Sequence tagged site marker-assisted selection for three bacterial blight resistance genes in rice

IR65598-112 and the two sister lines IR65600-42 and IR65600-96 are promising new plant type (NPT) rice lines with high yield potential. However, these lines are susceptible to bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo). To improve the resistance of the three NPT lines to Xoo, three bacterial blight (BB) resistance genes, xa5, xa13, and Xa21, were successfully transferred to the NPT lines via a marker-aided backcrossing procedure. Sequence tagged site (STS) markers for the two resistance genes were developed based on DNA sequences of their linked restriction fragment length polymorphism (RFLP) markers (RG556 and RG207 for xa5 and RG136 for xa13). Marker polymorphism for xa5 was detected after digestion of RG556 polymerase chain reaction (PCR) products with MaeII enzyme and digestion of RG136 PCR product with HinfI enzyme for xa13 The STS marker for Xa21 was designed previously from the sequence of a genomic clone RAPD248. Fifty-nine BC3F2 near-isogenic lines (NILs) in the three NPT backgrounds containing one to three BB resistance genes in various combinations were developed through marker-assisted selection (MAS) for the resistance genes and phenotypic selection for the NPT. The BC3F3 NILs having more than one BB resistance gene showed a wider resistance spectrum and manifested increased levels of resistance to the Xoo races, as compared with those having a single BB resistance gene. Results for two F2 populations and the progeny testing of their F3 lines showed that MAS reached an accuracy of 95 and 96% of identifying homozygous resistant plants for xa5 and xa13, respectively. These NPT NILs for BB resistance genes provided valuable materials for breeding and genetic studies of single-gene effects and interaction of several resistance genes. The results demonstrate the usefulness of MAS in gene pyramiding for BB resistance, particularly for recessive genes, such as xa5 and xa13, that are difficult to select through conventional breeding in the presence of a dominant gene such as Xa21