36th International Carrot Conference Abstract

Class II transposon insertion profiling differentiates cultivated carrots of various origin

Anna Nowicka, Alicja Macko-Podgórni, Ewa Grzebelus, Dariusz Grzebelus

Department of Genetics, Plant Breeding and Seed Science, University of Agriculture in Krakow, Poland

Transposable Elements (TEs) are DNA segments able to change their genomic localization. Miniature Inverted-Repeat Transposable Elements (MITEs) are small (>600bp) non-autonomous Class II mobile elements abundant in plant genomes. They are AT-rich, show potential to form secondary structures and frequently insert within gene-rich regions. These characteristics and a high level of intraspecific insertion polymorphism make MITEs a good source of molecular markers. Recently, we developed a robust and efficient Transposon Display system for carrot based on MITE insertion polymorphisms. Here, we applied that system for the identification of insertion polymorphisms of two MITE families, i.e. Krak and DcSto1. We investigated genomic distribution of these elements in 12 populations of cultivated carrots of various origin, each population being represented by one or two plants. We identified 246 and 243 insertion sites for Krak and DcSto1, respectively, of which 232 and 230 were polymorphic. For both families, we observed high levels of diversity and different patterns of MITE insertions, which could be in part attributed to their geographic origin. The populations could have been divided into three groups: (I) a group of cultivars and landraces of different origin, (II) cultivars ‘Balady’ and ‘Habitch’ from Egypt and Iran, respectively, and (III) landraces T-29 and ‘Red Carrot’ from Pakistan and Egypt, respectively, pointing at a possible higher diversity of cultivated carrots in the Mediterranean/Middle East region. In addition, we studied genomic distribution of MITEs using fluorescence in situ hybridization (FISH), which indicated that they were scattered on chromosome arms and mostly absent in pericentromeric and centromeric regions, while no clear differences in the abundance of hybridization signals could be seen, meaning that the differences of insertion patterns were of qualitative rather than quantitative nature.

Last updated Thursday, 25-Jul-2013 11:53:49 CDT