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Crop wild relatives, the wild progenitors and closely related cousins of cultivated plant species, are sources of valuable genetic resources for crop improvement. Persisting gaps in knowledge of taxonomy, distributions, and characterization for traits of interest constrain their expanded use in plant breeding and likewise negatively affect ex situ (in genebanks) and in situ (in natural habitats) conservation planning. We compile the state of knowledge on the taxonomy and distributions of the wild relatives of carrot (genus Daucus L.) natively occurring within Tunisia—a hotspot of diversity of the genus, containing 13 taxa (27% of species worldwide). We use ecogeographic information to characterize their potential adaptations to abiotic stresses of interest in crop breeding and assess their ex situ and in situ conservation status. We find substantial ecogeographic variation both across taxa and between populations within taxa, with regard to adaptation to high temperatures, low precipitation, and other traits of potential interest. We categorize three of the taxa high priority for further conservation both ex situ and in situ, five medium priority, and five low priority, with none currently considered sufficiently conserved. Geographic hotspots for species diversity, especially in the northern coastal areas, represent particularly high value regions for efficient further collecting for ex situ conservation and for in situ protection in Tunisia. [ABSTRACT FROM AUTHOR]

Daucus has traditionally been estimated to comprise 21–25 species, but a recent study expanded the genus to c. 40 species. The present study uses ten nuclear orthologues to examine 125 accessions, including 40 collections of 11 species (D. annuus , D. arcanus , D. decipiens , D. durieua , D. edulis , D. gracilis , D. minusculus , D. montanus , D. pumilus , D. setifolius and D. tenuissimus) newly examined with nuclear orthologues. As in previous nuclear orthologue studies, Daucus resolves into two well-defined clades, and groups different accessions of species together. Maximum likelihood and maximum parsimony analyses provide concordant results, but SVD quartets reveals many areas of disagreement of species within these two major clades. With maximum likelihood and maximum parsimony analyses Daucus montanus (hexaploid) is resolved as an allopolyploid between D. pusillus (diploid) and D. glochidiatus (tetraploid), whereas with SVD quartets it is resolved as an allopolyploid between D. glochidiatus and an unknown Daucus sp. We propose the new combination Daucus junceus (Durieua juncea) for a neglected species endemic to the south-western Iberian Peninsula often referred to as D. setifolius , and we place D. arcanus in synonymy with D. pusillus. Three lectotypes are also designated. [ABSTRACT FROM AUTHOR]

Tunisia, other countries in northwestern Africa, and the Iberian Peninsula, represent a center of diversity of Daucus. The genus traditionally has included about 20-25 species worldwide, but a recent molecular study redefined and expanded Daucus to include representatives from nine other genera. By this classification, Daucus now contains about 40 species, with some of them having winged fruits in addition to its traditionally recognized spiny fruits. The taxonomy of Daucus in Tunisia has recently been studied with morphological data, concluding that D. carota subsp. capillifolius is a subspecies that co-occurs and crosses with subsp. carota. The present study extends these findings with additional data from Genotyping-by-Sequencing (GBS) from 33 Tunisian accessions of D. carota (93 individuals with two to three replicates per accession), including the first collections of subsp. gummifer from Tunisia. Placed in the context of additional GBS data, D. carota subsp. gummifer has separate origins from other collections of subsp. carota in Tunisia and/or immediately adjacent areas to the north in Italy or its surrounding islands. Our results add support to the utility of large SNP datasets for species-level phylogenetic studies in Daucus. [ABSTRACT FROM AUTHOR]

* 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. [ABSTRACT FROM AUTHOR]

• 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. [ABSTRACT FROM AUTHOR]

Chromosome pairing relationships within cultivated potato (Solonum tuberosum) and its wild tuber-bearing relatives (Solanum sect. Petota) hove been interpreted by genome formulas, developed in the early 1900s, through techniques of classic meiotic analysis of interspecific hybrids. Here we reexamine potato genome hypotheses with the first phylogenetic analysis of all major genomes of sect. Petota using cloned DNA sequences of the single-copy nuclear gene GBSSI (waxy). Our results provide the first molecular confirmation of allopolyploidy in wild potato. They both support prior hypotheses and identify novel genome origins never before proposed. The data will be useful to help design crossing strategies to incorporate wild species germplasm into cultivated potato. [ABSTRACT FROM AUTHOR]

The use of genetic resources could be more effective and efficient if we were able to predict the presence or absence of useful traits in different populations or accessions. We analyzed the extent to which taxonomic, geographic and ecological factors can predict the presence of frost tolerance in wild potatoes. We used screening data for 1646 samples from 87 species that had been collected in 12 countries in the Americas. There was a strong association of frost tolerance with species and to a lesser extent with taxonomic series. There was significant geographic clustering of areas with wild potatoes with similar levels of frost tolerance. Areas with a high level of frost tolerance are the central and southern Peruvian Andes, the lowlands of Argentina and adjacent areas, and a small area in the central Chilean Andes. There is a greater chance of finding wild potatoes with high levels of frost tolerance in areas with a yearly mean minimum temperature below 3 °C than there is in warmer areas. However, temperature is only a weak predictor of frost tolerance. Temperature data alone did not predict observed frost tolerance in eastern Argentina/Uruguay and falsely predicted it in the southwestern United States. Because many wild potato species occur over small areas, taxonomic, ecological, and geographical factors are difficult to disentangle. [ABSTRACT FROM AUTHOR]

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The article discusses the authors' breeding research in potato which revealed unexpected result that led them to question the value of morphological diversity as a proxy for overall genetic diversity. Topics discussed include the evaluation of the F2 population for several morphological features such as tuber size, shape and eye depth and the dilemma from the study presented for managers of germplasm collections.