SEQUENCE VARIATIONS AND HAPLOTYPES OF THE BACTERIAL BLIGHT RESISTANCE GENE xa13 IN RICE
P. Yu, X.M. Wang, X.P. Yuan, C.H. Wang, Q. Xu, Y. Feng, H.Y. Yu, Y.P. Wang, X.H. Wei
The sequence variation diversity in the rice bacterial blight (BB) resistance locus xa13 was evaluated in 217 rice cultivars in this study. On the basis of 51 polymorphic sites in the promoter region, eighteen distinct haplotype groups were detected, with a haplotype diversity of 0.642. A 252 bp insertion in the −69 bp to −86 bp region of the promoter is useful for association with BB resistance. Six haplotype groups were developed from the five SNPs in the xa13 gene coding region. Alignment of the deduced amino acid sequences supported the existence of two XA13 protein haplotypes. The haplotypes of xa13 did not segregate in japonica and indica, the natural occurring alleles of xa13 had no independent origins in the two subspecies.