Analysis of DNA polymorphism and virulence in Philippine strains of Xanthomonas oryzae pv. oryzicola

Molecular tools were used to analyze the genetic diversity and population s tructure of Xanthomonas oryzae pv. oryzicola, the bacterial leaf streak pat hogen of rice in the Philippines. Representative pathogen strains were sele cted and used to assess resistance in rice germplasm. A partial genomic lib rary of X. oryzae pv. oryzicola was constructed, and a 459-bp clone contain ing the repetitive DNA element R41 was selected as a probe for restriction fragment length polymorphism (RFLP) analysis and sequenced. R41 shared 34% sequence homology with the putative transposase-gene of IS1112, an insertio n element cloned from X. oryzae pv. oryzae. Using R41 as a probe for RFLP a nalysis, 26 band profiles were discerned in a collection of 123 strains of X. oryzae pv. oryzicola. Analysis of PstI digestion patterns of DNA from th e same collection resolved 36 haplotypes. Several clusters of strains were detected after grouping of data based on either pR41 as a probe or Pst1 dig estion patterns. However, based on bootstrap analysis, the clusters were no t robust. Genetic diversity was high for the entire collection as well as w ithin spatially and temporally defined subsets of strains. Even a set of st rains collected from a single site at a single time was highly diverse. Str ains representing the different DNA types were inoculated to a set of diver se rice cultivars. Consistent rice varietal groupings were obtained from di sease reaction data, but there was no correlation between pathogen isolate cluster and host reaction across inoculation trials. Isozyme group I of ric e, representing tropical japonica and javanica germplasm, is a promising so urce of resistance to bacterial leaf streak.