Soybean is the world's largest animal protein feed and second largest vegetable oil source. Soybean cyst nematode (SCN) causes more yield loss than any other soybean pests in the US. Current resistance to SCN in soybean production is mainly derived from two sources, PI 88788 and Peking. Overuse of these resistances in production led to SCN populations overcoming the resistance. PI 437654 has broad SCN resistance to six races. Using a recombinant inbred line (RIL) population derived from Bossier × PI 437654, major QTLs on chromosomes (Chrs) 11 and 18 from PI 437654 were identified for resistance to both races 2 and 4, and a minor QTL on Chr 8 from Bossier to race 4. The Chr 18 QTL mapped to known resistance locus Rhg1. Epistatic interaction of QTLs from Chrs 11 and 18 provided resistance to SCN races 2 and 4 that was confirmed with additional RILs. Results provide QTL and SNP markers for developing cultivars. To pyramid rhg1 and Rhg4 genes with two QTLs from G. soja for soybean cultivar development, 10 pyramids were selected in two populations (Woodruff × LD09-30454, G00-3880 × LD0930454) using marker-assisted selection. A pyramid of cqSCN007 with the rhg1-b allele was identified that provided resistance across three races of SCN and moderate susceptibility to another. This pyramid is optimal for breeding with the small number of QTLs to select. To improve the SCN phenotyping efficiency and accuracy, an imaging system was developed for counting the cysts using enhanced GridFree software. A series of lights and filters were tested for the optimal combination to illuminate cysts. Accuracy of 95% was achieved through GridFree automated counting compared to manual counts. An editing step led to 98% accuracy. Sucrose is an easily digestible energy source, desired in livestock feed. Using fast neutron mutagenesis on elite line G00-3213, a Chr 16 deletion was identified as responsible for high sucrose content. The mutation was confirmed through a bulked segregant analysis and QTL mapping in a bi-parental population of Benning × G15FN-54. This mutation could help understand the genetic control of soybean sucrose content for genetic manipulation in soybean.