Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0806-x) contains supplementary material, which is available to authorized users.
Highlights
The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and their phylogeny and classification remains unresolved
Phylogeny inference The maximum likelihood (ML) phylogenetic reconstruction of Daucus with 10 or 30% missing imputed genotypes allowed us to determine the outgroup of the D. carota complex to be D. syrticus (Additional file 3: Figure S1 and Additional file 4: Figure S2), fully in agreement with prior molecular studies in Daucus [27, 35, 36, 88,89,90]
Maximum likelihood trees show that species Rouya polygama is placed within a monophyletic Daucus clade and is sister to a clade formed by the D. carota complex, and D. syrticus
Summary
The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and their phylogeny and classification remains unresolved. 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. More than 60 species have been proposed for the phenotypic variants observed within the D. carota complex [3]. 11 wild subspecies were recognized by Heywood [2, 17], five by Arenas and García-Martin [18], and five in the latest comprehensive morphoanatomical classification of Daucus by Sáenz [1] Pujadas Salvà [19] proposed nine subspecies for the Iberian Peninsula plus Balearic Islands Pujadas Salvà [19] proposed nine subspecies for the Iberian Peninsula plus Balearic Islands (subsp. carota, subsp. cantabricus, subsp. commutatus, subsp. gummifer, subsp. halophilus, subsp. hispanicus, subsp. majoricus, subsp. maximus, and subsp. sativus)
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call