RT Journal Article SR Electronic T1 Identifying the diamond in the rough: a study of allelic diversity underlying flowering time adaptation in maize landraces JF bioRxiv FD Cold Spring Harbor Laboratory SP 092528 DO 10.1101/092528 A1 J. Alberto Romero-Navarro A1 Martha Wilcox A1 Juan Burgueño A1 Cinta Romay A1 Kelly Swarts A1 Samuel Trachsel A1 Ernesto Preciado A1 Arturo Terron A1 Humberto Vallejo Delgado A1 Victor Vidal A1 Alejandro Ortega A1 Armando Espinoza Banda A1 Noel Orlando Gómez Montiel A1 Ivan Ortiz-Monasterio A1 Félix San Vicente A1 Armando Guadarrama Espinoza A1 Gary Atlin A1 Peter Wenzl A1 Sarah Hearne A1 Edward Buckler YR 2016 UL http://biorxiv.org/content/early/2016/12/13/092528.abstract AB 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.