Functional markers for bacterial blight resistance gene Xa3 in rice

Bacterial blight (BB) of rice ( Oryza sativa L.) caused by Xanthomonas oryzae pv . oryzae ( Xoo ) is a destructive disease in rice worldwide. Xa3 , a gene conferring resistance to BB at the booting stage of the rice plant, has been characterized previously using map-based cloning. We cloned and sequenced the Xa3/xa3 gene in the Korean cultivars Hwayeong, Ilmi, and Goun and conferred resistance or susceptibility to BB. We detected polymorphisms, and polymerase chain reaction-based functional markers were developed based on the single nucleotide polymorphism from the Xa3 and xa3 nucleotide sequence. Susceptible or resistant individuals from an F2 population developed from a cross between Milyang 244 and Ilmi, near-isogenic lines carrying BB resistance genes, were screened with functional markers. The BB3-RF and BB3-RR primers consistently amplified a resistance-specific fragment of 255 bp only in resistant plants, whereas the BB3-SF and BB3-SR primers were specific to susceptible plants. Genotyping results were co-segregated with phenotype by conducting the BB resistance test with the K 3 race. These markers could be effective for marker-assisted selection of the Xa3 gene in rice breeding programs.