The recent application of next generation deep sequencing technology (NGST) is beginning to significantly alter the landscape of genetic analysis of mutants, as it allows one-shot sequencing of the entire mutant’s genome, resulting in the detection of mutagen-induced sequence alterations compared to non-mutagenized reference genomes. Taking this notion a step further, whole genome sequencing (WGS) will also enable us to get at the molecular basis of mono- and multigenic traits, present in natural variants of a species, which are hard to molecularly identify through conventional mapping strategies. Therefore, identification of novel genes underlying some economically important qualitative & quantitative traits in Arabidopsis thaliana and Seminavis robusta using NGST are the major objectives of our research.