Extended studies of interspecific relationships of Daucus using DNA sequences from ten nuclear orthologs

Authors: FERNANDO MARTÍNEZ, FLORES - Universidad De Alicante; CRESPO, MANUEL - Universidad De Alicante; GEOFFRIAU, EMMANUEL - Institute Research Horticulture Seeds; ALLENDER, CHARLOTTE - University Of Warwick; Ruess, Holly; Simon, Philipp; Spooner, David

Submitted to: Botanical Journal of the Linnean Society
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2019
Publication Date: 11/25/2019
Citation: Fernando Martínez, F., Crespo, M.B., Geoffriau, E., Allender, C., Ruess, H.M., Simon, P.W., Spooner, D.M. 2019. Extended studies of interspecific relationships of Daucus using DNA sequences from ten nuclear orthologs. Botanical Journal of the Linnean Society. 164-187. https://doi.org/10.1093/botlinnean/boz042.
DOI: https://doi.org/10.1093/botlinnean/boz042

Interpretive Summary: Wild and cultivated carrots technically belong to the genus Daucus. There are about 25-40 species of wild carrots, depending on the classification, and they all have potential value as breeding stock to improve the cultivated carrot crop. This internationally collaborative study obtained DNA data of the nuclear genome to provide information about the relationships of wild and cultivated carrots, using a large collection of different species gathered from genebanks in England, France, and recent expeditions to Spain, where many wild carrots are native. The data results provide new information about wild carrot relationships, including new knowledge of the hybrid nature of one of the species, and knowledge of how one of the species is really two species. This new knowledge of the relationships of members of the genus Daucus provide carrot breeders with guideposts about Daucus species to use in their carrot breeding programs.

Technical Abstract: The genus Daucus traditionally has been estimated to contain 21-25 species, but a recent molecular study has expanded the genus to now contain about 40 species. This study uses ten nuclear orthologs that were recently chosen in Daucus to be efficient at the genus level. The focus of the present study is to expand recent studies using these nuclear orthologs, and other molecular markers, to study the interspecific relationships of Daucus, using 40 new collections, gathered from genebanks in England, France, and recent expeditions to Spain. Newly examined taxa using these 10 nuclear orthologs are D. arcanus, D. durieua, D. gracilis, D. montanus, D. setifolius, Melanoselinum decipiens, Monizia edulis, Pseudorlaya miniscula, Pseudorlaya pumila, Tornabena annua, and T. tenuissima. Due to the difficulty of making a concatenated data matrix of unlinked genes exhibiting allelic variants, we separated the data into two sets, A and B, randomly chosen to use in a concatenated matrix and then examined each of these separately. The trees were extremely similar, except for D. montanus that in one set resolved in a clade with D. pusillus, and in another with D. glochidiatus. Hence, we examined each of the ten alleles separately for each set (20 analyses in total), Relative to prior studies using these markers, D. arcanus is sister to D. pusillus, D. durieua to D. guttatus, D. gracilis, Tornabena annua, and T. tenuissima (along with D. syrticus) sister to D. carota, Melanoselinum decipiens and Monizia edulis sister to each other and these to a clade containing Pseudorlaya miniscula, P. pumila, and other species containing 2n = 18 chromosomes, and D. setifolius to D. crinitus. Daucus montanus (a hexaploid) is an allopolyploid between D. pusillus and D. glochidiatus.