Integrated molecular and morphological studies of Daucus

Authors: ATBIZU, C - University Of Wisconsin; Ruess, Holly; Senalik, Douglas; IORIZZO, M - University Of Wisconsin; Simon, Philipp; Spooner, David; REITSMA, K - Iowa State University

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/23/2015
Publication Date: 3/10/2017
Publication URL: http://handle.nal.usda.gov/10113/5695305
Citation: Atbizu, C.I., Ruess, H., Senalik, D., Iorizzo, M., Simon, P.W., Spooner, D.M., Reitsma, K. 2017. Integrated molecular and morphological studies of Daucus. Acta Horticulturae. 1153:265-271. doi: 10.17660/ActaHortic.2017.1153.39.

Interpretive Summary: Cultivated carrot is technically referred to by its formal scientific name Daucus carota. There are about 25 additional non-cultivated (wild) species in the genus Daucus. This paper summarizes published work on the taxonomy (determining how many species there are in a group and how they are related to each other) in the genus Daucus. We focus on two recent studies, one using DNA sequences of 94 genes from 89 separate collections of 13 species in the genus Daucus, and a second examining the same collections but examining the outward form of the plant (morphology). The DNA study was the largest of its kind in both the quantity and quality of data and the number of collections examined. It groups many of the different collections of the same species together and shows how they species are related to each other. The morphological study can distinguish most of these species, but shows how they are very similar by outward form. In a few species neither the DNA nor morphological data can distinguish the species, and we suspect this is because the taxonomy of these species is poorly determined. Our research also discovered misidentifications in some of the collections. These two coordinated studies show a useful subset of DNA and morphological data that are best to distinguish these Daucus species and point the need for larger studies needed to help define the difficult species. These data are needed to understand the species boundaries of the world’s collections of wild and cultivated carrot, which ultimately will better allow genebank managers and carrot breeders how to organize and use these collections.

Technical Abstract: Ninety-four nuclear orthologs were used to analyze phylogenetic structure in 89 accessions of 13 species and two subspecies of Daucus, and an additional ten accessions of related genera. A near parallel set of accessions were used for morphological analyses of germplasm planted in a common garden in Ames, Iowa. For DNA we analyzed 1) both alleles using ambiguity codes vs. a single allele with the highest coverage; 2) trimmed vs. untrimmed homopolymers; 3) pure exonic vs. pure intronic data; and 4) the use of all 94 markers vs. a reduced subset of markers. Morphological analyses included character state distributions, stepwise discriminant analyses, canonical variants analyses, and hierarchical cluster analyses. Our maximum parsimony and maximum likelihood DNA trees are highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They grouped multiple accessions of many different species as monophyletic with strong support, but failed to support some other taxa. The single allele analysis gave slightly better topological resolution in some clades, and is a logically more defendable analysis. Trimming homopolymers provided potentially more reliable data, but failed to increase taxonomic resolution. The pure exonic data, as expected, had a smaller proportion of parsimony-informative characters as compared to the pure intronic data. Similar phylogenetic results demonstrating the same dominant topology can be obtained with many fewer markers. Molecular and morphological analyses separated the outgroup taxa easily from the Daucus ingroup but, concordant with prior analyses, DNA data included Margotia gummifera and Pseudorlaya pumila as ingroup. Concordant with molecular analyses, most species form phenetic groups, but problems are shown in the recognition of 1) the subspecies of D. carota and D. capillifolius; 2) D. sahariensis and D. syrticus; and 3) D. broteri and D. guttatus. The status of D. broteri and D. guttatus is unresolved, with the present data supporting three taxa. Phenetic analyses, in combination with molecular data, support many other Daucus species. Our research highlights some difficult species groups in Daucus, and discovered misidentifications in germplasm collections. It highlights a useful subset of nuclear orthologs and methodological approaches for future studies of dominant topologies in Daucus, saving time and resources.