Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.
Bibliographical noteFunding Information:
The authors would like to thank T. Kono, S. Watson and M. Watson for photographs of inflorescences, P. Brown for help with QTL delineation, B.S. Gaut, A.M. Gonzales and two anonymous reviewers for comments on an earlier version of the manuscript and M. Grote for statistical advice. This work was supported by funding to the maize diversity project from the US National Science Foundation (NSF; IOS-0820619 to E.S.B., J.D. and M.D.M.) and USDA-ARS (to E.S.B., M.D.M. and D.W.), as well as from USDA Hatch Funds (to P.T. and N.M.S.), the Chinese 973 program (2007CB815701 to J.W.), the Chinese Ministry of Agriculture 984 program (2010-Z13 to G.Z.), the Shenzhen Municipal Government Basic Research Program (to J.W.), the US DOE Great Lakes Bioenergy Research Center (DOE Office of Science; BER DE-FC02-07ER64494), the Office of Science of the US DOE (contract DE-AC02-05CH11231 to the US DOE Joint Genome Institute) and by grants from the US NSF (IOS-0922703 to J.R.-I.) and the USDA–National Institute of Food and Agriculture (2009-01864 to J.R.-I.).