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A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture

Abstract

Although quantitative trait locus (QTL) mapping has been successful in describing the genetic architecture of complex traits1,2,3,4, the molecular basis of quantitative variation is less well understood, especially in plants such as maize that have large genome sizes. Regulatory changes at the teosinte branched1 (tb1) gene have been proposed to underlie QTLs of large effect for morphological differences that distinguish maize (Zea mays ssp. mays) from its wild ancestors, the teosintes (Z. mays ssp. parviglumis and mexicana)1,5,6,7. We used a fine mapping approach to show that intergenic sequences 58–69 kb 5′ to the tb1 cDNA confer pleiotropic effects on Z. mays morphology. Moreover, using an allele-specific expression assay, we found that sequences >41 kb upstream of tb1 act in cis to alter tb1 transcription. Our findings show that the large stretches of noncoding DNA that comprise the majority of many plant genomes can be a source of variation affecting gene expression and quantitative phenotypes.

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Figure 1: Introgression lines and effects on traits.
Figure 2: Allele-specific tb1 expression assay.

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Acknowledgements

We thank L. Rentmeester, B. Oldham, A.-C. Thuillet, K. Bomblies, Y. Vigouroux and other laboratory members for help with fieldwork and for suggestions that improved the experimental design, and K. Bomblies and S. Balasubramanian for comments on the manuscript. This work was supported by US National Institutes of Health grant GM-58816 (to J.D.) and National Institutes of Health award F32 GM-65008 (to R.M.C.).

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Correspondence to John Doebley.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Recombination breakpoints in the tb1 to PG3 region. (PDF 399 kb)

Supplementary Fig. 2

Trait means, sample sizes, and direction of effects. (PDF 936 kb)

Supplementary Table 1

Genealogies of Panindicuaro chromosome segments (PDF 39 kb)

Supplementary Table 2

P-values of tests for phenotypic differences in the means among genotypic classes within families segregating for Panindicuaro chromosome segments (PDF 43 kb)

Supplementary Table 3

Peak area measurements and adjusted expression ratios for allele-specific expression assay (PDF 64 kb)

Supplementary Table 4

Primers used for allele-specific PCR, genotyping, and localization of recombination breakpoints (PDF 48 kb)

Supplementary Table 5

Primers, polymorphisms, and loci used for genotyping Panindicuaro introgressions (PDF 38 kb)

Supplementary Methods (PDF 95 kb)

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Clark, R., Wagler, T., Quijada, P. et al. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet 38, 594–597 (2006). https://doi.org/10.1038/ng1784

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  • DOI: https://doi.org/10.1038/ng1784

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