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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: carrot Stowaway-like elements are abundant, diverse, and polymorphic

Authors
item Macko-Podgorni, Alicja -
item Nowicka, Anna -
item Grzebelus, Ewa -
item Simon, Philipp
item Grzebelus, Dariusz -

Submitted to: Genetica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 10, 2013
Publication Date: June 18, 2013
Repository URL: http://handle.nal.usda.gov/10113/58530
Citation: Macko-Podgorni, A., Nowicka, A., Grzebelus, E., Simon, P.W., Grzebelus, D. 2013. DcSto: carrot Stowaway-like elements are abundant, diverse, and polymorphic. Genetica. 141(4-6):255-267.

Interpretive Summary: Transposable elements are DNA segments capable of changing location in plant and animal chromosomes. They are present in genomes, the genetic material of almost all living organisms. In plants, they account for from 10% to over 90% of the genome. Transposable elements have been studied extensively for several plants, but not carrots. In this study, we investigated one family of carrot transposable elements called Stowaway-like elements. We estimated the number of copies of these elements in carrot chromosomes and their chromosomal locations. Results suggested possible functions of these elements in regulating the action of genes, based on their location. This study is of interest to biologists, geneticists, plant scientists, plant breeders, and seed companies.

Technical Abstract: We investigated nine families of Stowaway-like MITEs in the carrot genome, named DcSto1 to DcSto9. All of them were AT-rich and shared a highly conserved 6 bp-long TIR typical for Stowaways. The copy number of DcSto1 elements was estimated as ca. 5,000 per diploid genome. We observed preference for clustered insertions of DcSto and other MITEs. Distribution of DcSto1 hybridization signals revealed presence of DcSto1 clusters within euchromatic regions along all chromosomes. An arrangement of eight regions encompassing DcSto insertion sites, studied in detail, was highly variable among plants representing different populations of Daucus carota. All of these insertions were polymorphic which most likely suggests a very recent mobilization of those elements. Insertions of DcSto near carrot genes and presence of putative promoters, regulatory motifs, and polyA signals within their sequences might suggest a possible involvement of DcSto in the regulation of gene expression.

Last Modified: 8/22/2014
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