Analysis of nucleotide diversity among alleles of intronless bacterial blight resistant genes Xa27 and Xa23 in rice

Identifying novel effective alleles from different gene pools can provide a stress-free response in any crop plant by allele mining approach. Nucleotide diversity analysis through allele mining helps to study diverse function of genes and their role in disease resistance enhancement. The executor R genes; Xa27 and Xa23 provide resistance against several strains of the rice bacterial blight pathogen, Xanthomonas oryzae pv. Oryzae (Xoo). A total 114 wild relatives of Oryza species were examined to assess nucleotide diversities among the natural alleles of the two genes. Among these, 21 accessions were identified as homologous to Xa27, and 5 accessions were homologous to Xa23. Pathogenicity test was conducted to assess the resistance efficiency of the gathered wild accessions using disease scoring assays for phenotyping. Various parameters for the nucleotide diversity study, including polymorphic sites, InDels, number of haplotypes, single nucleotide polymorphisms, as well as Tajima's D and Fu and Li's D tests, were analyzed for the identified alleles in both the promoter, Effector Binding Element (EBE), and coding regions of these two genes. Xa27 alleles from the rice accessions such as CG86, CG105, CG180, and CG02 exhibit higher numbers of substitutions compared to other identified alleles. CG12 accession showed numerous nucleotide substitutions, indicating a possible novel allele unrelated to Xa23 alleles. Molecular mining of Xa27 and Xa23 in wild rice relatives will help to identify the major novel allele for the breeding program to enhance crop improvement.