Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) Arbizu, CI es_PE Ellison, SL es_PE Senalik, D es_PE Simon, PW es_PE Spooner, DM es_PE 2024-05-30T23:13:38Z 2024-05-30T23:13:38Z 2016
dc.description This work is supported by the USDA Agricultural Research Service. C. Arbizu is partly funded by the National Council of Science and Technology of Perú (Concytec).
dc.description.abstract Background. The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex. Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (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. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.
dc.description.sponsorship Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - Concytec
dc.identifier.isi 386313500002
dc.language.iso eng
dc.publisher BMC
dc.relation.ispartof BMC Evolutionary Biology
dc.rights info:eu-repo/semantics/openAccess
dc.subject Single nucleotide polymorphisms (SNPs)
dc.subject Carrot es_PE
dc.subject Daucus carota es_PE
dc.subject Genotyping-by-sequencing (GBS) es_PE
dc.subject Phylogeny es_PE
dc.title Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)
dc.type info:eu-repo/semantics/article