Pigeonpea, a member of family Fabaceae, is one of the important food legumes cultivated in tropical and subtropical regions. Due to its inherent properties to withstand harsh environments, it plays a critical role in ensuring sustainability in the subsistence agriculture. Furthermore, plasticity in the maturity duration imparts it a greater adaptability in a variety of cropping systems. In the post genomics era, the importance of pigeonpea is further evident from the fact that pigeonpea has emerged as first non-industrial legume crop for which the whole genome sequence has been completed. It revealed 605.78 Mb of assembled and anchored sequence as against the predicted 833 Mb genome consequently representing 72.8 % of the whole genome. In order to perform genetic and genomic analysis various molecular markers like random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), diversity array technology (DArT), single feature polymorphism (SFP), and single nucleotide polymorphism (SNP) were employed. So far four transcriptome assemblies have been constructed and different sets of EST-SSRs were developed and validated in a panel of diverse pigeonpea genotypes. Extensive survey of BAC-end sequences (BESs) provided 3,072 BES-SSRs and all these BES-SSRs were further used for linkage analysis and trait mapping. To make the available linkage information more useful, six intra-specific genetic maps were joined together into a single consensus genetic map providing map positions to a total of 339 SSR markers at map coverage of 1,059 cM. However, earlier very few linkage maps were available in the crop because of non-availability of genomic resources. Several quantitative trait loci (QTLs) associated with traits of agronomic interest including QTLs for sterility mosaic disease, fertility restoration, plant type and earliness have been identified and validated. To strengthen the traditional breeding, plenty of genomics ...