Abundant polymorphism in the flanking regions of two loci for basic PR-1 proteins as markers for indica-japonica differentiation in rice (Oryza sativa L.)

In an attempt to use new sources of disease resistance, genomic sequences o f two genes Rpr1-1(t) and Rpr1-2(t) of PR-1 proteins, which are one of the major pathogenesis-related (PR) proteins in plants, were obtained by TAIL-P CR on the basis of a registered genomic sequences and from expressed sequen ce tag (EST) data, respectively. The genetic loci of Rpr1-1(t) and Rpr1-2(t ) were identified on chromosome 1 and 5, respectively, using recombinant in bred lines (RILs) from an indica-japonica cross. Abundant sequence polymorp hism between alleles of indica and japonica cultivars were found in the two genes. Polymorphic insertions including the Tnr1 (transposable element in rice #1) sequence in indica cultivars and a minor insertion in japonica cul tivars were detected in the ORF flanking regions of Rpr1-1(t), In the ORF f lanking regions of Rpr1-2(t), a unique insertion of 827 bp was found in jap onica cultivars, while two insertions were found in an indica cultivar, Mil yang 23, Despite such diversity in the flanking regions, only a few amino-a cid residues were different between the alleles, Based on a test for polymo rphism among some cultivars, it was found that variation of inserted/delete d sequences may provide a useful molecular tool for investigating indica-ja ponica differentiation in rice.