Genetic signals of origin, spread, and introgression in a large sample of maize landraces

TLDR

Maize was domesticated from Balsas teosinte in southwestern Mexico, yet the closest cultivars are found in highlands, suggesting primary diffusion from highlands rather than lowlands, a paradox unresolved by earlier evidence. The study reexamines the geographic origins of early maize using a large SNP dataset of teosinte and maize accessions. The authors analyzed a large SNP dataset from many teosinte and maize accessions to investigate early maize geography. Gene flow between maize and teosinte significantly alters inferred geographic origins, and differentiation analysis aligns with ecological, archaeological, and genetic evidence for early maize cultivation.

Abstract

The last two decades have seen important advances in our knowledge of maize domestication, thanks in part to the contributions of genetic data. Genetic studies have provided firm evidence that maize was domesticated from Balsas teosinte ( Zea mays subspecies parviglumis ), a wild relative that is endemic to the mid- to lowland regions of southwestern Mexico. An interesting paradox remains, however: Maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where subspecies parviglumis does not grow. Genetic data thus point to primary diffusion of domesticated maize from the highlands rather than from the region of initial domestication. Recent archeological evidence for early lowland cultivation has been consistent with the genetics of domestication, leaving the issue of the ancestral position of highland maize unresolved. We used a new SNP dataset scored in a large number of accessions of both teosinte and maize to take a second look at the geography of the earliest cultivated maize. We found that gene flow between maize and its wild relatives meaningfully impacts our inference of geographic origins. By analyzing differentiation from inferred ancestral gene frequencies, we obtained results that are fully consistent with current ecological, archeological, and genetic data concerning the geography of early maize cultivation.