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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: Development of EST based markers for exploiting the carrot genome

Authors
item Iorizzo, Massimo -
item Bowman, Megan -
item SIMON, PHILIPP
item Cavagnaro, Pablo -
item SENALIK, DOUGLAS
item Carputo, Domenico -
item Van Deynze, Allen -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 8, 2010
Publication Date: January 15, 2011
Citation: Iorizzo, M., Bowman, M., Simon, P.W., Cavagnaro, P., Senalik, D.A., Carputo, D., Van Deynze, A. 2011. Development of EST based markers for exploiting the carrot genome [abstract]. Plant and Animal Genome Conference. p. 175.

Technical Abstract: Carrot is the most economically important member of the Apiaceae family and a major source of provitamin A in the human diet. Breeding and genetic studies are ongoing to improve quantitative and qualitative traits. However, carrot molecular resources are relatively underdeveloped, hampering progress in genetic studies. Recently, a next generation sequence approach was used to develop the first extensive carrot Expressed Sequence Tag (EST) collection. Here we report the development and evaluation of EST based SNP and SSR markers. Computational analyses of EST sequences provided the identity of about 23,000 SNP and 8,700 SSR candidate markers. About 80% of SNP mutations were transitions. Trinucleotide repeats were the most abundant class of SSR motifs in carrot ESTs. A set of 354 SNP and 200 SSR primer pairs were tested, with 212 SNP and 110 SSR markers verified as having the expected sequence. Screening of verified SNP markers within two mapping populations identified 70 segregating markers. Mapping of SNPs and testing of SSR markers within F2 mapping populations is ongoing. The F2 segregating SSR and SNP markers derived from EST sequences will be placed on genetic linkage maps allowing the development of the first carrot EST based genetic map and integration of previously constructed maps.

Last Modified: 7/28/2014
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