We accumulated different candidate genes (CG) involved in quantitative resistance using advanced backcross populations of Vandana/Moroberekan and evaluated them in multi-location environments for resistance to rice blast. Using sequence information and molecular markers from the Rice Genome Program and Gramene, we were able to design gene-based markers and identify SSRs co-localizing with CGs. These markers were used to conduct a genome scan to determine introgression of Moroberekan alleles for CGs into the progenies. We are using in-silico analysis to determine phylogeny, to characterize protein sequences as well as to identify cis-elements related to defense response in the 1kb upstream regions of each gene. For each gene, there was variation in the copy number of cis-elements related to biotic stress responses, such as W box, WNPR1, and WRKY, indicating that these genes have potential associations with the response of rice to pathogen infection such as the blast fungus. To identify the functional variants in CGs genes important for conditioning resistance in rice, we are sequencing these genes from a wide variety of rice germplasm.