Soybean is one of the few promising crops that are both an important source of protein and oil in the world. It is a source of several rare nutrients that can prevent chronic diseases becoming common by the day. Certain challenges such as poor seed longevity, susceptibility to mechanical damage, beany flavor, and trypsin inhibitor activity still affect preference for soybean among consumers and farmers. This scenario can change only when breeders focus on handling these productivity-related challenges through thorough genetic analysis and advanced breeding approaches. Breeders are trying to address these problems using marker-assisted technologies and genomic studies. As a result of these efforts, a Kunitz trypsin inhibitor genotype NRC 127 has been released for several soybean growing states, a high oleic acid containing variety IC 210 has been developed for coronary heart disease patients, and gene introgression for the mosaic disease has been done in JS-335 variety. It is expected that genomics and marker-assisted breeding will further improve the productivity of already popular soybean varieties.