Seed development and composition is an important determinant of grain yield and grain utilization. We have utilized recurrent selection populations, structured bi-parental populations, association panels, and qualitative mutants to characterize the genetic basis of endogenous variation for seed weight and composition in maize. This research has been supported by transcription analysis using RNAseq and microarrays, whole genome re-sequencing, high density genotyping using a genotype-by-sequencing approach, and high resolution mapping. In this presentation, I will describe the insights that we have gained through this research, and some of the challenges encountered in integrating genomic information.