Domesticated maize and its wild ancestor (teosinte) differ strikingly
in morphology and afford an opportunity to examine the
connection between strong selection and diversity in a major crop
species. The tb1 gene largely controls the increase in apical dominance
in maize relative to teosinte, and a region of the tb1 locus
5 to the transcript sequence was a target of selection during maize
domestication. To better characterize the impact of selection at a
major ‘‘domestication’’ locus, we have sequenced the upstream tb1
genomic region and systematically sampled nucleotide diversity
for sites located as far as 163 kb upstream to tb1. Our analyses
define a selective sweep of 60–90 kb 5 to the tb1 transcribed
sequence. The selected region harbors a mixture of unique sequences
and large repetitive elements, but it contains no predicted
genes. Diversity at the nearest 5 gene to tb1 is typical of that for
neutral maize loci, indicating that selection at tb1 has had a
minimal impact on the surrounding chromosomal region. Our data
also show low intergenic linkage disequilibrium in the region and
suggest that selection has had a minor role in shaping the pattern
of linkage disequilibrium that is observed. Finally, our data raise
the possibility that maize-like tb1 haplotypes are present in extant
teosinte populations, and our findings also suggest a model of tb1
gene regulation that differs from traditional views of how plant
gene expression is controlled.