found in URP ( r = 1.000), followed by ISSR ( r = 0.813) and RAPD ( r = 0.784). The combined analysis of all three marker systems showed high cophenetic correlation ( r = 0.848), which indicated a good fit of the data for genetic diversity analysis. Hence, combined use of three marker systems would be more sensitive and reliable in characterizing genetic variability in B. oryzae strains.