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

V. vermiformis est une amibe libre répandue dans l'environnement et les milieux artificiels comme les réseaux d'eau chaude sanitaire (RECS). Il est maintenant bien établi qu'elle joue un rôle de réservoir pour des bactéries pathogènes, comme L. pneumophila. Le contrôle de V. vermiformis dans les RECS représente donc un enjeu sanitaire important. Les amibes libres peuvent passer d'une forme métaboliquement active (trophozoïte) à une forme de résistance, le kyste, lorsque les conditions sont défavorables ce qui leur confère une résistance aux traitements. Malgré la haute prévalence de V. vermiformis dans les RECS, les processus de différenciation et la résistance de ses kystes aux traitements n'ont été que peu étudiés. Nous avons donc investigué les changements morphologiques et ultrastructuraux qui s'opèrent lors de l'enkystement et désenkystement de V. vermiformis. Il en ressort que l'enkystement est un phénomène rapide (9 h) qui conduit à la formation de kystes entourés d'une paroi double couche. Lors du désenkystement, les trophozoïtes n'émergent pas à travers un ostiole comme c'est le cas chez Acanthamoeba. Puis, nous avons étudié l'effet des conditions environnementales et de la concentration cellulaire sur l'enkystement. Nous avons observé que plus la concentration cellulaire est élevée plus l'enkystement est rapide, ce qui suggère l'existence de mécanismes de communication intercellulaire. Enfin, nous avons étudié la résistance des kystes aux traitements utilisés dans les RECS et aux protéases. Ces traitements étaient efficaces, in vitro, pour inactiver les kystes de V. vermiformis. Ces travaux ont permis d'apporter des connaissances de bases sur les processus de d / Vermamoeba vermiformis is a free-living amoeba (FLA) widespread in the environment and artificial environments such as hot water networks. It is now well established that it acts as a reservoir for many pathogenic bacteria, such as Legionella pneumophila. The control of V. vermiformis in artificial environments represents an important health issue. FLA can turn from a metabolic active form (trophozoite) to a resistance form, called cyst, when conditions are unfavorable. Cysts are more resistant to treatments. Despite the high prevalence of V. vermiformis in hot water networks, the processes of differentiation and the resistance of cysts to disinfection treatments have been poorly studied. Therefore we investigated morphological and ultrastructural changes occurring during encystment and excystment of V. vermiformis. It appears that encystment is a fast process (9 h) which leads to the formation of cysts surrounded by a double-layered wall. During excystment, trophozoites do not emerge through an ostiole as is the case with Acanthamoeba. Then, we studied the effect of environmental conditions and cell concentration on encystment. We observed that the higher cell concentration was, the faster the encystment was, which suggests the existence of intercellular communication. Finally, we studied the resistance of cysts to conventional disinfection treatments used in hot water networks and to innovative treatment with proteases. These treatments were effective, in vitro, to inactivate V. vermiformis cysts. This work provides new finding regarding differentiation processes and cysts resistance of V. vermiformis, a free-living amoeba poorly studied.