Technical Abstract: Rapid advances in post-Sanger sequencing technology have brought the $1000 human genome within reach while providing the raw sequencing output for researchers to revolutionize the way populations are genotyped. To capitalize on these advancements, genotyping-by-sequencing (GBS) has been developed as rapid and robust approach for reduced representation sequencing of multiplexed samples that combines marker discovery and genotyping. The flexibility and low-cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding. Here we address some of the new research opportunities that are becoming more feasible with GBS. Further, we highlight areas where GBS will become more powerful with the continued increase of sequencing output, development of reference genomes, and improved bioinformatics. The ultimate goal of plant biology scientists is to understand the connection between the material of inheritance (DNA) and the observable characteristics (phenotype) and make informed predictions of the expected phenotype resulting from a given DNA compliment. Furthering our understanding of the connection between heritable genetic factors and the resulting phenotypes will enable genomics-assisted breeding to exist on the scale needed to increase global food supplies in the face of decreasing arable land and climate change.