Gene expression is typically understood to be controlled by their promoters. What controls promoter function is less understood, thus limiting the ability to modify gene expression in plants to obtain desired changes in trait performance. The discovery of cis-regulatory DNA elements is starting to change our approach to this challenge. These are DNA sequences elsewhere in the genome that affect the ability of promoters to control genes and their expression. We are using newly developed single-cell genomic methods to systematically and precisely identify, analyze, and validate cis-regulatory DNA elements important for soybean seed development, including the synthesis and accumulation of oil and protein and their precursors as well as for understanding responses to soybean cyst nematode infection. We collected soybean tissue from eleven different developmental stages and identified the location of cis-regulatory elements. We are currently analyzing these data with plans to release them publicly to all soybean researchers via Soybase and via publication in a peer-reviewed journal. We also innovated methods to isolate soybean cells after infection with soybean cyst nematodes so we can study how cells respond to this devasting disease. In parallel, we have identified cis-regulatory DNA elements associated with key genes important for protein and oil production in the seed. These cis-regulatory elements are being targeted by genome editing methods to produce plants with more or less gene expression and potentially expand the tissues and organs in which the genes are expressed. We cannot at this time predict which of these events will occur, but what we can do is select plants with desired alterations to protein or oil production.