The genomic origin of early maize in eastern North America

Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize’s domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize. [Display omitted] •Ancient maize genomes reveal eastward dispersal into eastern North America•Modern lineage of Northern Flint linked to 900-year-old maize from the Ozarks•Starch metabolic pathway was repeatedly under selection during maize domestication Ancient maize genomes reveal recurrent northward movements from its domestication center, culminating in two dispersals of US Southwest maize into the Ozark rockshelters in eastern North America. The 1,000-year-old maize genomes from the Ozarks provide insights into the origin of Northern Flints and the selection history of the wx1 gene, part of the starch metabolic pathway.