Identification of a functional transposon insertion in the maize domestication gene tb1

Abstract

Genetic diversity created by transposable elements is an important source of functional variation upon which selection acts during evolution1,2,3,4,5,6. Transposable elements are associated with adaptation to temperate climates in Drosophila7, a SINE element is associated with the domestication of small dog breeds from the gray wolf8 and there is evidence that transposable elements were targets of selection during human evolution9. Although the list of examples of transposable elements associated with host gene function continues to grow, proof that transposable elements are causative and not just correlated with functional variation is limited. Here we show that a transposable element (Hopscotch) inserted in a regulatory region of the maize domestication gene, teosinte branched1 (tb1), acts as an enhancer of gene expression and partially explains the increased apical dominance in maize compared to its progenitor, teosinte. Molecular dating indicates that the Hopscotch insertion predates maize domestication by at least 10,000 years, indicating that selection acted on standing variation rather than new mutation.

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Figure 1: Teosinte and maize plants.
Figure 2: The phenotypic additive effects for seven intervals across the tb1 genomic region.
Figure 3: Sequence diversity in maize and teosinte across the control region.
Figure 4: Constructs and corresponding normalized luciferase expression levels.

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Acknowledgements

We thank members of the Doebley laboratory for technical assistance, especially H. Wang. We also thank A.J. Eckert, K. Thornton, G. Coop and R.A. Cartwright for helpful discussion and J. Holland for statistical advice. This work is supported by US Department of Agriculture Hatch grant MSN101593 and US National Science Foundation grant DBI0820619.

Author information

A.S. and J.D. designed the experiments and wrote the paper. A.S., J.R.-I. and Q.Z. performed population genetic analyses. Genetic mapping, transient assays, sequencing and informatics were done by A.S.

Correspondence to John Doebley.

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The authors declare no competing financial interests.

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Supplementary Figures 1 and 2 and Supplementary Tables 1–5. (PDF 651 kb)

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Studer, A., Zhao, Q., Ross-Ibarra, J. et al. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 43, 1160–1163 (2011). https://doi.org/10.1038/ng.942

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