The Complex Inheritance of Maize Domestication Traits and Gene Expression

The genetic basis for morphological change in divergent species is a central question in evolutionary biology. The domestication of maize from its wild progenitor, teosinte, is an excellent system to address this question. We explore the large effect on domestication phenotypes of a poorly understood region of the maize genome using a chromosome five specific mapping population. Unlike other large effect regions of the maize genome, many traits have multiple QTL that do not stack on a single locus suggesting multiple genes on the fifth chromosome influence domestication traits. Simulation studies show clear evidence for limited power to detect QTL for highly polygenic traits that do not accurately portray the true complexity of the underlying genetic architecture. Two QTL in different locations were chosen for fine mapping studies to identify the underlying causative genes. While a single gene was not identified for either QTL, both were successfully narrowed to less than three centimorgan intervals with relatively few genes and evidence of positive selection during maize domestication. Finally, the first genome-wide effort to characterize cis and trans regulatory change between a domesticated crop and its wild progenitor found extensive regulatory variation with relatively few genes having consistent cis differences, which were determined to be under positive selection during the domestication and crop improvement of maize. Consistent with loss of diversity during the domestication bottleneck, cis expression variation explained by the maize parent is reduced in comparison to teosinte with an even greater reduction seen in cis candidate genes. A general increase in the expression of maize alleles was also observed suggesting domestication in maize may have led to a general increase in gene expression. Collectively, these experiments shed light on the evolution of divergent phenotypes and gene regulation in the domesticated maize and its wild progenitor.