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

Alicja Macko-Podgórni; Massimo Iorizzo; Krzysztof Smółka; Philipp W Simon; Dariusz Grzebelus

doi:10.18388/abp.2014_1917

Alicja Macko-Podgórni Institute of Plant Biology and Biotechnology, University of Agriculture Krakow, Kraków, Poland.;
Massimo Iorizzo Department of Horticulture, University of Wisconsin-Madison, Madison, USA.;
Krzysztof Smółka Institute of Plant Biology and Biotechnology, University of Agriculture Krakow, Kraków, Poland.;
Philipp W Simon Department of Horticulture, University of Wisconsin-Madison, Madison, USA and USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, Madison, USA.;
Dariusz Grzebelus Institute of Plant Biology and Biotechnology, University of Agriculture Krakow, Kraków, Poland.;

DOI: https://doi.org/10.18388/abp.2014_1917

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 understood. 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 these polymorphisms, showing the strongest evidence for directional selection in the course of domestication, and converted it into a co-dominant 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.