Application of repetitive extragenic palindromic (REP)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis to the identification and classification of Japan and Thai local isolates of Bradyrhizobium japonicum, Shinorhizobium meliloti, Rhizobium leguminosarum

Abstract

Repetitive extragenic palindromic (REP)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis was applied to the identification and classification of local isolates of 44 Bradyrhizobium japonicum, 7 Sinorhizobium meliloti, 10 Rhizobium leguminosarum strains from Japan and Thai. Using genomic DNA of the 61 strains, both REP and ERIC primers induced reproducible PCR band patterns, although REP-PCR generated more bands and appeared to be more useful for distinguishing the isolates from each other. Using mixed matrix data from both REP- and ERIC-PCR data, it become possible to distinguish all the isolates analyzed in this experiment from each other. When cluster analysis was applied to both PCR matrix data of 44 B. japonicum isolates, only the REP-PCR dendrogram showed a grouping profile corresponding to the exo-polysaccharide phenotype with a exceptions. When the matrix data of R. leguminosarum and S. meliloti were subjected to cluster analysis, S. meliloti appeared to form a different subgroup from R. leguminosarum in the dendrogram of REP-PCR data except for one strain. In the case of ERIC-PCR, isolates of R. leguminosarum from northern Thailand formed a separate subgroup from other R. leguminosarum and S. meliloti which were dispersed in the dendrogram. These data suggest that REP-PCR and ERIC-PCR were effective for the identification of individual isolates even though the isolates showed a wide genetic diversity and the same phenotype. When the data of the local isolates from Japan and Thailand were subjected to cluster analysis, REP- and ERIC-PCR analysis revealed different grouping characteristics.