Subspecies variation of Daucus carota coastal (“gummifer”) morphotypes using genotyping-by-sequencing

Authors: FLORES, FERNANDO - Universidad De Alicante; CRESPO, MANUEL - Universidad De Alicante; Simon, Philipp; Ruess, Holly; REITSMA, KATHLEEN - Iowa State University; GEOFFRIAU, EMMANUEL - Agrocampus Ouest; ALLENDER, CHARLOTTE - University Of Warwick; MEZGHANI, NAJLA - Food And Agriculture Organization Of The United Nations (FAO); Spooner, David

Submitted to: Systematic Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2020
Publication Date: 8/11/2020
Citation: Flores, F.M., Crespo, M.B., Simon, P.W., Ruess, H.M., Reitsma, K., Geoffriau, E., Allender, C., Mezghani, N., Spooner, D.M. 2020. Subspecies variation of Daucus carota coastal (“gummifer”) morphotypes using genotyping-by-sequencing. Systematic Botany. Volume 45, Number 3, September 2020, pp. 688-702(15). https://doi.org/10.1600/036364420X15935294613527.
DOI: https://doi.org/10.1600/036364420X15935294613527

Interpretive Summary: The genus Daucus, wild and cultivated carrot, is widely distributed worldwide, but with a concentration of diversity in the Mediterranean Region. One of these Daucus species, Daucus carota, contains a group of subspecies called the Daucus carota gummifer complex, and there is widespread disagreement of how many subspecies it contains. We here study the gummifer complex in great detail, using 287 accessions of the gummifer complex and related subspecies from around the Mediterranean Region and worldwide, using a DNA technique called genotyping by sequencing. Members of the gummifer complex all occur in the Mediterranean Region and surrouding areas, are loosely morphologically similar sharing a relatively short stature, thick, broad, sometimes highly glossy leaf segments, and usually flat or convex fruiting umbels. These results support independent selection of the gummifer morphotypes in these narrowly restricted maritime environments, but from localized populations of other subspecies of Daucus carota subspecies carota or subspecies maximus. Daucus annuus (=Tornabenea annua) and Daucus tenuissimus (=Tornabenea tenuissima; Cape Verde) also fall firmly within Daucus carota, supporting their classification as morphologically well-defined variants of that species.

Technical Abstract: The genus Daucus is widely distributed worldwide, but with a concentration of diversity in the Mediterranean Region. The D. carota complex presents the greatest taxonomic problems in the genus. We focus on a distinctive phenotypic group of coastal morphotypes of D. carota, strictly confined to the margins to within about 1 km of the Mediterranean Sea and the Atlantic Ocean, which we here refer to as coastal morphotypes or D. carota subsp. “gummifer” complex, the earliest name for taxa in this group. They are loosely morphologically coherent, sharing a relatively short stature, thick, broad, sometimes highly glossy leaf segments, and usually flat or convex fruiting umbels. We analyzed 287 accessions, including 112 accessions not examined before, obtained from genebanks in England, France, and an expedition to Spain in 2017, covering the Mediterranean and Atlantic coasts and Balearic Islands, where much of the gummifer complex variation occurs. Genotyping-by-sequencing (GBS) identified 29,041 filtered SNPs. Maximum Likelihood and Structure analysis identified three main clades with subclades in clade 3-. The gummifer morphotypes are intercalated with members of Daucus carota subspecies carota and subspecies maximus in two of these main clades, including a clade containing accessions from Tunisia (also including subsp. D. carota subsp. capillifolius) and a clade containing accessions from western Europe, southern Europe and Balearic Islands, Iberian Peninsula and Morocco. These results support independent selection of the gummifer morphotypes in these narrowly restricted maritime environments. Daucus annuus (=Tornabenea annua) and Daucus tenuissimus (=Tornabenea tenuissima; Cape Verde) also fall firmly within Daucus carota, supporting their classification as morphologically well-defined variants of that species.