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. 2004 Jan 20;101(3):700-7.
doi: 10.1073/pnas.2237049100. Epub 2003 Dec 30.

Pattern of diversity in the genomic region near the maize domestication gene tb1

Richard M Clark  1 , Eric Linton, Joachim Messing, John F Doebley
Affiliations

Pattern of diversity in the genomic region near the maize domestication gene tb1

Richard M Clark et al. Proc Natl Acad Sci U S A. .

Abstract

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 approximately 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.

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Figures

Fig. 1.
Fig. 1.
Genomic region and gene structure. (A) A schematic representation of the tb1 region indicating predicted genes and repetitive sequence features. (B)vista plots compare identity of maize genomic sequence for tb1 with that of sorghum and rice (similarity indicated by shading). The position of the previously identified cDNA (7) is shown with putative start and termination sites for translation. The location of a possible 5′ exon is as indicated (open box, “?”; ref. 7). The locations of sites surveyed for diversity in the current study (2.5-, 1.7-, and 0.4-kb and 5′ cDNA sites) are shown at the bottom.
Fig. 2.
Fig. 2.
Diversity survey. (A) The location of sampled sites relative to sequence features in the gene 3 to tb1 region. (B) The levels of nucleotide diversity (π) for maize and teosinte. (C) The relative ratio of π in maize to teosinte. Values of π for teosinte were calculated from combined subsp. parviglumis and subsp. mexicana sequences. ND, regions for which teosinte data are not determined.
Fig. 3.
Fig. 3.
Phylogenies. Neighbor-joining trees are shown for 10 sites in the tb1 region with percent bootstrap support indicated at nodes when >50%. In the absence of an outgroup for all sites, we used midpoint rooting to generate tree outputs that facilitate comparisons of topologies. Teosinte samples are indicated as either Par (subsp. parviglumis) or Mex (subsp. mexicana), and Z. diploperennis samples (Dip) are shown for sites where full-length sequence was obtained. Multiple alleles recovered from heterozygous teosinte plants are indicated (sample name plus A1 or A2). For the 0.4-kb and 5′ cDNA sites, sample names that end with L, LA, or LB are from Wang et al. (7). However, sample maize 1L from the previous study (7) was changed to BOV396 to facilitate discussion (see text).
Fig. 4.
Fig. 4.
LD. Within- and between-region pairwise LD comparisons for maize (A) and within-region pairwise LD comparisons for teosinte (B). Magnitude of mean r2 is indicated by shading (see scale, A). No pairwise comparisons (NC) could be calculated where insufficient polymorphism was present.
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