The present investigation has been initiated to combine bacterial blight (BB) and blast resistance with the high yield potential of a short duration rice variety, MTU1010 (Cottondora Sannalu) of India. B95-1 carrying BB resistance genes (xa13 and Xa21) and NLR145 carrying blast resistance genes (Pi54 and Pi1) were selected for making crosses. B95-1 was validated for the presence of target genes, xa13 and Xa21 by using primers viz., xa13 promotor (functional marker-FM) and pTA 248 (STS marker), while NLR145 was validated by using primers viz., Pi54 MAS (functional marker-FM) and RM 224 (gene linked marker-GLM). These primers were also used to study polymorphism between resistant (B95-1 & NLR145) and susceptible (MTU1010) parents for the target genes. Two F₂ segregating populations viz., MTU1010 x B95-1 and MTU1010 x NLR145 were evaluated during dry season, 2012. Foreground selection was carried out and the plants carrying the target genes in homozygous condition were identified. Genotyping revealed that BB and Blast resistance genes exhibited Mendelian pattern of segregation in 1:2:1 ratio and exhibited goodness of fit. Phenotypic studies for BB and Blast progenies in two F₃ populations resulted in identification of resistant plants.