Genome Dynamics and Marker-Trait Associations in Two Soybean Breeding Programs at the University of Guelph.

Understanding marker-trait association within a breeding program and the population structure underlying these associations is important in making informed selections in a breeding program. The objective of this study is to assess genetic diversity and genomic changes due to selection in two soybean breeding programs (Ridgetown and Guelph) at the University of Guelph, Ontario, Canada. A total of 288 soybean genotypes will be genotyped using genotyping-by-sequencing (GBS).  The full 288 line panel is comprised of lines from all parts of the breeding program and different periods that include: founder lines, exotic plant introductions (PI), historical varieties,  modern elite cultivars and breeding lines and lines with specialty market classes such as tofu and natto soybeans. The purpose is to capture the range of genetic diversity for various traits that have been the focus of breeders at different periods in order to better understand the effects of selection on overall as well as specific genomic diversity. In this paper, GBS data from the first set of 96 lines will be presented along with a complete pedigree of all material in the project. The initial genome-wide association has been conducted for seed traits, which will be followed by multi-location field trials to study other traits of interest. It is expected that the results of this study will lead to the development of knowledge and genomic tools for more effective selection of crossing parents to maximize gains from selection in the breeding program.