Artificial Selection and the Genome: “Deep Pedigree” Analysis In An Elite Soybean Cultivar.

Modern Soybean [Glycine max (L.) Merr.] breeding programs are based on shallow gene pools as a result of a well-defined population bottleneck event. How subsequent artificial selection from breeding activities has shaped the genome is largely unknown as it pertains to cultivar improvement. The analysis of  “deep pedigrees” can be used to address this question. OAC Bayfield was a highly successful commercial cultivar developed by the University of Guelph’s soybean breeding program and released in 1993. Among elite soybean cultivars, OAC Bayfield stands out because of its high yield stability and longevity in the seed market. OAC Bayfield’s pedigree was genotyped with SSR markers across the genome to investigate various genetic parameters related to plant breeding theory. Genotyping data showed very limited genetic diversity within the pedigree with an average of four alleles/locus. Clustering of genotypes based on marker data revealed a shallow shift away from a core set of ancestral lines indicating genotypes which have not contributed as much genetically to the current breeding lines. Furthermore, the current breeding lines did not capture many of the rare alleles from the most genetically distinct ancestral lines but rather are composed of favourable linkage blocks built-up through multiple generations of breeding.