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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY Title: Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.)

Authors
item Iorizzo, Masssimo -
item Senalik, Douglas
item Ellison, Shelby -
item Grzebelus, Dariusz -
item Cavagnaro, Pablo -
item Spooner, David
item Van Deynze, Allen -
item Simon, Philipp

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 13, 2012
Publication Date: January 14, 2013
Citation: Iorizzo, M., Senalik, D.A., Ellison, S.L., Grzebelus, D., Cavagnaro, P., Spooner, D.M., Van Deynze, A., Simon, P.W. 2013. Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.) [abstract]. Plant and Animal Genome Conference. Paper No. P0762.

Technical Abstract: The rapid advancement in high-throughput SNP genotyping technologies along with next generation sequencing (NGS) platforms has decreased the cost, improved the quality of large-scale genome surveys, and allowed specialty crops with limited genomic resources such as carrot (Daucus carota) to access these technologies. Here, we designed 4,000 Single Nucleotide Polymorphisms markers (SNPs) from carrot transcriptome sequences data to characterize the genetic diversity in a geographically well dispersed subset of wild and cultivated carrots using the Kbioscience (Hoddesdon, England) platform. Overall, 3636 SNPs (91%) produced distinct genotypic clusters. Preliminary structure analysis indicated a clear separation between wild and cultivated accessions. Phylogenetic analysis is ongoing. Evaluation of seven mapping populations revealed that the rate of polymorphism ranged from 24.9% to 47.9%. Marker analyses in three segregating populations allowed us to map 1,242 SNPs. Analysis of mapping data along with phenotypic data are ongoing. This study provides the first genome wide molecular characterization of genetic diversity in carrot. In addition, mapped traits of agronomic interest will provide a framework for the upcoming carrot genome sequence analysis.

Last Modified: 10/24/2014
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