Molecular analysis of bacterial blight resistance genes in elite lines of rice

The resistance to rice bacterial blight (BB) of classical elite lines, IR varieties and new plant types (NPT) of rice was analysed using molecular and phenotypic approaches. PCR [polymerase chain reaction]-based molecular markers linked to known bacterial blight resistance genes were used to detect the presence of xa4, xa5, xa7, xa13 and xa21 genes while rice Xanthomonas oryzae pv. oryzae (Xoo) interaction expressed in lesion length was used to determine the phenotype of each line. The xa4 gene was present in most of the elite lines singly or in combination with xa5 and to an unidentified gene conferring resistance to Xoo race 9a (PX0339). Lines with xa4 alone are susceptible to race 9a. xa7 was also detected in two of the elite lines. The detection of xa gene(s) in each line are confirmed by the reaction to Xoo since the phenotype of these lines are the same when compared with near-isogenic lines bearing the same gene(s). Pedigree analyses of each lines show the possible donors of the xa genes detected. The xa21 gene was detected in seven lines in combination with xa4 or xa5. These lines had the parental line Oryza barthii, a wild relative of rice and O. largistaminata, donor of xa21. Phenotype analysis shows that the xa21 detected does not confer a broad spectrum of resistance to Xoo races even in combination with other xa genes. Forty-four IR and PSBRc varieties including IR5 and IR8 were also tested for resistance to bacterial blight. Previous studies on the resistance to BB of these IR varieties used phenotypic approaches involving only six to eight races of Xoo. The present study made use of ten races of Xoo as well as molecular markers linked to known xa genes. Most IR varieties have resistance to race 1 (PX061) as indicated by short lesion lengths against PX061 and the presence of xa4 detected by molecular markers. None of the markers detected any xa gene in IR5, IR56, and IR70 although phenotype analyses show resistance of these lines to race 9a. PSBRC82 showed high level resistance to all races of Xoo except PXO99. This is due to the presence of both xa4 and xa5 genes. Eighty-four new plant type (NPT) elite lines as well as 17 NPT parental lines belonging to the tropical japonica group were also characterized for bacterial blight resistance. Molecular analysis showed the presence of xa4, xa5, xa7, and xa13 genes in these lines. However, some lines with the gene combinations xa4, xa4/xa7 and xa5/xa7 in tropical japonica background alone have susceptible reactions with Xoo. Two lines carry four-gene combinations xa4/xa5/xa7/xa13 and have very short lesions against all Xoo races. Putative markers for the xa3 gene were also identified using rice microsatellite markers and resistance gene-analogs (RGA). RM144 showed polymorphism between IRBB3 and other NILs with xa genes from rice chromosome 2. The same band in IRBB3 was observed in Malagkit Sungsong which is reported to have xa3 as well as in one of the NPT lines. Polymorphism was observed between IR24 and IRBB3 when RGA primers based in leucine-rich repeats of clone resistance genes were used to amplify genomic DNA