Expanding the Genomic Perspective of Domestication and Subsequent Adaptation in Maize

The recent assembly of numerous crop reference genomes has allowed for important inferences regarding domestication. For example, comparative genomic studies of crops and their wild relatives based on resequencing data have characterized both genome-wide loss of diversity and localized signatures of selection during domestication.  While these initial resequencing studies have indeed been informative, many domestication questions remain to be explored. Here we describe our efforts to untangle additional complexities of maize domestication.  We first report progress on the de novo assembly of a teosinte (i.e., wild maize) genome and discuss the potential of such de novo assemblies for assessing the importance of structural variation during domestication. We then report evidence that gene flow from wild relatives was a strong adaptive force during the first spread of maize from its center of origin. Finally, we describe how the genome of maize continued to evolve as it spread more widely, colonizing a number of distinct environments across the Americas.