Molecular mapping of marker-aided backcrossing of bacterial blight resistance genes to the new plant type of rice (Oryza sativa L.)

Two bacterial blight (BB) resistance genes, xa-5 and xa-13 of chromosome 5 and 8 respectively, were fine-mapped to identify restriction fragment length polymorphism (RFLP) markers suitable for conversion to sequence-tagged site (STS) markers. STS markers for xa-5 were developed based on clone sequences of flanking markers RG556 and RG207. RG556 STS was mapped to be 1.7 cM from xa-5 and RG207STS was 2.2 cM on the other side. Polymerase Chain Reaction (PCR) products of STS markers for xa-13 were monomorphic and none out of the 48 enzymes tried was able to detect polymorphism. STS primers based on Bacterial Artificial Chromosome (BAC) clones linked to xa-13 failed to amplify consistently in a segregating population. The STS marker used for marker-aided backcrossing of xa-13 was based on the linked RFLP marker RG136. Polymorphism was detected after digestions of the PCR products with Hinfl enzyme. RG136STS was mapped to be 5.5 cM from xa-13. The STS marker for the Xa-21 was based on a published work of J. Chunwongse. The STS markers obtained were used to screen for resistance alleles in the backcross progenies of the three new plant type lines. Fifty-nine BC3F2 plants containing one to three BB resistance genes in various combinations were identified based on STS marker analysis. The selected BC3F2 plants exhibit resistance to the various races of Xoo depending on the resistance gene present. F3 progeny testing showed 95 percent and 95.8 percent accuracies of identifying homozygous resistant plants by molecular marker for xa-5 and for xa-13, respectively. Chromosomal introgression around the two resistance genes xa-5 and xa-13 among the BC3F1 progenies varied in size. Introgressed segment of the chromosome could be as small as to be limited to a single marker or as large as to include all the molecular markers studied around the BB resistance gene. The results show that marker-assisted selection for bacterial blight, resistance using STS markers can be done successfully. However, better PCR-based markers are needed to circumvent the lower amount of polymorphism observed in STS markers and the restriction digestion needed for a PCR-based RFLP