Allele Profiling of Bacterial Blight Resistance Genes Xa4, Xa38, and Xa21 in Selected Sri Lankan Rice Germplasm

In rice, resistance to bacterial blight (BB) is conveyed by several Xa genes, among which Xa4, Xa21 and Xa38 convey durable resistance. Most Sri Lankan rice germplasm is uncharacterized for the alleles carried at Xa genes. Knowledge on the allele profile of major Xa genes of rice accessions/varieties is essential for making informed decisions in rice breeding programs. In the current study, the allele profiles of 42 Sri Lankan rice accessions/varieties were developed targeting three Xa genes (Xa4, Xa21, and Xa38) using intragenic/linked markers amplifying known resistance/susceptible alleles. According to allele profiles, the rice accessions/varieties were grouped into 11 allele-haplotypes. The varieties, Bg 250, Bg 251 and At 354 carried resistance alleles at Xa4, Xa21, and Xa38 (H1 and H3). Most other accessions/varieties reported either one (Xa4- H8 and Xa38- H10) or two resistance alleles (Xa4 and Xa21- H2; Xa4 and Xa38- H9; Xa21 and Xa38- H11). Three allele-haplotypes were reported with a novel allele at Xa4 (H4, H5, and H6). Ma wee and Kuru wee reported susceptible alleles at all three Xa genes (H7). A significant association (p≤0.05) between the Xa allele-haplotypes and the BB disease response was not observed. To achieve durable BB disease resistance in rice, it is recommended to introgress resistance alleles of the major Xa genes when releasing rice varieties, for which the reported allele profile of Xa4, Xa21 and Xa38 genes in the selected panel of Sri Lankan rice varieties/accessions will be of great importance.