Molecular population genetics of maize regulatory genes during maize evolution

Selection is the key driving force for the adaptive evolution of organisms. Domestication is a selection process for the adaptation of animal or plant species to the cultivated environment under human influence. During domestication, artificial selection was directed by humans at genes controlling agronomically favorable traits and has largely reduced genetic variation at theses genes and their adjacent genomic regions.; Maize was domesticated from its wild ancestor less than 10000 years ago. Strong artificial selection during maize domestication resulted in a dramatic and rapid morphological divergence between maize and teosinte. Identification of maize genes under artificial selection is important for understanding the genetic basis of rapid maize evolution and the role of selection in shaping genetic variation at the targets of selection and their adjacent genomic regions.; The primary goal of this study is to identify candidates for targets of selection during maize domestication based on the prediction that selected genes exhibit a significant loss of genetic diversity. We utilized population genetic approaches to search for targets of selection in several groups of candidate genes and assess whether some specific classes of genes can be major targets of selection. First, we studied the transcription factor family of MADS-box genes and found that MADS-box genes were likely more often targets of selection than average genes in the maize genome. Second, we investigated sequence evolution of two documented maize domestication genes, tb1 and tga1, and one strong candidate for domestication gene, ba1, and found strong signatures of selection at these three genes and their adjacent genomic regions. Third, we analyzed sequence data of 23 characterized or putative maize developmental genes and identified five genes as candidates for targets of selection during domestication. Finally, we studied 72 maize genes with sequence homology to known regulatory genes. Our analysis of these genes suggested that regulatory genes overall may not be a more frequent target of selection for maize domestication traits than the average maize genes.