Genetic Diversity, Linkage Disequilibrium, and Genome Evolution in a Soft Winter Wheat Population

Understanding genetic diversity is fundamental for efficient use breeding populations. The development of new high-density genotyping systems offers the opportunity to expand the scope and depth of these studies. The objective of this study was to analyze the genetic diversity of two soft winter wheat populations adapted to the Eastern U.S. The historical population (HP) consisted of 187 lines released or developed from 1808 to 2005. The elite population (EP) consisted of 449 elite modern lines from the Ohio State University breeding program. The HP was genotyped with SNP and DArT markers to create the HPs and HPd data sets, respectively, while the EP was genotyped with DArT markers to create the EPd data set. Evidence of structure was observed in both populations, with five subgroups in HP using either SNP or DArT markers and up to nine in EP. Year of release (in HP), class (red and white wheat) and pedigree partly explained structure. Linkage disequilibrium decay (r² = 0.2) extended consistently to around 5cM in both populations. Interestingly, diversity appeared to increase with time and an estimated 11% of the genome exhibited a pronounced linear change over time while evidence of more subtle changes abound. In conclusion, soft winter wheat in the eastern U.S. has a moderate level of structure, appears quite diverse, and diversity may be increasing.