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Mutator-Based Transposon Display: A Genetic Tool for Evolutionary and Crop-Improvement Studies in Maize

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Abstract

Transposable elements account for up to 85% of the maize genome and have significant implications in crop-improvement and evolutionary analyses. The Mutator (Mu) transposon superfamily, a class of DNA transposons, comprises the most complex and active elements in the maize genome, suggesting a special role in plant evolution. Here, we designed a set of Mu-specific primers based on terminal invert repeats and used a transposon display (TD) method for genotyping. We analyzed the distribution pattern of Mu insertions in teosinte (wild relative), sorghum (distant relative), and domesticated maize accessions (dent, sweet, and waxy). The MU-TD analysis suggested the presence of high polymorphic insertions among the species and subspecies, indicating the utility of the method in studying genetic variation and species relationships. Furthermore, we analyzed 80 maize recombinant inbred line populations. Mu-TD generated an average of 60% Mu-anchored polymorphic fragments in which insertions appeared to be segregating in significantly high numbers. The amplification profile was highly reproducible, confirming the utility of Mu elements as a new set of TD markers for developing high-density genetic maps.

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Acknowledgements

This study was supported by the Cooperative Research Program for Agriculture Science & Technology Development (Project Title #PJ01177601, Project #PJ011776), Rural Development Administration, Republic of Korea.

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  1. Rahul Vasudeo Ramekar and Kyong-Cheul Park have contributed equally to this work.

Authors and Affiliations

  1. Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 24341, South Korea

    Rahul Vasudeo Ramekar, Kyu Jin Sa & Ju Kyong Lee

  2. Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, 24341, South Korea

    Kyong-Cheul Park

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  1. Rahul Vasudeo Ramekar
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Correspondence to Ju Kyong Lee.

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12033_2018_118_MOESM1_ESM.jpg

Online Resource 1—Mu-specific primer designing scheme. a) Grouping of TIR sequences based on a phylogenetic tree, b) TIR regions were further subgrouped and were aligned to obtain a consensus region, c) Primers were designed based on the consensus region covering the TIR group (JPG 439 KB)

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Ramekar, R.V., Park, KC., Sa, K.J. et al. Mutator-Based Transposon Display: A Genetic Tool for Evolutionary and Crop-Improvement Studies in Maize. Mol Biotechnol 60, 799–809 (2018). https://doi.org/10.1007/s12033-018-0118-z

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