Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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


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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

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.


  1. 1

    Naito, K. et al. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461, 1130–1134 (2009).

    CAS  Article  Google Scholar 

  2. 2

    Xiao, H., Jiang, N., Schaffner, E., Stockinger, E.J. & van der Knaap, E. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319, 1527–1530 (2008).

    CAS  Article  Google Scholar 

  3. 3

    White, S.E., Habera, L.F. & Wessler, S.R. Retrotransposons in the flanking regions of normal plant genes: A role for copia-like elements in the evolution of gene structure and expression. Proc. Natl. Acad. Sci. USA 91, 11792–11796 (1994).

    CAS  Article  Google Scholar 

  4. 4

    Bejerano, G. et al. A distal enhancer and an ultraconserved exon are derived from a novel retrotransposon. Nature 441, 87–90 (2006).

    CAS  Article  Google Scholar 

  5. 5

    Mackay, T.F.C., Lyman, R.F. & Jackson, M.S. Effects of P element insertions on quantitative traits in Drosophila melanogaster. Genetics 130, 315–332 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6

    Torkamanzehi, A., Moran, C. & Nicholas, F.W. P element transposition contributes substantial new variation for a quantitative trait in Drosophila melanogaster. Genetics 131, 73–78 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7

    González, J., Karasov, T.L., Messer, P.W. & Petrov, D.A. Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet. 6, e1000905 (2010).

    Article  Google Scholar 

  8. 8

    Gray, M.M., Sutter, N.B., Ostrander, E.A. & Wayne, R.K. The IGF1 small dog haplotype is derived from Middle Eastern grey wolves. BMC Biol. 8, 16 (2010).

    Article  Google Scholar 

  9. 9

    Britten, R.J. Transposable element insertions have strongly affected human evolution. Proc. Natl. Acad. Sci. USA 107, 19945–19948 (2010).

    CAS  Article  Google Scholar 

  10. 10

    Doebley, J. The genetics of maize evolution. Annu. Rev. Genet. 38, 37–59 (2004).

    CAS  Article  Google Scholar 

  11. 11

    Doebley, J., Stec, A. & Gustus, C. Teosinte branched1 and the origin of maize: Evidence for epistasis and the evolution of dominance. Genetics 141, 333–346 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12

    Cubas, P., Lauter, N., Doebley, J. & Coen, E. The TCP domain: a motif found in proteins regulating plant growth and development. Plant J. 18, 215–222 (1999).

    CAS  Article  Google Scholar 

  13. 13

    Doebley, J., Stec, A. & Hubbard, L. The evolution of apical dominance in maize. Nature 386, 485–488 (1997).

    CAS  Article  Google Scholar 

  14. 14

    Clark, R.M., Nussbaum Wagler, T., Quijada, P. & Doebley, J. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat. Genet. 38, 594–597 (2006).

    CAS  Article  Google Scholar 

  15. 15

    Clark, R.M., Linton, E., Messing, J. & Doebley, J.F. Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc. Natl. Acad. Sci. USA 101, 700–707 (2004).

    CAS  Article  Google Scholar 

  16. 16

    Hudson, R.R., Kreitman, M. & Aguade, M. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153–159 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    Zhao, Q. Molecular Population Genetics of Maize Regulatory Genes During Maize Evolution. PhD Thesis, University of Wisconsin–Madison (2006).

  18. 18

    Fukunaga, K. et al. Genetic diversity and population structure of teosinte. Genetics 169, 2241–2254 (2005).

    CAS  Article  Google Scholar 

  19. 19

    Thomson, R. et al. Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data. Proc. Natl. Acad. Sci. USA 97, 7360–7365 (2000).

    CAS  Article  Google Scholar 

  20. 20

    Hudson, R.R. The variance of coalescent time estimates from DNA sequences. J. Mol. Evol. 64, 702–705 (2007).

    CAS  Article  Google Scholar 

  21. 21

    Clark, R.M., Tavare, S. & Doebley, J. Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Mol. Biol. Evol. 22, 2304–2312 (2005).

    CAS  Article  Google Scholar 

  22. 22

    Pi, W. et al. Long-range function of an intergenic retrotransposon. Proc. Natl. Acad. Sci. USA 107, 12992–12997 (2010).

    CAS  Article  Google Scholar 

  23. 23

    Chung, H. et al. Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics 175, 1071–1077 (2007).

    CAS  Article  Google Scholar 

  24. 24

    Schmidt, J.M. et al. Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus. PLoS Genet. 6, e1000998 (2010).

    Article  Google Scholar 

  25. 25

    McClintock, B. The significance of responses of the genome to challenge. Science 226, 792–801 (1984).

    CAS  Article  Google Scholar 

  26. 26

    Tenaillon, M.I. et al. Patterns of DNA sequence polymorphism along chromsome 1 of maize (Zea mays ssp. mays L). Proc. Natl. Acad. Sci. USA 98, 9161–9166 (2001).

    CAS  Article  Google Scholar 

  27. 27

    Thompson, J.D., Higgins, D.G. & Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994).

    CAS  Article  Google Scholar 

  28. 28

    Rozas, J., Sanchez-DelBarrio, J.C., Messeguer, X., Rozas, R. & Dna, S.P. DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496–2497 (2003).

    CAS  Article  Google Scholar 

  29. 29

    Zhao, Q., Weber, A.L., McMullen, M.D., Guill, K. & Doebley, J. MADS-box genes of maize: frequent targets of selection during domestication. Genet. Res. (Camb.) 93, 65–75 (2011).

    CAS  Article  Google Scholar 

  30. 30

    Excoffier, L. & Lischer, H.E.L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567 (2010).

    Article  Google Scholar 

  31. 31

    Teacher, A.G.F. & Griffiths, D.J. HapStar: automated haplotype network layout and visualization. Mol. Ecol. Resour. 11, 151–153 (2011).

    CAS  Article  Google Scholar 

  32. 32

    Thornton, K. Libsequence: a C. class library for evolutionary genetic analysis. Bioinformatics 19, 2325–2327 (2003).

    CAS  Article  Google Scholar 

  33. 33

    Benfey, P.N. & Chua, N. The cauliflower mosaic virus 35S promoter: combinatorial regulation of transcription in plants. Science 250, 959–966 (1990).

    CAS  Article  Google Scholar 

Download references


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.

Corresponding author

Correspondence to John Doebley.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

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

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing