Five populations were investigated. The first population was 18 H. tuberosus individuals collected from UMore Park in Rosemount, MN. The second was a set of 187 interspecific F1 hybrids between H. annuus and H. tuberosus. The interspecific hybrids were developed during the years 2003–2006 ( Hulke and Wyse, 2008) by crossing the 18 H. tuberosus (perennial) parents with three inbred H. annuus (annual) lines (CMS HA 89 [PET1], HA 89 (released by the USDA-ARS in 1971) and HA 434 ( Miller et al., 2004)). HA 89 and HA 434 were used as male parents and CMS HA 89 was used as a female parent (Supplementary Table 1). The third population was a derivative of the second, as the F1 hybrids were intermated to form an intermated F1 population (designated as the IM1F1 population). This population was developed in 2007 by Hulke and Wyse (2008) (Supplementary Table 1). The fourth population was a backcross of the interspecific F1 to the inbred lines HA 434 and HA 89 (designated as the BC1F1 population). This population was developed in 2006 by Hulke and Wyse (2008) (Supplementary Table 1). The fifth population was 31 H. tuberosus plants from the seed stocks of the United States Department of Agriculture Germplasm Resources Information Network (GRIN) that were collected from a diverse set of geographical locations (Supplementary Table 1) ( USDA, 2012).