Soybean oil contains contaminants like free fatty acids that significantly reduce the efficiency of biodiesel production by poisoning the catalysts in the transesterification reaction. Soybean seed derived protein products contain compounds that have been shown to have physiological effects on humans and animals that ingest these products. Manipulation of soybean seed composition to provide speciality cultivars suited to different purposes is a long term goal for soybean improvement. Using the Essex by Forrest genomic resources eight loci (QTL) controlling isoflavone content, seven controlling seeed yield, six controlling protein content, five underlying seed size, four underlying oil content and four underlying biodiesel catalysis efficiency were identified. Genotypes varied in free fatty acid content and the degree of increase in the amount after storage. Protein was inversely correlated with oil and yield. Transgressive segregants were identified for each trait. Isogeneic germplasm was developed with elevated and reduced isoflavone content and elevated and reduced free fatty acid content in an otherwise isogeneic protein and oil matrix. In addition candidate genes underlying the QTL were identified. Using the genomic resources at SoyGD (http:/soybeangenome.siu.edu) an ortholog of KASI that encoded beta-ketoacyl-ACP synthase was found in a region underlying a protein and oil QTL. However, the gene appeared to be a transcriptionally silent pseudo-gene. Examination of surrounding sequences identified a cluster of genes that are candidates to underlie the QTL. The research has lead to the identification of nearly isogeneic soybeans, in which seed content can be managed for specific needs within the research community, and later the human health and biofuel industries. This research may expand the usefulness of soy products.