Rice is a staple food crop providing energy for more than fifty percent of the world population. Considering the world population growth rate and declining of arable area of crops, increasing the yield is utmost requisite for the rice breeders. Yield is a quantitative trait influenced by many minor genes. Among the agronomic traits, the rice grain size is the most important factors for yield and quality. It is reported to be controlled by many genes which showed continuous variation. Therefore, identification and characterization of novel genes for grain size would be useful for enhancing the yield and grain quality. Here, a known gene POS1 from Tomatilo plant for fruit size encoding two AP2 domain were used to identify homologous gene(s) in rice genome through in-silico analysis. A total of 87 protein coding genes were identified in rice genome of which eight gene were found to be encoding double AP2 domains which would be useful to understand the role of grain size in rice. Using the full-length gene sequence of these eight genes, SSR markers were developed for genetic mapping and marker assisted breeding in rice breeding programme. There were quit variable number of exon and intron among the homolog genes indicating the diverse role of genes. In Silico analysis of the protein sequences revealed the non-membranous nature and might be played an important role in gene expression and regulation. Therefore, cloning and functional characterization of these genes would facilitates bridging the gap between gene identification and breeding application.