Bacterial blight caused by Xanthomonas oryzae pv.oryzae(Xoo)is one of the most devastating diseases of rice worldwide.We found that a pair of rice alleles on the ZA locus had opposite roles in rice-Xoo interaction.Overexpressing ZAI resulted in rice more susceptible to Xoo,while overexpressing ZA2 promoted rice resistance to Xoo.The intron of ZA1 had an insertion of transposon.Overexpressing ZA1 was accompanied with accumulation of small interfering RNAs(siRNAs)generated from the transposon.Rice ST1 gene carries the complementary sequence of the siRNAs.The susceptibility of ZA1-overexpressing(oe)plants was associated with suppressed expression of ST1 and increased DNA methylation level of ST1.In contrast,the enhanced resistance of ZA2-oe plants was associated with induced ST1.These results suggest that induction of ST1 is required for ZA-mediated resistance.ZA1 intron-derived siRNAs may suppress ST1 by RNA-directed DNA methylation,which results in the two alleles function differently in rice resistance to Xoo.