TY - JOUR T1 - Identifying the diamond in the rough: a study of allelic diversity underlying flowering time adaptation in maize landraces JF - bioRxiv DO - 10.1101/092528 SP - 092528 AU - J. Alberto Romero-Navarro AU - Martha Wilcox AU - Juan Burgueño AU - Cinta Romay AU - Kelly Swarts AU - Samuel Trachsel AU - Ernesto Preciado AU - Arturo Terron AU - Humberto Vallejo Delgado AU - Victor Vidal AU - Alejandro Ortega AU - Armando Espinoza Banda AU - Noel Orlando Gómez Montiel AU - Ivan Ortiz-Monasterio AU - Félix San Vicente AU - Armando Guadarrama Espinoza AU - Gary Atlin AU - Peter Wenzl AU - Sarah Hearne AU - Edward Buckler Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/12/13/092528.abstract N2 - Landraces (traditional varieties) of crop species are a reservoir of useful genetic diversity, yet remain untapped due to the genetic linkage between the few useful alleles with hundreds of undesirable alleles1. We integrated two approaches to characterize the genetic diversity of over 3000 maize landraces from across the Americas. First, we mapped the genomic regions controlling latitudinal and altitudinal adaptation, identifying 1498 genes. Second, we developed and used F-One Association Mapping (FOAM) to directly map genes controlling flowering time across 22 environments, identifying 1,005 genes. In total 65% of the SNPs associated with altitude were also associated with flowering time. In particular, we observed many of the significant SNPs were contained in large structural variants (inversions, centromeres, and pericentromeric regions): 29.4% for flowering time, 58.4% for altitude and 13.1% for latitude. The combined mapping results indicate that while floral regulatory network genes contribute substantially to field variation, over 90% of contributing genes likely have indirect effects. Our strategy can be used to harness the diversity of maize and other plant and animal species. ER -