Assessment of genetic variability and strain identification of Xanthomonasoryzae pv. oryzae using RAPD-PCR and IS1112-based PCR

Sixteen isolates of Xanthomonas oryzae pv, oryzae (X.o. pv. oryzae) represe nting different geographical locations in India along with 2 isolates from the Philippines were analysed using polymorphic RAPDs. The primers OPA-03, OPA-04, OPA-10, OPA-11, OPK-7, OPK-12 and OPK-17 generated simple, specific and reproducible fingerprint patterns, indicating usefulness of RAPD marke rs in differentiating X, o, pv. oryzae isolates. At a similarity index of 0 .5 the isolates were grouped into only 2 clusters, suggesting that these pr imers are not very efficient in grouping isolates. Primers PJEL1 and PJEL2, used in insertion sequence IS1112-based PCR, also generated specific and r eproducible fingerprint patterns for the same set of the X,o, pv, oryzae is olates. Based on the RAPD-PCR (seven primers) and IS1112-PCR (two primers) data, at a similarity of 0.57, sixteen out of 18 isolates were grouped into 5 different clusters and 2 isolates were loosely grouped with them. The da ta using RAPD-PCR and IS1112-based PCR approaches revealed their potential in rapid identification of isolates, in assessment of genetic variation in the Indian pathogen population and in generating unique DNA fragments speci fic to 8 isolates of X.o. pv. oryzae.