Genetic architecture of domestication-related traits in maize

Authors: XUE, SHANG - North Carolina State University; Bradbury, Peter; CASSTEVENS, TERRY - Cornell University; Holland, Jim - Jim

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2016
Publication Date: 9/1/2016
Citation: Xue, S., Bradbury, P., Casstevens, T., Holland, J.B. 2016. Genetic architecture of domestication-related traits in maize. Genetics. 204:99-113.

Interpretive Summary: Maize was domesticated from its wild ancestor, teosinte, more than 5000 years ago. Domestication radically transformed the morphology of the plant. Nevertheless, some of the traits presumed to be important under domestication retain variation in maize. We tested if the remaining variation is due to genes in regions known to differentiate maize and teosinte. We found no major effect loci remaining, but many small effect genes outside of the known domestication genome regions affect variation in domestication-related traits.

Technical Abstract: Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genetic basis of this could be sequence variation at the same key genes controlling maize-teosinte differentiation (due to lack of fixation or arising as new mutations after domestication), distinct loci with large effects, or polygenic background variation. Previous studies permit annotation of maize genome regions associated with the major differences between maize and teosinte or that exhibit population genetic signals of selection during either domestication or post-domestication improvement. Genome-wide association studies and genetic variance partitioning analyses were performed in two diverse maize inbred line panels to compare the phenotypic effects and variances of sequence polymorphisms in regions involved in domestication and improvement to the rest of the genome. Additive polygenic models explained most of the genotypic variation for domestication-related traits; no large effect loci were detected for any trait. Most trait variance was associated with background genomic regions lacking previous evidence for involvement in domestication. Improvement sweep regions were associated with more trait variation than expected based on the proportion of the genome they represent. Selection during domestication eliminated large effect genetic variants that would revert maize toward a teosinte type. Small effect polygenic variants (enriched in the improvement sweep regions of the genome) are responsible for most of the standing variation for domestication-related traits in maize.