Examinando por Materia "Daucus"

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Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae)
(TUBITAK, 2022-04-25) Yildiz, Mehtap; Arbizu Berrocal, Carlos Irvin
Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon markers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The manual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and a principal coordinate analysis (PCoA) indicated the presence of four clusters. The Daucus species with 2n = 18 chromosome (subclade A´) separated from the other two species D. pusillus and D. muricatus, which were positioned into two individual clusters. The other clade includes the Daucus from the B group. It was also noticed that few accessions were intermixed amongst clusters. Different genetic diversity parameters were estimated based on the four clusters (populations) defined by STRUCTURE software, demonstrating that clusters 3 and 4 possessed the lowest and highest diversity values, respectively. AMOVA showed variation between and within clusters of 41.85% and 58.15%, respectively. The highest population divergence (Fst) was observed between clusters 2 and 3 (0.579), on the other hand, clusters 1 and 4 depicted the lowest Fst with 0.160. Our research highlighted that iPBS markers were successful and effective to study Daucus genetic diversity. These results will contribute to the genetic improvement of carrots and sustainable management of its diversity.
Morphometrics of Daucus (Apiaceae): A counterpart to a phylogenomic study
(John Wiley & Sons, 2014-11-01) Arbizu Berrocal, Carlos Irvin; Reitsma, Kathleen R.; Simon, Philipp W.; Spooner, David M.
•Premise of study: Molecular phylogenetics of genome‐scale data sets (phylogenomics) often produces phylogenetic trees with unprecedented resolution. A companion phylogenomics analysis of Daucus using 94 conserved nuclear orthologs supported many of the traditional species but showed unexpected results that require morphological analyses to help interpret them in a practical taxonomic context. •Methods: We evaluated character state distributions, stepwise discriminant analyses, canonical variate analyses, and hierarchical cluster analyses from 40 morphological characters from 81 accessions of 14 taxa of Daucus and eight species in related genera in an experimental plot. •Key results: Most characters showed tremendous variation with character state overlap across many taxa. Multivariate analyses separated the outgroup taxa easily from the Daucus ingroup. Concordant with molecular analyses, most species form phenetic groups, except the same taxa that are problematical in the molecular results: (1) the subspecies of D. carota, (2) D. sahariensis and D. syrticus, and (3) D. broteri and D. guttatus. •Conclusions: Phenetic analyses, in combination with molecular data, support many Daucus species, but mostly by overlapping ranges of size and meristic variation. The subspecies of D. carota are poorly separated morphologically, are paraphyletic, and all could be recognized at the subspecies rank under D. carota. Daucus sahariensis and D. syrticus are so similar morphologically that they could be placed in synonymy. Combined molecular and morphological data support three species in accessions previously identified as D. broteri and D. guttatus. Molecular and morphological results support the new combination Daucus carota subsp. capillifolius.
Phylogenetic Prediction of Alternaria Leaf Blight Resistance in Wild and Cultivated Species of Carrots
(John Wiley & Sons, 2017-09-14) Arbizu Berrocal, Carlos Irvin; Tas, Pamela M.; Simon, Philipp W.; Spooner, David M.
Plant scientists make inferences and predictions from phylogenetic trees to solve scientific problems. Crop losses due to disease damage is an important problem that many plant breeders would like to solve, so the ability to predict traits like disease resistance from phylogenetic trees derived from diverse germplasm would be a significant approach to facilitate cultivar improvement. Alternaria leaf blight (ALB) is among the most devastating diseases of carrots (Daucus spp., Apiaceae) worldwide. Thus, new approaches to identify resistant germplasm to this disease are needed. In a study of 106 accessions of wild and cultivated Daucus and related genera, we determined plant height is the best explanatory variable to predict ALB resistance using a phylogenetic linear regression model. Using the estimated area under the disease progress curve, the most resistant species to ALB were the non-carrot relative Ammi visnaga (L.) Lam. and the wild carrot relative D. crinitus Desf. A permutation tail probability test was conducted considering phylogenetic signal to evaluate the strength of association between the Daucus phylogeny and ALB resistance. We found that species belonging to clade A, which includes carrots and other Daucus possessing 2n = 18, 20, or 22 chromosomes, are slightly more resistant to ALB than members of other clades of the Daucus phylogeny.
Phylogenomics of the Carrot Genus (Daucus, Apiaceae)
(John Wiley & Sons, 2014-10-01) Arbizu Berrocal, Carlos Irvin; Ruess, Holly; Senalik, Douglas; Simon, Philipp W.; Spooner, David M.
•Premise of the study: We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species. •Methods: We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; the use of all 94 markers vs. a reduced subset of markers; and analysis of a concatenated data set vs. a coalescent (species tree) approach. •Key results: Our maximum parsimony and maximum likelihood trees were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They resolved multiple accessions of many different species as monophyletic with strong support, but failed to support other species. The single allele analysis gave slightly better topological resolution; trimming homopolymers failed to increase taxonomic resolution; the exonic data had a smaller proportion of parsimony‐informative characters. Similar results demonstrating the same dominant topology can be obtained with many fewer markers. A Bayesian concordance analysis provided an overall similar phylogeny, but the coalescent analysis provided drastic changes in topology to all the above. •Conclusions: Our research highlights some difficult species groups in Daucus and misidentifications in germplasm collections. It highlights a useful subset of markers and approaches for future studies of dominant topologies in Daucus.