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Title: Conversion of a diversity arrays technology marker differentiating wild and cultivated carrots to a co-dominant cleaved amplified polymorphic site marker

Author
item MACKO-PODGORNI, ALICJA - Agricultural University Of Poland
item IORIZZO, MASSIMO - University Of Wisconsin
item SMOLKA, KRYSZTOF - Agricultural University Of Poland
item Simon, Philipp
item GRZEBELUS, DARIUSZ - Agricultural University Of Poland

Submitted to: Acta Biochimica Polonica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2014
Publication Date: 3/17/2014
Publication URL: http://handle.nal.usda.gov/10113/60221
Citation: Macko-Podgorni, A., Iorizzo, M., Smolka, K., Simon, P.W., Grzebelus, D. 2014. Conversion of a diversity arrays technology marker differentiating wild and cultivated carrots to a co-dominant cleaved amplified polymorphic site marker. Acta Biochimica Polonica. 61(1):19-22.

Interpretive Summary: DNA-based molecular markers are useful in identifying genes involved in traits important in health, agriculture, and evolution. In this study, a large number of DNA-based markers called DArTs was used to evaluate DNA of a collection of cultivated carrots, and a collection of wild carrots, which is the same species of cultivated carrots. Evaluation of these markers demonstrated that one DArT marker, referred to as cult, was nearly completely associated with cultivated carrots, but never in wild carrots. This suggests that the cult gene, or another gene close to it on the same chromosome, accounts for some of the genetic differences between wild and cultivated carrots. This research is of interest to carrot researchers and botanists.

Technical Abstract: Cultivated carrot and its wild ancestor co-occur in most temperate regions of the world and can easily hybridize. The genetic basis of the process of domestication in carrot is not well recognized. Recent results of an investigation on genetic diversity structure of cultivated and wild carrot and signatures for domestication using Diversity Arrays Technology (DArT) allowed identification of polymorphisms differentiating wild and cultivated accessions. We selected one of those polymorphisms, showing the strongest evidence for directional selection in the course of domestication, and converted it into a codominant cleaved amplified polymorphic site (CAPS) marker named cult. To achieve that, we designed site-specific primers anchored in sequences flanking the original DArT clone, amplified and sequenced the PCR products derived from cultivated and wild carrot. A PstI restriction site present in the ‘cultivated’ variant and absent in the ‘wild’ was subsequently used for routine differentiation the two variants. We validated the cult marker on 88 accessions of cultivated and wild carrot, each represented by five individuals. The allelic variant associated with the wild phenotype was only rarely observed in cultivated carrot, mostly in purple-rooted accessions originating Turkey and Iran, possibly indicating that the physical association between the diagnostic polymorphism and the putative ‘domestication gene’ has been broken in a group of Eastern carrots.