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Marker utility of transposable elements for plant genetics, breeding, and ecology: a review

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An Erratum to this article was published on 17 March 2015

Abstract

Variation is the primary source for plant and animal breeding and evolution, and hence, the detection of variation is an integral part of genetics, breeding, and ecology. Various molecular marker systems have been developed to detect genetic variation. They detect sequence variations (e.g., restriction fragment length polymorphism, randomly amplified polymorphic DNA, amplified fragment length polymorphism) or simple sequence motif variations. However, a large portion of genomic variation is derived from the transposition of transposable elements (TEs), which are major denizens of most eukaryote genomes. Therefore, molecular markers derived from TEs are valuable resources for dissecting genomes in plants and animals. Because class I retrotransposons transpose by a “copy-and-paste” semi-conservative manner, retrotransposon-based markers (e.g., Inter-retrotransposon amplified polymorphism, retrotransposon-microsatellite amplified polymorphism, sequence-specific amplified polymorphism) can reveal highly accurate phylogenetic relationships among related taxa as well as among accessions within a species. Transposon display based on class II DNA transposons has also been used in various genetics fields. A large amount of fairly accurate genome sequences are now being generated, and computational biology allows us to mine the TEs on a genome-wide scale. Thus, TE-based molecular markers are adding another venue to the other marker systems used for the molecular dissection of genomes.

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Acknowledgments

This work was funded by a grant from Golden Seed Project, Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development of Korea (RDA), and Korea Forest Service (KFS).

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  1. Department of Molecular Biosciences, Kangwon National University, Chucheon, 200-701, Korea

    Neha Samir Roy, Ji-Yeong Choi, Sung-Il Lee & Nam-Soo Kim

  2. Institute of Bioscience and Biotechnology, Kangwon National University, Chucheon, 200-701, Korea

    Nam-Soo Kim

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Roy, N.S., Choi, JY., Lee, SI. et al. Marker utility of transposable elements for plant genetics, breeding, and ecology: a review. Genes Genom 37, 141–151 (2015). https://doi.org/10.1007/s13258-014-0252-3

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