ArticleMolecular genetics and genomics : MGG2007
Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives.
Article in Molecular genetics and genomics : MGG, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 29 citations in OpenAlex.
- Terminal-Repeat Retrotransposons in Miniature (TRIMs) in bivalves.Scientific reports · 2019Article
- BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species.BMC research notes · 2014Article
- Article
- R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements.Mobile DNA · 2012Article
- Development of new molecular markers for the Colletotrichum genus using RetroCl1 sequences.World journal of microbiology & biotechnology · 2012Article
- A novel family of terminal-repeat retrotransposon in miniature (TRIM) in the genome of the red harvester ant, Pogonomyrmex barbatus.PloS one · 2012Article
- Characterizing the walnut genome through analyses of BAC end sequences.Plant molecular biology · 2012Article
- Epigenetic QTL mapping in Brassica napus.Genetics · 2011Article
- Karyotype and identification of all homoeologous chromosomes of allopolyploid Brassica napus and its diploid progenitors.Genetics · 2011Article
- Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication.Genome biology · 2009Article
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Authors and funding
14 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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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