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Pattern of Diversity in the Genomic Region near the Maize Domestication Gene tb1
Richard M. Clark, Eric Linton, Joachim Messing and John F. Doebley
Proceedings of the National Academy of Sciences of the United States of America
Vol. 101, No. 3 (Jan. 20, 2004), pp. 700-707
Published by: National Academy of Sciences
Stable URL: http://www.jstor.org/stable/3148440
Page Count: 8
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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.
Proceedings of the National Academy of Sciences of the United States of America © 2004 National Academy of Sciences