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Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives

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Abstract

We have developed a display system using a unique sequence of terminal repeat retrotransposon in miniature (TRIM) elements, which were recently identified from gene-rich regions of Brassica rapa. The technique, named TRIM display, is based on modification of the AFLP technique using an adapter primer for the restriction fragments of BfaI and a primer derived from conserved terminal repeat sequences of TRIM elements, Br1 and Br2. TRIM display using genomic DNA produced 50–70 bands ranging from 100 to 700 bp in all the species of the family Brassicaceae. TRIM display using B. rapa cDNA produced about 20 bands. Sequences of 11 randomly selected bands, 7 from genomic DNA and 4 from cDNA, begin with about 104 bp of the terminal repeat sequences of TRIM elements Br1 or Br2 and end with unique sequences indicating that all bands are derived from unique insertion sites of TRIM elements. Furthermore, 7 of the 11 unique sequences showed significant similarity with expressed gene. Most of the TRIM display bands were polymorphic between genera and about 55% (132 of 239 bands) are polymorphic among 19 commercial F1 hybrid cultivars. Analysis of phylogenetic relationships shows clear-cut lineage among the 19 cultivars. Furthermore, a combination of 11 polymorphic bands derived from only one primer combination can clearly distinguish one cultivar from the others. TRIM display bands were reproducible and inheritable through successive generations that is revealed by genetic mapping of 6 out of 27 polymorphic TRIM markers on the genetic map of Brassica napus. Collective data provide evidence that TRIM display can provide useful DNA markers in Brassica relatives because these markers are distributed in gene-rich regions, and are sometimes involved in the restructuring of genes.

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Acknowledgments

This work was partly supported by a grant from the BioGreen 21 Program (20050301034438), Rural Development Administration, and the National Institute of Agricultural Biotechnology (04-1-12-2-4), Korea. We thank Dawn Holligan for technical advice and assistance.

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Authors and Affiliations

  1. Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB), RDA, Suwon, 441-707, South Korea

    Soo-Jin Kwon, Dong-Hyun Kim, Myung-Ho Lim, Ki-Byung Lim, Jin-A Kim, Jung Sun Kim, Mina Jin, Ho-Il Kim, Tae-Jin Yang & Beom-Seok Park

  2. National Key Laboratory of Crop Genetics Improvement, University of Huazhong Agricultural, Wuhan, 430070, China

    Yan Long & Jin-Ling Meng

  3. Department of Agronomy, Chungnam National University, Daejeon, 305-764, Korea

    Sang-Nag Ahn

  4. Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA

    Susan R. Wessler

  5. Deparatment of Plant Science, College of Agriculture and Life Science, Seoul National University, Seoul, 151-921, Korea

    Tae-Jin Yang

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  1. Soo-Jin Kwon
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  2. Dong-Hyun Kim
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  3. Myung-Ho Lim
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  4. Yan Long
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  6. Ki-Byung Lim
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  7. Jin-A Kim
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  8. Jung Sun Kim
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  11. Sang-Nag Ahn
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  12. Susan R. Wessler
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  13. Tae-Jin Yang
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  14. Beom-Seok Park
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Corresponding authors

Correspondence to Tae-Jin Yang or Beom-Seok Park.

Additional information

Communicated by M.-A. Grandbastien.

GenBank accession nos.: AC190326 (TRIM display fragment gCP01); AC190327 (TRIM display fragment gCP02); AC190328 (TRIM display fragment gCP02) AC190329 (TRIM display fragment gCP04) AC190330 (TRIM display fragment gDP01); AC190331 (TRIM display fragment gDP02); AC190332 (TRIM display fragment gDP03); AC190333 (TRIM display fragment gDP04); AC190334 (TRIM display fragment gDP05); AC190335 (TRIM display fragment gDP06); AC190336 (TRIM display fragment gDP07).

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Kwon, SJ., Kim, DH., Lim, MH. et al. Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives. Mol Genet Genomics 278, 361–370 (2007). https://doi.org/10.1007/s00438-007-0249-6

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