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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Characterization, Taxonomy, and Acquisition of Genetic Resources for Carrot, Potato, and Their Related Wild Species

Location: Vegetable Crops Research Unit

Title: Integrated molecular and morphological studies of Daucus

Authors
item Arbizu, Carlos -
item Ruess, Holly
item Senalik, Douglas
item Simon, Philipp
item Spooner, David

Submitted to: Botany
Publication Type: Abstract Only
Publication Acceptance Date: April 15, 2014
Publication Date: July 26, 2014
Citation: Arbizu, C., Ruess, H.M., Senalik, D.A., Simon, P.W., Spooner, D.M. 2014. Integrated molecular and morphological studies of Daucus [abstract]. Botany. Paper No. 172.

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.

Last Modified: 11/21/2014
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