The objective of this thesis was to investigate the genomic changes that have occurred due to the effects of long-term artificial selection applied by soybean breeders. A total of 42 cultivars from six different breeding programs, comprising the multi-generational pedigree of OAC Bayfield were genotyped with molecular markers and chromosomal inheritance was tracked throughout the pedigree. The graphical genotype profile of the 20 chromosomes revealed substantial allelic structure that has been built up in certain chromosomes, in the form of specific linkage blocks, which have been conservatively inherited. A selective sweep analysis using microsatellite markers was performed using the members of OAC Bayfield’s pedigree to identify genomic regions that have retained a molecular selective signature through OAC Bayfield in the varieties derived from it. Overall, there was a high level of agreement between the identified quantitative trait loci (QTL) and the phenotypic traits that would have been expected to be under breeders’ selection.

This thesis is the first report linking differential distribution of cadmium (Cd) among tissues of hydroponically-grown soybean with Cd amendments – lower seed Cd-accumulating OAC Champion and higher seed Cd-accumulating OAC Bayfield – and the mechanisms responsible for these differences. OAC Champion retains 94% (64% for OAC Bayfield) of accumulated Cd in the root stock and Cd in its xylem sap is eleven-fold less concentrated than OAC Bayfield by seed fill. Though the movement of Cd to shoots is more restricted in OAC Champion, the concentration in some seed still approximates or exceeds 0.1 mg Cd • kg-1, indicating that in soils with elevated available Cd, there is potential for many cultivars of soybean to exceed the new suggested maximum for soybean, under an amendment to regulation (EC) No 1881/2006. Phytic acid was also assayed in seed tissue and OAC Bayfield was found to contain the highest concentrations.