Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)

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1 Department of Plant Sciences, University of California, Davis, California, USA
2 Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, USA
3 Department of Biology, University of Oulu, Oulu, Finland
4 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
5 Center for Population Biology and Genome Center, University of California, Davis, California, USA
DOI
10.7287/peerj.preprints.685v1
Published
Accepted
Subject Areas
Agricultural Science, Ecology, Evolutionary Studies, Genetics
Keywords
transposable element, domestication, teosinte, teosinte branched1, maize
Copyright
© 2014 Vann et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Vann L, Kono T, Pyhäjärvi T, Hufford MB, Ross-Ibarra J. 2014. Natural variation in teosinte at the domestication locus teosinte branched1 (tb1) PeerJ PrePrints 2:e685v1

Abstract

The teosinte branched1 (tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene’s expression, causing reduced tillering in maize. Observations of the maize tb1 allele in teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in teosinte. We assessed the prevalence of the Hopscotch element across an Americas-wide sample of 837 maize and teosinte individuals using a co-dominant PCR assay. Additionally, we calculated population genetic summaries using sequence data from a subset of individuals from four teosinte populations and collected phenotypic data using seed from a single teosinte population where Hopscotch was found segregating at high frequency. Genotyping results indicate the Hopscotch element is found in a number of teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on the tb1 locus revealing a potential ecological role, but a greenhouse experiment does not detect a strong association between the Hopscotch and tillering in teosinte. Our findings suggest the role of Hopscotch differs between maize and teosinte. Future work should assess tb1 expression levels in teosinte with and without the Hopscotch and more comprehensively phenotype teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in teosinte.

Author Comment

This manuscript has been submitted to PeerJ for review.

Supplemental Information

Accessions included in study

Accessions of Zea mays ssp. mexicana (RIMME) and Zea mays ssp. parviglumis (RIMPA) sampled. RIHY is a Zea mays ssp. parviglumis and Zea mays ssp. mays hybrid

DOI: 10.7287/peerj.preprints.685v1/supp-1

Hopscotch frequency in maize

Hopscotch frequency in sampled Zea mays ssp. mays (RIMMA).

DOI: 10.7287/peerj.preprints.685v1/supp-2

Depiction of tb1 region sequenced

Representation of the upstream regulatory region of tb1, showing the tb1 coding region (green) and the Hopscotch insertion (red). Arrows show the location of primer sets; in black, primers used for amplification and sequencing (Region 1; within the 5' UTR, and Region 2; 66,169 bp upstream from the tb1 ORF); in blue, primers used to genotype the Hopscotch insertion.

DOI: 10.7287/peerj.preprints.685v1/supp-3

Neighbor-joining tree based on tb1 sequences

Neighbor-joining tree of the sequenced region in the 5' UTR (right; Region 1) and the 66,169 bp upstream region (left; Region 2) of tb1. Individuals with genotype data are colored: Homozygous for the teosinte (no Hopscotch) allele (red), homozygous for the maize (Hopscotch) allele (blue), heterozygotes (purple). TILs (teosinte inbred lines) are colored in green, with stars indicating the 3 TILs known to have the Hopscotch insertion. Black indicates individuals not genotyped for the Hopscotch insertion. EjuA refers to individuals from population Ejutla A, EjuB from Ejutla B, SLO from San Lorenzo, and MSA from La Mesa. Remaining individuals are lines of maize (Zea mays ssp. mays)

DOI: 10.7287/peerj.preprints.685v1/supp-4

Gel image of PCR products

Agarose gel image of amplification products using our primer sets. Genotypes are indicated at the top of the gel.

DOI: 10.7287/peerj.preprints.685v1/supp-5