Whole-genome variation of transposable element insertions in a maize diversity panel

Yinjie Qiu; Christine H O’Connor; Rafael Della Coletta; Jonathan S Renk; Patrick J Monnahan; Jaclyn M Noshay; Zhikai Liang; Amanda Gilbert; Sarah N Anderson; Suzanne E McGaugh; Nathan M Springer; Candice N Hirsch

doi:10.1093/g3journal/jkab238

G3: Genes, Genomes, Genetics (Jun 2021)

Whole-genome variation of transposable element insertions in a maize diversity panel

Yinjie Qiu,
Christine H O’Connor,
Rafael Della Coletta,
Jonathan S Renk,
Patrick J Monnahan,
Jaclyn M Noshay,
Zhikai Liang,
Amanda Gilbert,
Sarah N Anderson,
Suzanne E McGaugh,
Nathan M Springer,
Candice N Hirsch

Affiliations

Yinjie Qiu: ORCiD; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
Christine H O’Connor: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
Rafael Della Coletta: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
Jonathan S Renk: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
Patrick J Monnahan: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
Jaclyn M Noshay: ORCiD; Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
Zhikai Liang: Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
Amanda Gilbert: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
Sarah N Anderson: Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
Suzanne E McGaugh: Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
Nathan M Springer: ORCiD; Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
Candice N Hirsch: ORCiD; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA

DOI: https://doi.org/10.1093/g3journal/jkab238
Journal volume & issue: Vol. 11, no. 10

Abstract

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AbstractIntact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome-wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short-read sequencing data from 509 diverse inbred lines to classify the presence/absence of 445,418 nonredundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e.R2

Published in G3: Genes, Genomes, Genetics

ISSN: 2160-1836 (Online)
Publisher: Oxford University Press
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General): Genetics
Website: https://academic.oup.com/g3journal

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