Comparative Genomics of the Genomic Region Controlling Resistance to Puccinia Polysora Underw. in Zea Mays L

Polysora rust (Southern Corn Rust) is a major disease of maize in tropical and subtropical region causing yield loss in excess of 45%. The loci governing resistance (Rpp9, RppQ and RppD) have been mapped to 10.01 bins on short arm of maize chromosome 10, which also has genes for common rust resistance like Rp1 and Rp5. With the publication of maize draft genomic sequence we tried to annotate the region spanning these genes using comparative genomic tools. We constructed a physical map using the various loci and the corresponding markers, BAC clones and contigs reported from the previous researchers and using MaizeGDB. The sequence for this region was downloaded from maizesequence.org. The sequence was scanned for coding regions using GENSCAN and the CDS and peptides obtained along with the whole sequence (in bits of 1 MB) was subjected to BLAST analysis in NCBI-nBLAST, NCBI-pBLAST, COGE-BLAST and MaizeGDB BLAST. The region when located on a physical map, had all the loci governing Polysora rust resistance in a overlapping position and was around 3 MB size. Two loci RppQ and RppD covered large portion of the 3MB region whereas Rpp9 was 82769 bp long. The BLAST results indicated the similarity of the region to many loci responsible for disease resistance like PR protein, Serine/threonine kinase protein, rust resistance protein (rp3-1), receptor kinases and zein cluster. The region shared homology with rice, sorghum and brachypodium grass and we found some orthologs having NB-LRR domain. Hence from this analysis it could be concluded that the region is responsible for disease resistance and host many other genes linked with resistance to various diseases.