Comparative analysis of the genomic regions flanking Xa21 locus in indica and japonica ssp. of rice (Oryza sativa L.)

Abstract

Comparative analysis of a 100 kb region flanking of major bacterial blight resistance gene Xa21 (3.57 kb) was performed in the two subspecies of rice Oryza sativa L. ssp. japonica cv. Nipponbare and Oryza sativa L. ssp. indica cv. 93-11 to understand the evolution and divergence of Xa21 locus. A total of 12 genes in japonica and 14 genes in indica were predicted and annotated in this region. Functional annotation revealed the presence of 4 genes and 8 genes in japonica and indica, respectively, which could be putatively associated with disease resistance in the 100 kb region of Xa21 locus. The study also revealed that 50% of japonica genes and 42.8% of indica genes in the genomic region of interest were transposable elements protein coding genes. Analysis of each predicted gene in this region revealed more or less similar GC content in both the subspecies. A total of 109 SSRs have been identified in the region of interest in both indica and japonica. The numbers of repeated motifs were observed to decrease with the increased number of nucleotides. Interestingly, most of the leucine rich repeat (LRR) gene products were predicted to be localized in the plasma membrane and the transposable element related protein coding genes were localized in the nucleus. Phylogenetic tree analysis revealed that the majority of predicted genes with similar functions of both the subspecies were grouped together.