Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)
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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.
Cite this as
2014. Natural variation in teosinte at the domestication locus teosinte branched1 (tb1) PeerJ PrePrints 2:e685v1 https://doi.org/10.7287/peerj.preprints.685v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This manuscript has been submitted to PeerJ for review.
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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
Hopscotch frequency in maize
Hopscotch frequency in sampled Zea mays ssp. mays (RIMMA).
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.
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)
Gel image of PCR products
Agarose gel image of amplification products using our primer sets. Genotypes are indicated at the top of the gel.
Additional Information
Competing Interests
Jeffrey Ross-Ibarra is an Academic Editor for PeerJ.
Author Contributions
Laura Vann performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Thomas Kono performed the experiments, analyzed the data, reviewed drafts of the paper.
Tanja Pyhäjärvi analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Matthew B. Hufford conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Jeffrey Ross-Ibarra conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Figshare <http://dx.doi.org/10.6084/m9.figshare.776926>, <http://dx.doi.org/10.6084/m9.figshare.779707>. Sanger sequencing data will be uploaded to Figshare prior to publication
Data Deposition
The following information was supplied regarding the deposition of related data:
Figshare: <http://dx.doi.org/10.6084/m9.figshare.1166630>, <http://dx.doi.org/10.6084/m9.figshare.776926>, <http://dx.doi.org/10.6084/m9.figshare.1165577>.
Funding
Funding was provided by the Department of Plant Sciences at UC Davis for graduate student research funding to LEV and for research funds supporting the project, and by UC Mexus for a postdoctoral scholar grant to MBH and JR-I. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
