Background The progress in tagging/mapping of genes in crops like Arabidopsis, rice, maize etc. is far ahead when compared to the major legume crops viz. groundnut, chickpea, redgram, greengram, soyabean etc., even in the post release period of legume genome sequence databases. This can be attributed mainly to low level of available molecular genetic diversity in these crops. Methods The study of transferability of Rice yield gene tagged markers to Peanut was carried out by employing17 diverse groundnut genotypes. ANOVA revealed significant differences for six yield and seven seed quality traits studied which indicates availability of ample amount of variability among the genotypes. Molecular analysis was conducted to analyse the transferability of known rice yield, grain size and micronutrient content (Fe and Zn) controlling gene tagged markers (GTMs) to peanut by using 45 GTMsthat targets 24 known functional genes. Results Of 45 markers, 31 (76%) were transferable to peanut, denotes very high conservation at functional regions. The extent of amplification of rice GTMs at individual groundnut genotype level was observed from 79.17% for the cultivated varieties (2n = 4x) Nithya Haritha, Greeshma, Prasuna, Kalahasti, Narayani and with a wild genotype, Arachis villosa(2n = 2x) to 91.67% for Dheeraj variety. The analysis on transferable efficiency of individual rice GTM revealed that 17 markers belong to 14 rice genes showed amplification among all the 17groundnut genotypes (100%) under study. Conclusions Hence, focusing research on the available knowledge of functionally characterized genes of molecular model crops and vast list of annotated orthologous genes present in ‘Omics’ databases, widens the scope to tag the genes at molecular level and thereby to improve the cropslike groundnutthat has meager progress in gene tagging;by pyramiding of desirable genes with high veracity.