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Title: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

item ARBIZU, CARLOS - University Of Wisconsin
item ELLISON, SHELBY - University Of Wisconsin
item Senalik, Douglas
item Simon, Philipp
item Spooner, David

Submitted to: BMC Evolutionary Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2016
Publication Date: 10/28/2016
Publication URL:
Citation: Arbizu, C.I., Ellison, S.L., Senalik, D., Simon, P.W., Spooner, D.M. 2016. Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae). BMC Evolutionary Biology. 16(1):234. doi: 10.1186/s12862-016-0806-x.

Interpretive Summary: Cultivated carrot, Daucus carota, has a wild species relative of the same name. Wild Daucus carota grows worldwide, but its taxonomic classification is unresolved. This study uses a new and powerful molecular method, called Genotyping by Sequencing (GBS) to investigate the taxonomy of wild forms of Daucus carota, as well as very closely related wild species related to it, with 162 accessions obtained from the US germplasm collection of Daucus. To obtained a total of 10,814 data points (DNA characters). Consistent with prior results from prior studies, all accessions of D. carota grouped together apart from other Daucus species, but unlike prior studies it separated the subspecies of D. carota into geographically-defined regions, showing the power of this technique to understand the taxonomy of Daucus carota. Our study shows, for the first time, the utility of this new molecular technique that is being investigated further to investigate a broader array of collections of Daucus carota. The results will help advise breeders and other users of the Daucus collection on natural groups of germplasm to choose for carrot improvement programs.

Technical Abstract: Premise of study: Premise of study: The taxonomic classification of the subspecies of Daucus carota is unresolved. Intercrosses among traditionally recognized subspecies has been well-documented, as have intercrosses with other Daucus species containing 2n = 18 chromosomes (D. sahariensis and D. syrticus). A previous study using 94 nuclear orthologs and another study using morphology were unable to clearly distinguish the subspecies of D. carota. In this study we explore the utility of a large number of single nucleotide polymorphism (SNP) markers to infer the phylogeny of the subspecies of D. carota. Methods: We used genotyping-by-sequencing (GBS) to obtain SNPs covering all nine Daucus chromosomes. We examined 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 SNPs with a maximum of 10% missing rate; and to classify the subspecies of Daucus, we employed two data sets containing 144 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) missing data of 30% totaling 43,713 SNPs. Missing data were imputed using Beagle software. Key results: Consistent with prior results, the topology of both data sets separated the 2n = 18 chromosome species from all other species examined. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade, but in contrast to a recent study using 3,326 transcriptomic SNPs generated by KASPar genotyping; our study places the wild members of D. carota from Central Asia together with eastern members of subsp. sativus, but does not recover a subsp. sativus monophyletic clade with other subspecies of D. carota as a sister clade. Rather, the other subspecies of D. carota were clustered into four geographic groups as follows: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Conclusions: Our study, combined with prior morphological data, suggests that (1) the morphotypes identified as D. carota subspecies gummifer are all confined to areas near the Atlantic and Mediterranean Oceans, and have separate origins from geographically contiguous members of other subspecies of D. carota, (2) indicates that the eastern cultivated carrots have origins from wild carrots from central Asia, and (3) large SNP data sets are suitable for low-level phylogenetic studies.