Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

Authors: GRZEBELUS, DARIUSZ - University Of Krakow; IORIZZO, MASSIMO - University Of Wisconsin; Senalik, Douglas; ELLISON, SHELBY - University Of Wisconsin; CAVAGNARO, PABLO - Consejo Nacional De Investigaciones Científicas Y Técnicas(CONICET); MACKO-PODGORNI, ALICJA - University Of Krakow; HELLER-USZYNSKA, KASIA - Diversity Arrays Technology; KILIAN, ANDRZEJ - Diversity Arrays Technology; NOTHNAGEL, THOMAS - Julius Kuhn Institute; ALLENDER, CHARLOTTE - University Of Warwick; Simon, Philipp; BARANSKI, RAFAL - University Of Krakow

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/18/2013
Publication Date: 3/1/2014
Publication URL: http://handle.nal.usda.gov/10113/58533
Citation: Grzebelus, D., Iorizzo, M., Senalik, D.A., Ellison, S., Cavagnaro, P., Macko-Podgorni, A., Heller-Uszynska, K., Kilian, A., Nothnagel, T., Allender, C., Simon, P.W., Baranski, R. 2014. Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers . Molecular Breeding. 33(3):625-637.

Interpretive Summary: Modern genetic analysis and improvement of crop plants relies upon DNA-based molecular markers. There are many types of molecular marker systems, and one that has become popular, because of its ease of use and low cost, is the Diversity Arrays Technology (DArT) marker system. DArT markers have not been developed and tested for carrot, and in this research we accomplished that. Molecular markers are used to assess genetic diversity or relatedness among geographically widespread individual, and the evaluation of DArT markers in this study demonstrated that they provide results similar to other types of molecular markers. Molecular markers are also used to develop genetic maps of chromosomes, and carrot DArT markers generate a carrot genetic map comparable to those of other molecular marker systems. Overall these results demonstrated that DArT markers are a useful addition to the collection of molecular marker systems available for carrot genetics and breeding, to complement other molecular marker systems already in place. This research is of interest to plant breeders and geneticists performing not only more fundamental research, but also breeders.

Technical Abstract: Carrot is one of the most economically important vegetables worldwide, however, genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to develop a saturated genetic linkage map of carrot. We analyzed a set of 900 DArT markers in a collection of plant materials comprising 94and 65 cultivated and wild carrot accessions, respectively. The accessions were attributed to three separate groups, i.e. wild, Eastern cultivated and Western cultivated. Twenty-seven markers showing signatures for selection were identified. They showed a directional shift in frequency from the wild to the cultivated, likely reflecting diversifying selection imposed in the course of domestication. A genetic linkage map constructed using 188 F2 plants comprised 431 markers with an average distance of 1.1 cM, divided into nine linkage groups. Using previously anchored SNPs, the linkage groups were physically attributed to the nine carrot chromosomes. A cluster of markers mapping to chromosome 8 showed significant segregation distortion. Two of the 27 DArT markers with signatures for selection were segregating in the mapping population and were localized on chromosomes 2 and 6. Chromosome 2 was previously shown to carry Vrn1 gene governing biennial growth habit essential for cultivated carrot. Results reported here provide background for further research on the history of carrot domestication and identify genomic regions potentially important for modern carrot breeding.