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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY

Location: Vegetable Crops Research Unit

Title: DcSto, stowaway-like miniature inverted-repeat transposable elements (MITEs), are abundant and polymorphic in the carrot genome

Authors
item Podgorni, Macko -
item Mschichowska, A -
item Grzebelus, E -
item Grzebelus, D -
item SIMON, PHILIPP

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 12, 2009
Publication Date: January 9, 2010
Citation: Podgorni, M., Mschichowska, A., Grzebelus, E., Grzebelus, D., Simon, P.W. 2010. DcSto, stowaway-like miniature inverted-repeat transposable elements (MITEs), are abundant and polymorphic in the carrot genome [abstract]. Plant and Animal Genome Conference. p. 205.

Technical Abstract: Transposable elements constitute a large fraction of plant genomes and strongly influence gene and genome evolution. Stowaway elements, a group of MITEs present in high copy number, are preferentially located in the vicinity of coding regions. Stowaway elements are characterized by short length, similar terminal inverted repeat (TIR) sequences and formation of two-nucleotide ‘TA’ target site duplications (TSD). Like other MITEs, Stowaways have no coding capacity. Their mobilization depends on a transposase encoded by related DNA (class II) transposons belonging to the Tc1 Mariner superfamily. The first member of the DcSto family of carrot Stowaway-like MITEs was identified as a 272-long insertion in the first intron of acid soluble invertase isozyme II (invII). A TIR-specific primer was used to amplify and clone related elements from different genetic backgrounds, including cultivated carrot and wild Daucus. Length of 53 copies of DcSto cloned in this study was 252 to 288 bp and their average full length sequence similarity was 89.2%. Abundance of DcSto elements in the carrot genome was estimated by means of fluorescent in situ hybridization and by PCR-based screening of a BAC carrot genomic DNA library. DcSto elements are present in the carrot genome in thousands of copies distributed over the whole genome. Insertional polymorphism of DcSto elements was observed in an F2 population, using Transposon Display. DcSto insertions were highly polymorphic. The high copy number of DcSto elements and their preference for insertion close to coding regions makes them a potentially valuable source of molecular markers.

Last Modified: 9/10/2014