Natto and sprout soybeans are produced using small-seeded soybeans and their production is a high value alternative to grow grain soybeans for food in U.S. The development of soybean cultivars with improved natto and sprout quality is crucial for maintaining and increasing the soyfood market. However, there is insufficient information on sprout soybean characteristics. Therefore, the first objective of this study was to evaluate seed and sprout traits as potential selection criteria and study the storage effect on sprout quality. Seeds can be a vehicle for transmission of pathogens capable of causing human illness. That is why, the second objective was to identify seed-borne pathogens on a commercial soybean cultivar and to evaluate different seed decontamination treatments. Finally, seed coat deficiency is an undesirable trait for natto soybean seeds because it causes inferior appearance of the product. Thus, the third objective was to identify quantitative trait loci (QTL) underlying seed coat deficiency (SCD) and associated markers. Results showed that seed size, high-, average- and low-quality sprout percentage, hypocotyl thickness and length and sprout yield are the most important variables for breeding sprout cultivars; and one-year seed storage at room temperature reduced sprout quality. Fusarium, Alternaria and Diaphorte were the most frequent genera isolated from soybean seeds, and 2% calcium hypochlorite and 5% acetic acid were promising seed disinfection treatments. A stable QTL, qSCD20_1, was identified across two years explaining up to 25% of the variation of SCD; and eight molecular markers tightly linked and nearby qSCD20_1 were identified. Information presented will be helpful for sprout and natto soybean cultivar development. / Master of Science / Natto and sprout soybeans are produced using by small-seeded soybeans and their production is a high value alternative to grow grain soybeans for feed in U.S. The development of soybean cultivars with improved natto and sprout quality is crucial for maintaining and increasing the soyfood market. However, there is insufficient information on sprout soybean characteristics. Therefore, the first objective of this study was to evaluate important seed and sprout traits as potential selection criteria of soybean cultivars and study the storage effect on sprout quality. Seeds can be contaminated with fungi capable of causing human illness. So, the second objective was to identify fungus species associated with seeds of a sprout soybean cultivar and evaluate different seed disinfection treatments. Finally, seed coat deficiency is an undesirable trait for natto soybean seeds because it causes inferior appearance of the product. Thus, the third objective was to identify molecular markers associated with seed coat deficiency. Results showed that seed size, high-, average- and low-quality sprout percentage, hypocotyl thickness and length and sprout yield are the most important variables for breeding sprout cultivars; and one-year seed storage at room temperature reduced sprout quality. Fungal species that may cause human illness were isolated from sprout soybean seeds and calcium hypochlorite and acetic acid are promising seed disinfection treatment for reducing fungus incidence. Finally, eight molecular markers associated with seed coat deficiency were identified which may be potentially used in selecting natto soybean cultivars with low seed coat deficiency. Information presented will be helpful for sprout and natto soybean cultivar development.