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—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.

The Potato Introduction Station in Sturgeon Bay Wisconsin has maintained herbarium specimens as part of its operations. These specimens mostly were grown from seeds in the field plots or greenhouses, but also include original specimens made during germplasm collecting expeditions. The herbarium of the Station (herbarium acronym PTIS) has been transferred from the potato genebank in Sturgeon Bay Wisconsin to the Wisconsin State Herbarium (acronym WIS) in Birge Hall, University of Wisconsin-Madison where it is now fully integrated and curated and funded by WIS; PTIS is discontinued and is no longer maintained as a separate herbarium. Separately, maps and taxonomic literature that were used by the potato taxonomist in Madison were transferred to the Potato Station in Sturgeon Bay.

24 Páginas 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. INTRODUCTION. MATERIAL AND METHODS. RESULTS. DISCUSSION. NOMENCLATURAL PROPOSALS. REFERENCES

—The genus Daucus is widely distributed worldwide, but with a concentration of diversity in the Mediterranean Region. The D. carota complex presents the greatest taxonomic problems in the genus. We focus on a distinctive phenotypic group of coastal morphotypes of D. carota, strictly confined to the margins to within about 0.5 km of the Mediterranean Sea and the Atlantic Ocean, which we here refer to as coastal morphotypes or D. carota subsp. “gummifer” complex. They are loosely morphologically coherent, sharing a relatively short stature, thick, broad, sometimes highly glossy leaf segments, and usually flat or convex fruiting umbels. We analyzed 288 accessions obtained from genebanks in England, France, and the USA, and an expedition to Spain in 2016, covering the Mediterranean and Atlantic coasts and Balearic Islands, where much of the gummifer complex variation occurs. Our study includes 112 accessions not examined before in this context. Genotyping-by-sequencing identified 29,041 filtered SNPs. Based on high bootstrap support from maximum likelihood and Structure analysis we highlight three main clades. The gummifer morphotypes are intercalated with members of Daucus carota subspecies carota and subspecies maximus in two of these main clades, including a clade containing accessions from Tunisia (also including D. carota subsp. capillifolius) and a clade containing accessions from western Europe (including the British Isles), southern Europe (including the Balearic Islands and the Iberian Peninsula) and Morocco. These results support five independent selections of the gummifer morphotypes in these restricted maritime environments in the Mediterranean and nearby Atlantic coasts. Daucus annuus (=Tornabenea annua) and Daucus tenuissimus (=Tornabenea tenuissima) also fall firmly within D. carota, supporting their classification as morphologically well-defined subspecies of D. carota, which are accepted here under the new combinations Daucus carota subsp. annuus and D. carota subsp. tenuissimus, respectively. Types are indicated for most of treated names, including designation of four lectotypes and three epitypes, which fix their further use.

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.

9 Páginas 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. INTRODUCTION. MATERIALS AND METHODS. RESULTS. DISCUSSION. References.

PREMISE OF THE STUDY We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences. METHODS We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP). KEY RESULTS Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations. CONCLUSIONS Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.

Our paper analyzes full plastid DNA sequence data of 202 wild and cultivated diploid potatoes, Solanum section Petota, to explore its phylogenetic utility compared to prior analyses of the same accessions using genome-wide nuclear SNPs, and plastid DNA restriction site data. The present plastid analysis discovered the same major clades as the nuclear data but with some substantial differences in topology within the clades. The considerably larger plastid and nuclear data sets add phylogenetic resolution within the prior plastid DNA restriction site data, highlight plastid/nuclear incongruence that supports hypotheses of hybridization/introgression to help explain the taxonomic difficulty in the section.

Cultivated carrot (Daucus carota subsp. sativus) is one of about 25–40 related wild species in the genus Daucus depending on the classification. It is part of a widely distributed and taxonomically complex family Apiaceae (Umbelliferae) containing 466 genera and 3820 species that is one of the largest families of seed plants. Members of the Apiaceae, particularly the genus Daucus, have been the subject of intensive recent molecular studies on the structure and genetics of plastids and mitochondria. This chapter summarizes organellar (plastids and mitochondria) structure, function, mutational rates, and inter-organelle DNA transfer in the Apiaceae and inheritance in the genus Daucus, with a wider focus on the Apiaceae and the sister family Araliaceae, and places these data in the context of other studies in the angiosperms.

Cultivated carrot (Daucus carota subsp. sativus) is the most important member in the Apiaceae family in terms of economy and nutrition and is considered the second most popular vegetable in the world after potato. Despite its global importance, the systematics of Daucus remains under active revision at the species, genus, and subtribal levels. The phylogenetic relationships among the species of Daucus and close relatives in the Apioideae have been clarified recently by a series of molecular studies using DNA sequences of the plastid genes rbcL and matK; plastid introns rpl16, rps16, rpoC1; nuclear ribosomal DNA internal transcribed spacer (ITS) sequences; and plastid DNA restriction sites. Of these DNA markers, the ITS region consisting of ITS1, the intervening spacer, and ITS2 has served as the main marker used. Recently, next-generation DNA sequencing methodologies have been used. We review these techniques and how they are impacting the taxonomy of the genus Daucus.

The third most important food crop worldwide, potato (Solanum tuberosum L.) is a tetraploid outcrossing species propagated from tubers. Breeders have long been challenged by polyploidy, heterozygosity, and asexual reproduction. It has been assumed that tetraploidy is essential for high yield, that the creation of inbred potato is not feasible, and that propagation by seed tubers is ideal. In this paper, we question those assumptions and propose to convert potato into a diploid inbred line–based crop propagated by true seed. Although a conversion of this magnitude is unprecedented, the possible genetic gains from a breeding system based on inbred lines and the seed production benefits from a sexual propagation system are too large to ignore. We call on leaders of public and private organizations to come together to explore the feasibility of this radical and exciting new strategy in potato breeding. S.H. Jansky, USDA–ARS Vegetable Crops Research Unit, Dep. of Horticulture, Univ. of Wisconsin, 1575 Linden Dr., Madison, WI; A.O. Charkowski, Dep. of Plant Pathology, Univ. of Wisconsin, Madison, WI; D.S. Douches, Dep. of Plant, Soil, and Microbial Sciences, Mich. State Univ., East Lansing, MI; G. Gusmini, Pepsico, St. Paul, MN; C. Richael, Simplot Plant Sciences, Boise, ID; P.C. Bethke and D.M. Spooner, USDA–ARS Vegetable Crops Research Unit, Dep. of Horticulture, Univ. of Wisconsin, Madison, WI; R.G. Novy, USDA– ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, ID; H. De Jong, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada (retired); W.S. De Jong, School of Integrative Plant Sciences, Cornell Univ., Ithaca, NY; J.B. Bamberg USDA–ARS, Dep. of Horticulture, Univ. of Wisconsin, Madison, WI, and US Potato Genebank, Sturgeon Bay, WI; A.L. Thompson, Dep. of Plant Sciences, North Dakota State Univ.; B. Bizimungu, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada; D.G. Holm, Dep. of Horticulture and Landscape Architecture, Colorado State Univ., San Luis Valley Research Center, Center, CO; C.R. Brown, USDA– ARS, Prosser, WA; K.G. Haynes, USDA–ARS, Beltsville, MD; V.R. Sathuvalli, Dep. of Crop and Soil Science, Oregon State Univ., Hermiston Agricultural Research and Extension Center, Hermiston, OR; R.E. Veilleux, Dep. of Horticulture, Virginia Tech, Blacksburg, VA; J.C. Miller, Jr., Dep. of Horticultural Sciences, Texas AM J.M. Bradeen, Dep. of Plant Pathology, Univ. of Minnesota, St. Paul, MN; J. Jiang, Dep. of Horticulture, Univ. of Wisconsin, Madison, WI. G. Gusmini is an employee of PepsiCo, Inc.; the views expressed in this presentation are those of the author and do not necessarily reflect the position or policy of PepsiCo Inc. C. Richael is an employee of Simplot Plant Sciences; the views expressed in this presentation are those of the author and do not necessarily reflect the position or policy of Simplot Plant Sciences. Received 3 Dec. 2015. Accepted 25 Jan. 2016. *Corresponding author (shelley.jansky@ars. usda.gov; shjansky@wisc.edu). Abbreviations: CIP, International Potato Center; ILs, introgression lines; RILs, recombinant inbred lines; TPS, true potato seed. Published in Crop Sci. 56:1412–1422 (2016). doi: 10.2135/cropsci2015.12.0740 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Published July 7, 2016

The Daucus guttatus complex includes two to four species growing from central and northern Italy to the Middle East. They are characterized by being typically annuals up to 50 cm high; with primary umbels up to 7 cm in diameter with fewer than 25(35) rays; discolored umbels frequent, bearing one to several dark colored umbellules which form different color patterns; and mericarps relatively small, ca. 2.0–4.5 mm. The taxonomy of this complicated group has not been satisfactorily resolved to date and is the focus of current research. Seven names of species belonging to the D. guttatus complex occurring in the central and eastern Mediterranean basin are typified here: Daucus guttatus, Daucus bicolor, Daucus involucratus, Daucus setulosus, Daucus broteri, Daucus hirsutus, and Daucus speciosus. Historical data are reported to justify lectotype and/or epitype selection, and selected morphological and distributional data are used to facilitate identification. The resulting typifications will enable pro...

In a previous study using 94 nuclear orthologs, we reported the species status of the Daucus guttatus complex to be unresolved, partitioned into three clades. In the present study, a subset of ten of these 94 orthologs was used to infer the phylogeny of the D. guttatus complex and related species. A near parallel set of accessions, planted in a common garden, was used for morphological analyses. The molecular trees are highly resolved for most of the clades, grouping accessions of the D. guttatus complex into four clades. Bayesian concordance analysis and a coalescent approach gave slightly different topologies. Morphological data likewise support four taxa in the complex. Moreover, herbarium research from a companion study informs nomenclature for taxa of the complex. We identify these four clades as D. bicolor, D. conchitae, D. guttatus, and D. setulosus; internested in or among these segregates are the phenetically distinctive species D. glochidiatus, D. involucratus, D. littoralis, and D. pus...

Solanum section Petota has been the subject of intensive taxonomic work since the description of the cultivated potato in 1753. In total, there are 494 epithets for wild taxa and 626 epithets for cultivated taxa. Different taxonomists applied various taxonomic philosophies and species concepts to the section. Hypotheses of the number of species and their interrelationships have differed greatly among authors. A taxonomic treatment of section Petota by Jack Hawkes in 1990 recognized 228 wild species and seven cultivated species, divided into 21 taxonomic series. In 2014 Spooner and collaborators more than halved this number to 107 wild species and four cultivated species, partitioned into four clades; not using series. The purpose of this paper is to provide a retrospective of the methods and philosophies that have resulted in this drastic decrease in the number of species and their infrasectional classification.

With ca. 200 species, the informally named Potato clade represents one of the larger subgroups of the estimated 1500 species of Solanum. Because its members include the potato (S. tuberosum), tomato (S. lycopersicum), and pepino (S. muri- catum), it is the most economically important clade in the genus. These crop species and their close relatives have been the focus of intensive research, but relationships among major lineages of the Potato clade remain poorly understood. In this study, we use sequences from the nuclear ITS and waxy (GBSSI), and plastid trnT-trnF and trnS-trnG to estimate a phylogeny and further explore relationships within the Potato clade. With increased sampling over past studies, the Potato clade emerges as a strongly supported clade and comprises 12-13 subclades which, for the most part, correspond to traditionally recognized sections. Solanum sect. Regmandra is sister to the rest of the lineages of the Potato clade which are, in turn, organized into two major subclades: (1) sections Anarrhichomenum, Articulatum, Basarthrum, Etuberosum, Juglandifolia, Lycopersicoides, Lycopersicon, and Petota, and (2) sections Herpystichum and Pteroidea. As in all other studies including these groups, sections Etuberosum, Juglandifolia, Lycopersicoides, Lycopersicon, and Petota form a strongly supported clade. Solanum oxycoccoides, a high-elevation species endemic to north-central Peru, was tentatively assigned to several groups within Solanum based on morphological evidence, but instead the species represents an independent lineage within the Potato clade, sister to the first major subclade. A key to the sections of the Potato clade is provided.

In a recent issue of PNAS, Hardigan et al. (1) state that the genetic diversity of the potato is much greater than that of other major crops, based on 68.9 million SNPs identified from the resequencing of 67 accessions of wild and cultivated potatoes. We questioned this conclusion based on our own original analysis of wild and cultivated potato species (2) and estimates of genomic SNPs in other major crops by next-generation resequencing with a few to 15 million SNPs. Examples include soybean (3), pigeon pea (4), cotton (5), tomato (6), and potato (2) (Table 1). To explore this further, we reanalyzed the raw data from ref. 1 using standard, stricter methods to filter SNPs … [↵][1]1To whom correspondence may be addressed. Email: binquan.huang{at}plants.ox.ac.uk, David.Spooner{at}ars.usda.gov, or liangqiqi{at}novogene.com. [1]: #xref-corresp-1-1

Wild potato species have substantial phenotypic and physiological diversity. Here, we report a comprehensive assessment of wild and cultivated potato species based on genomic analyses of 201 accessions of Solanum section Petota . We sequenced the genomes of these 201 accessions and identified 6 487 006 high-quality single nucleotide polymorphisms (SNPs) from 167 accessions in clade 4 of Solanum section Petota , including 146 wild and 21 cultivated diploid potato accessions with a broad geographic distribution. Genome-wide genetic variation analysis showed that the diversity of wild potatoes is higher than that of cultivated potatoes, and much higher genetic diversity in the agronomically important disease resistance genes was observed in wild potatoes. Furthermore, by exploiting information about known quantitative trait loci (QTL), we identified 609 genes under selection, including those correlated with the loss of bitterness in tubers and those involved in tuberization, two major domesticated traits of potato. Phylogenetic analyses revealed a north-south division of all species in clade 4, not just those in the S. brevicaule complex, and further supported S. candolleanum as the progenitor of cultivated potato and the monophyletic origin of cultivated potato in southern Peru. In addition, we analyzed the genome of S. candolleanum and identified 529 genes lost in cultivated potato. Collectively, the molecular markers generated in this study provide a valuable resource for the identification of agronomically important genes useful for potato breeding.

Solanum L. es uno de los géneros que posee una alta riqueza de especies dentro de la flora peruana y dentro de los Andes tropicales en general. Presentamos una lista revisada de 276 especies de Solanum para el Perú, de estas 253 son nativas, mientras que 23 son introducidas y/o cultivadas. Un total de 74 especies de Solanum (29% de las especies nativas) son endémicas de Perú. Además 58 especies se encuentran solamente en pequeñas poblaciones fuera del Perú, y estas especies están designadas aquí como casi endémicas para destacar el rol importante del Perú en la futura protección de estas especies. El pico de diversidad de especies es observado entre 2500 – 3000 m de elevación, pero la diversidad de especies endémicas es más alta entre 3000 – 3500 m. Cajamarca tiene el más alto número de especies (130 spp.) y de especies endémicas (29 spp.), incluso si se considera el efecto del área. Centros de diversidad de especies endémicas se localizan en las provincias de Cajamarca (Cajamarca), Huaraz y Carhuaz (Ancash), Canta y Huarochirí (Lima). Centros de endemismos secundarios con una alta concentración tanto de especies endémicas y de casi endémicas se encuentran en San Ignacio y Cutervo (Cajamarca), Santiago de Chuco (La Libertad), Oxapampa (Pasco), y Cusco (Cusco): Los actuales patrones de diversidad están altamente correlacionados con la densidad de colecciones, por lo que es necesario una mayor colecta en todas las regiones, especialmente en Arequipa, Ayacucho, Puno, Ancash, Huánuco, Amazonas y Cajamarca, donde se indican altos niveles de diversidad y endemismo de especies, pero de las cuales existen pocas colecciones.

The common potato, Solanum tuberosum L., is the third most important food crop and is grown and consumed worldwide. Indigenous cultivated (landrace) potatoes and wild potato species, all classified as Solanum section Petota, are widely used for potato improvement. Members of section Petota are broadly distributed in the Americas from the southwestern United States to the Southern Cone of South America. The latest comprehensive taxonomic treatment of section Petota was published by John (Jack) Hawkes in 1990; it recognized seven cultivated species and 228 wild species, divided into 21 taxonomic series. Since 1990, intensive field collections from throughout the range of the group, coupled with morphological and molecular studies, have halved the number of species and elucidated new ingroup and outgroup relationships. The recent sequencing of the potato genome has greatly accelerated investigation of all aspects of potato biology and allows us to address new questions not conceivable before. The purpose of this review is to provide a historical overview and update since 1990 of the systematics, diversity, genetics, domestication, evolution, and breeding of Solanum section Petota that will serve as a reference for the next generation of studies in the potato.

12 Páginas •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. INTRODUCTION. MATERIALS AND METHODS. RESULTS. DISCUSSION. LITERATURE CITED.

DNA-based marker analysis of plant genebank material has become a useful tool in the evaluation of levels of genetic diversity and for the informed use and maintenance of germplasm. In this study, we quantify levels of amplified fragment length polymorphism (AFLP) in representative accessions of wild and cultivated potato species of differing geographic origin, ploidy, and breeding system. We generated 449 polymorphic AFLP fragments in 619 plants, representing multiple plants (16–23) from 17 accessions of 14 potato taxa as well as single plants sampled from available accessions (from 3 to 56) of the same 14 taxa. Intra-accession diversities were compared to those of a synthetic ‘taxon-wide’ population comprising a single individual from a variable number of available accessions of each sampled taxon. Results confirm the expected considerably lower levels of polymorphism within accessions of self-compatible as compared to self-incompatible taxa. We observed broadly similar levels of ‘taxon-wide’ polymorphism among self-compatible and self-incompatible species, with self-compatible taxa showing only slightly lower rates of polymorphism. The most diverse accessions were the two cultivated potato accessions examined, the least diverse being the Mexican allohexaploids Solanum demissum and S. iopetalum. Generally allopolyploid self-compatible accessions exhibited lower levels of diversity. Some purported self-incompatible accessions showed relatively low levels of marker diversity, similar to the more diverse self-compatible material surveyed. Our data indicate that for self-compatible species a single plant is highly representative of a genebank accession. The situation for self-incompatible taxa is less clear, and sampling strategies used will depend on the type of investigation. These results have important implications for those seeking novel trait variation (e.g., disease resistance) in gene banks as well as for the selection of individuals for genomics studies. We also show that AFLPs, despite having been largely replaced by other marker types, is highly suitable for the evaluation of within and between accession diversity in genebanks.

In recent years there has been an effort towards the development of genomicresources in carrot. The number of available sequences for carrot in publicdatabases has increased recently. This has allowed the design of SSRs markers,COS markers and a high-throughput SNP assays for genotyping. Additionalmolecular tools include the first high-throughput DArT array and the fullsequence of organelle genomes. These molecular resources have been successfullyused to gain new insights into carrot genetic diversity, organelle genomeevolution and to establish the first dense sequence-based linkage maps. Supported by a consortium of private companies, sequencing of the carrot genomeis currently ongoing. Its release, will establish a solid framework for carrotgenomic studies, opening a new challenging and exciting era for the carrot scientific community. Fil: Iorizzo, Massimo. University of Wisconsin; Estados Unidos Fil: Ellison, S.. University of Wisconsin; Estados Unidos Fil: Van Deynze, Allen. University of California; Estados Unidos Fil: Stoffel, K.. University of California; Estados Unidos Fil: Ashrafi, Hamid. University of California; Estados Unidos Fil: Iovene, M.. Centre National de la Recherche Scientifique; Francia. Institute for Bioscience and Biotechnology Research; Italia Fil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina Fil: Cheng, S.. Instituto de Genómica de Pekín; China Fil: Zheng, P.. Instituto de Genómica de Pekín; China Fil: Zheng, Z.. Instituto de Genómica de Pekín; China Fil: Senalik, Douglas A.. University of Wisconsin; Estados Unidos Fil: Spooner, D.M.. University of Wisconsin; Estados Unidos Fil: Simon, P. W.. University of Wisconsin; Estados Unidos

Potato cyst nematodes (PCN) collected in six localities in the Leningrad region of North West Russia were identified as Globodera rostochiensis pathotype Ro1 and were used for subsequent resistance tests. Seventy-nine accessions of cultivated and closely related wild potato species from the VIR collection in Russia were screened on resistance to G. rostochiensis pathotype Ro1 and on the presence of molecular markers for H1 and Gro1-4 resistance genes. No associations were detected between the resistance level of diploid and tetraploid Andean and tetraploid Chilean potato landraces (indigenous cultivars) and their related wild species and their geographical distribution or presence of PCR-based markers that are associated with the H1 and Gro1-4 genes. At the same time, all susceptible genotypes lacked such markers. New sources of resistance were found and could be used in breeding.

The genus Daucus includes about 20 recognized species. The most widespread and economically important species, Daucus carota L., occurs on almost every continent. The cultivated carrot, subsp. sativus (Hoffm.) Schubl. and G. Martens, has been selected from wild populations that are extremely diverse, especially in the western Mediterranean. The predominant outcrossing and the lack of sexual isolating mechanisms among recognized infraspecific taxa complicate the taxonomy and identification of the wild populations, resulting in widely different interpretations of the number of infraspecific taxa. We measured 36 morphological characters from multiple individuals within each of 155 accessions of D. carota and from the morphologically similar species D. capillifolius (both species 2n = 18) alongside other species for comparison (D. aureus Desf., 2n = 22; D. broteri Ten., 2n = 20; D. involucratus Sm., 2n = 20; and D. littoralis Sm., 2n = 20) in an experimental field plot. Within D. carota, multivariate analyses were able to identify only two subspecies, but even these showed great overlap of individual characters. Because of the ease of crossability of wild D. carota to the domestic landraces and cultivars and because of the taxonomic challenges, the purpose of our study is to explore morphological support for subspecies within D. carota, including the phenetically similar D. capillifolius, which is part of the same clade as D. carota, with the long-term goal of resolving taxonomic disagreements and developing a practical system to classify variation within this economically important species.

We explored the phylogenetic utility of entire plastid DNA sequences inWe used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade ofOur data have allowed us to (1) produce a well-resolved plastid phylogeny of

Morphology has long provided key data to assess diversity in landrace collections in genebanks worldwide. We explored, through an F2 cross between two inbred diploid potato clones, the utility of tuber morphology to assess diversity of potato landraces. We assessed the F2 population created by self-pollinating an F1 clone from a cross between two diploid (2n = 2x = 24) potato clones: DM, a completely homozygous clone derived from somatically doubling an androgenic monoploid of a cultivated potato, and M6, a highly inbred clone derived from seven generations of self-pollination of the wild diploid potato relative Solanum chacoense. We evaluated the F2 population for tuber size, shape and eye depth; skin and flesh colors; and dry matter content. Phenotypic segregation in this F2 population is astonishing. This single cross displayed a range of tuber traits approaching the entire diversity of potato landraces. Morphological characterization of potato used to classify accessions in genebanks is not representative of underlying genetic diversity. This is in agreement with other studies that have shown a lack of correlation between morphological/taxonomic classification and neutral genetic diversity, and a lack of correlation between either morphology or neutral genetic diversity and functional, trait-related genetic diversity in several species. We need better strategies for combining phenotypic and genetic characterization of accessions to develop predictive models that plant breeders can use to identify promising accessions for traits of interest.

Fruits present major morphological characters used to define genera and species within the Apiaceae. Northern Africa represents a major center of diversity of Daucus, with Tunisia containing at least 12 species and six subspecies. We assessed 14 mature fruit characters from the Daucus L. germplasm collection at the National Gene Bank of Tunisia. Quantification of variability for each character was investigated using the standardized Shannon–Weaver diversity index (H′). Diversity was established by factorial analysis of correspondence and cluster analysis. The computing H′ index ranged from 0.31 for stylopodium shape to a maximum of 0.81 for spine shape. A mean diversity index for all traits recorded across all populations averaged 0.58 indicating existence of an important genetic diversity within the collection. Multivariate analysis of factorial correspondence and cluster analysis on morphological descriptors permitted the subdivision of the Daucus collection into five distinct groups including one single accession group, two groups with six accessions, one group of nine accessions and one large group with 81 accessions corresponding each one to a species among Daucus except the large group corresponding to D. carota and D. capillifolius. The grouping of populations did not reflect bioclimatic and geographic patterns, suggesting adaptation of populations to local environments. Of equal importance, our study shows the effectiveness of fruit characters alone to identify species in this collection of Daucus.

We studied the phylogeny of 22 accessions of Daucus and seven accessions in related genera, with DNA sequences from eight nuclear orthologs and one plastid (psbA/trnH) region. Maximum parsimony and maximum likelihood analyses of the concatenated data matrix of 7,212 aligned nucleotides provided excellent bootstrap support for many clades. Concordant with prior molecular results Pseudorlaya pumila was firmly imbedded within Daucus, as was Margottia gummifera, a new finding. All accessions of D. capillifolius, D. carota, and D. sahariensis formed a 2n = 18 clade with all other species within the Daucus clade with chromosome numbers of = 20, 22, and 44 (D. glochidiatus). Sister to the D. carota clade was a clade containing Margottia gummifera and Pseudorlaya pumila, sister to these species was D. crinitus, sister to all the above was D. muricatus, and sister to all of the above was a clade containing the remaining Daucus species. Bayesian analyses of individual regions analyzed separately and averag...

The origin of cultivated potatoes has remaining questions. In this study, 237 accessions of all cultivated species and 155 accessions of wild species closely related to cultivated potatoes, including their putative ancestors, were analyzed using 15 plastid microsatellites (SSRs) to investigate genetic diversity and their relationships with the wild species. We here used polymorphic plastid SSRs we developed from potato plastid genome sequences as well as already known plastid SSR markers. All 15 loci were polymorphic and identified a total of 127 haplotypes. Dramatic decreases in levels of genetic diversity were revealed in landraces in comparison with wild ancestor species. The plastid SSR results showed a decrease in haplotype number and diversity from Peru to both north and south. Phylogenetic analysis revealed two distinct groups. One of them, group A, contained the majority of accessions of cultivated species of the Solanum tuberosum Andigenum group including all accessions of cultivated diploid and triploid cytotypes of this group (S. chaucha, S. phureja, and S. stenotomum by a former taxonomic system) and most of tetraploid accessions of the S.tuberosum Andigenum group (S. tuberosum subsp. andigenum), and the majority of accessions of wild ancestors from the northern members of the S. brevicaule complex. Another group B comprised most of the wild species accessions and almost exclusively hybrid cultivated species which have introgressed plastid genomes from the other wild gene pools. Lack of clustering of traditional cultivated species (as used above) support a revised group classification of S. tuberosum.

Solanum L. section Petota Dumort., which includes the cultivated potato (S. tuberosum L.) and its wild relatives, has been the subject of intensive taxonomic research in the last 25 years. The last comprehensive taxonomic treatment by Hawkes (1990) recognized seven cultivated and 225 wild species, yet the latest estimate is four cultivated and about 100 wild species. These changes have all involved synonymy of preexisting names, but our intensive nomenclatural research in the mega-diverse Solanum (1000+ species) revealed a name, Solanum stipuloideum Rusby, that is the earlier valid name for the species long known as Solanum circaeifolium Bitter. Because this latter name is frequently used in the literature we here present a taxonomic treatment of S. stipuloideum with complete synonymy in order to clarify nomenclature and species circumscription for this common species; this study also highlights the value of genus-wide taxonomic treatments.

Transfer of DNA between different compartments of the plant cell, i.e., plastid, mitochondrion and nucleus, is a well-known phenomenon in plant evolution. Six directions of inter-compartmental DNA migration are possible in theory, however only four of them have been previously reported. These include frequent cases of mitochondrion and plastid to nucleus transfer, plastid to mitochondrion transfer, and rare nucleus to mitochondrion migrations. The connection between the plastid and mitochondrial genomes in flowering plants has been viewed as a one way road. Contrary to these observations we found that a sequence widespread in the carrot mitochondrial genome, designated as DcMP, was transferred to the plastid genome of a carrot ancestor. Interestingly, DcMP was integrated into a tRNA promoter of the plastid trnV gene, replacing the original promoter sequence. The rearrangement of the plastid genome is specific for carrot and closely related species belonging Scandiceae clade. The structure of the sequence and the presence of a 6 nt target site duplication led us to speculate that the transfer was a result of a transposition event of a non-LTR retrotransposon. These findings open interesting questions about the evolution of organellar genomes and mobile genetic elements and provide a useful plastid marker to phylogenetically delineate species relationships within the Scandiceae clade.

The objective of this collection o fpotatoes expedition was to collect germplasm of potatoes wild species for their conservation and regeneration to put them available to the international scientific community as well as to gather field data to carry on taxonomic studies. Atotal of accessions of five species was collected. Thirteen accessions of Solanum agrimonifolium were collected in the Huehuetenango, San Marcos, Quetzaltenango, Totonicapán, Sololá and Chimaltenango provinces located in altitudes ranging from 2,340 to 3,300 meters above sea level (masl); six accessions of S. bulbocastanum subsp. partitum were gotten in the Huehuetenango and Baja Verapaz provinces; 17 accessions of S. clarum were found in the Huehuetenango, San Marcos, Sololá, and Totonicapán provinces in altitudes extending from 3,000 to 3,500 masl; on1y one accession of S. demissum was found in Totonicapán province; and six accessions of S. morelliforme were gotten in Huehuetenango, San Marcos and Totonicapán provinces in altitudes ranging from 2,900 to 3,050 masl. The habitats where these species grow are very dist urbed due to deforestation and changes in the use of the soil. As a result, the guatemalan potato wild species are endangered species. It is notorious that in many locations where 50 years ago wild germplasm was gathered it no longer exist.

We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation. EEA La Consulta Fil: Iorizzo, Massimo. University of Wisconsin. Department of Horticulture; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados Unidos Fil: Ellison, Shelby L. University of Wisconsin. Department of Horticulture; Estados Unidos Fil: Senalik, Douglas A. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos Fil: Peng, Zeng. Beijing Genomics Institute–Shenzhen; China Fil: Satapoomin, Pimchanok. University of Wisconsin. Department of Horticulture; Estados Unidos Fil: Jiaying, Huang. Beijing Genomics Institute–Shenzhen; China Fil: Bowman, Megan. Michigan State University. Department of Plant Biology; Estados Unidos Fil: Iovene, Marina. Consiglio Nazionale delle Ricerche. Istituto di Bioscienze e Biorisorse; Italia Fil: Sanseverino, Walter. Sequentia Biotech; España Fil: Cavagnaro, Pablo Federico. . Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Yildiz, Mehtap. Yuzuncu Yil University. Faculty of Agriculture. Department of Agricultural Biotechnology; Turquía Fil: Macko-Podgórni, Alicja. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia Fil: Moranska, Emilia. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia Fil: Grzebelus, Ewa. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia Fil: Grzebelus, Dariusz. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia Fil: Ashrafi, Hamid. University of California. Seed Biotechnology Center; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados Unidos Fil: Zhijun, Zheng. Beijing Genomics Institute–Shenzhen; China Fil: Shifeng, Cheng. Beijing Genomics Institute–Shenzhen; China Fil: Spooner, David M. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos Fil: Deynze, Allen Van. University of California. Seed Biotechnology Center; Estados Unidos Fil: Simon, Philipp W. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos

The natural history of epiphytic plant species has been extensively studied. However, little is known about the physiology and genetics of epiphytism. This is due to difficulties associated with growing epiphytic plants and the lack of tools for genomics studies and genetic manipulations. In this study, tubers were generated from 223 accessions of 42 wild potato Solanum species, including the epiphytic species S. morelliforme and its sister species S. clarum. Lyophilized samples were analyzed for 12 minerals using inductively coupled plasma optical emission spectrometry. Mineral levels in tubers of S. morelliforme and S. clarum were among the highest for 10 out of the 12 elements evaluated. These two wild potato relatives are native to southern Mexico and Central America and live as epiphytes or in epiphytic-like conditions. We propose the use of S. morelliforme and S. clarum as model organisms for the study of mineral uptake efficiency. They have a short life cycle, can be propagated vegetatively via tubers or cuttings, and can be easily grown in controlled environments. In addition, genome sequence data are available for potato. Transgenic manipulations and somatic fusions will allow the movement of genes from these epiphytes to cultivated potato.

With 7 figures and 1 table Abstract The causal agent of potato wart (Synchytrium endobioticum) is an obligate parasitic chytrid fungus. It is included as a quarantine pathogen in 55 countries, with losses in susceptible cultivars reaching 50–100%. The aim of our study was to characterize the resistance to S. endobioticum pathotype 1 in cultivated potatoes from a well-characterized subset of the Vavilov Institute of Plant Industry collection and to determine whether this resistance is associated with cultivated potato species taxonomy, with ploidy, with geographic distance or with a molecular marker Nl25-1400 proposed for molecular screening for resistance to pathotype 1 of S. endobioticum. Within the diversity of 52 landrace genotypes, our work shows a lack of such predictive associations with wart resistance. High intraspecific variation of wart diseases resistance allows the selection of extremely resistant and susceptible genotypes available for future genetic and breeding studies.

Wild potato ( Solanum L. sect. Petota Dumort.) species contain diploids (2n = 2x = 24) to hexaploids (2n = 6x = 72). J.G. Hawkes classified all hexaploid Mexican species in series Demissa Bukasov and, according to a classic five-genome hypothesis of M. Matsubayashi in 1991, all members of series Demissa are allopolyploids. We investigated the genome composition of members of Hawkes’s series Demissa with genomic in situ hybridization (GISH), using labeled DNA of their putative progenitors having diploid AA, BB, or PP genome species or with DNA of tetraploid species having AABB or AAAaAa genomes. GISH analyses support S. hougasii Correll as an allopolyploid with one AA component genome and another BB component genome. Our results also indicate that the third genome of S. hougasii is more closely related to P or a P genome-related species. Solanum demissum Lindl., in contrast, has all three chromosome sets related to the basic A genome, similar to the GISH results of polyploid species of series Acaulia Juz. Our results support a more recent taxonomic division of the Mexican hexaploid species into two groups: the allopolyploid Iopetala group containing S. hougasii, and an autopolyploid Acaulia group containing S. demissum with South American species S. acaule Bitter and S. albicans (Ochoa) Ochoa.

The Enigma of Solanum maglia in the Origin of the Chilean Cultivated Potato, Solanum tuberosum Chilotanum Group. Landrace potato cultivars occur in two broad geographic regions: the high Andes from western Venezuela south to northern Argentina (Solanum tuberosum Andigenum Group, “Andigenum”), and lowland south-central Chile (S. tuberosum Chilotanum Group, “Chilotanum”), with a coastal desert and 560 km between southernmost populations of Andigenum and Chilotanum. Unlike Andigenum landraces, Chilotanum landraces are adapted to long days and carry a 241 base pair plastid DNA deletion. However, Andigenum and Chilotanum landraces are morphologically similar. We investigated a hypothesis that Chilotanum landraces arose from Solanum maglia, a rare tuber-bearing species found in Chile and Argentina. This hypothesis was formulated first based on morphological analyses of starch grains of extant and preserved (12,500 years before present) S. maglia, and on putative sympatry of extant S. maglia and Chilotanum landraces. Our new starch grain analyses fail to support this hypothesis; we could find no evidence of current sympatric distributions, and S. maglia lacks the 241-bp plastid deletion. However, microsatellite data group all accessions of S. maglia exclusively with Chilotanum, which is supported by our previous observation at the single locus of the waxy gene. These results could be interpreted in various ways, but all explanations have problems. One explanation is that S. maglia is a progenitor of Chilotanum. However, the plastid deletion in Chilotanum but not S. maglia cannot be easily explained. Another explanation is that Chilotanum was formed by hybridization between S. maglia and pre-Chilotanum, but this conflicts with prior cladistic analyses. These new data shed light on aspects of this question and highlight various evolutionary scenarios, but the origin of Chilotanum and the involvement of S. maglia in its origin remain an enigma.

The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next-generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at a fraction of the cost relative to traditional Sanger sequencing. As costs and capabilities of these technologies continue to improve, we are only beginning to see the possibilities of NGS platforms, which are developing in parallel with online availability of a wide range of biological data sets and scientific publications and allowing us to address a variety of questions not possible before. As techniques and data sets continue to improve and grow, we are rapidly moving to the point where every organism, not just select "model organisms", is open to the power of NGS. This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications for large genebank collections.