AFLP analysis reveals a lack of phylogenetic structure within <Emphasis Type="Italic">Solanum</Emphasis> section <Emphasis Type="Italic">Petota</Emphasis>

Background  

The secondary genepool of our modern cultivated potato (Solanum tuberosum L.) consists of a large number of tuber-bearing wild Solanum species under Solanum section Petota. One of the major taxonomic problems in section Petota is that the series classification (as put forward by Hawkes) is problematic and the boundaries of some series are unclear. In addition, the classification has received only partial cladistic support in all molecular studies carried out to date.     

Comparative analysis of 343 plastid genomes of Solanum section Petota: Insights into potato diversity,phylogeny, and species discrimination

Common potato (Solanum tuberosum L.) and its wild relatives belong to Solanum section Petota. This section's phylogeny and species delimitation are complicated due to various ploidy levels, high heterozygosity, and frequent interspecific hybridization. Compared to the nuclear genome, the plastid genome is more conserved, has a haploid nature, and has a lower nucleotide substitution rate, providing informative alternative insights into the phylogenetic study of section Petota. Here, we analyzed 343 potato plastid genomes from 53 wild and four cultivated species. The diversity of sequences and genomes was comprehensively analyzed. A total of 24 species were placed in a phylogenetic tree based on genomic data for the first time. Overall, our results not only confirmed most existing clades and species boundaries inferred by nuclear evidence but also provided some distinctive species clade belonging and the maternally inherited evidence supporting the hybrid origin of some species. Furthermore, the divergence times between the major potato clades were estimated. In addition, the species discriminatory power of universal barcodes, nuclear ribosomal DNA, and whole and partial plastid genomes and their combinations were thoroughly evaluated; the plastid genome performed best but had limited discriminatory power for all survey species (40%). Overall, our study provided not only new insights into phylogeny and DNA barcoding of potato but also provided valuable genetic data resources for further systematical research of Petota.     

Collapse of species boundaries in the wild potatoSolanum brevicaule complex (Solanaceae, S. sect.Petota): Molecular data

TheSolanum brevicaule complex is a group of morphologically very similar wild and cultivated potato taxa (Solanum sect.Petota). This study uses single to low-copy nuclear RFLPs and RAPDs to investigate their species boundaries and relationships. Cladistic analyses of both data sets are largely concordant with each other and with a recently published phenetic analyses of the same accessions using morphology. All three data sets separate members of the complex into populations from Peru and immediately adjacent northwestern Bolivia, including most cultivated species accessions, and populations from northwestern Bolivia to Argentina. The molecular results suggest that the complex is paraphyletic as currently circumscribed. Many species of theS. brevicaule complex should be relegated to synonymy.     

Greatly reduced phylogenetic structure in the cultivated potato clade (Solanum section Petota pro parte)

Premise of the Study

The species boundaries of wild and cultivated potatoes are controversial, with most of the taxonomic problems in the cultivated potato clade. We here provide the first in‐depth phylogenetic study of the cultivated potato clade to explore possible causes of these problems.

Methods

We examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned data set of 14,072 DNA characters, 2171 of which are parsimony‐informative. We analyzed the data to produce phylogenies and perform concordance analysis and goodness‐of‐fit tests.

Key Results

There is good phylogenetic structure in clades traditionally referred to as clade 1+2 (North and Central American diploid potatoes exclusive of Solanum verrucosum), clade 3, and a newly discovered basal clade, but drastically reduced phylogenetic structure in clade 4, the cultivated potato clade. The results highlight a clade of species in South America not shown before, ‘neocardenasii’, sister to clade 1+2, that possesses key morphological traits typical of diploids in Mexico and Central America. Goodness‐of‐fit tests suggest potential hybridization between some species of the cultivated potato clade. However, we do not have enough phylogenetic signal with the data at hand to explicitly estimate such hybridization events with species networks methods.

Conclusions

We document the close relationships of many of the species in the cultivated potato clade, provide insight into the cause of their taxonomic problems, and support the recent reduction of species in this clade. The discovery of the neocardenasii clade forces a reevaluation of a hypothesis that section Petota originated in Mexico and Central America.     

Seed protein electrophoresis of some cultivated and wild species of <Emphasis Type="Italic">Chenopodium</Emphasis>

Seed protein profiles of 40 cultivated and wild taxa of Chenopodium have been compared by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The relative similarity between various taxa, estimated by Jaccard’s similarity index and clustered in UPGMA dendrogram, is generally in accordance with taxonomic position, crossability relationships and other biochemical characters. Eight accessions of C. quinoa studied are clustered together and show genetic similarity with closely related C. bushianum and C. berlandieri subsp. nuttalliae. The taxa included under C. album complex are clustered in two groups which show that these taxa are a heterogenous assemblage and their taxonomic affinities need a reassessment. Other wild species studied are placed in the dendrogram more or less according to their taxonomic position.     

The use and limits of AFLP data in the taxonomy of polyploid wild potato species in Solanum series Conicibaccata

Solanum sect. Petota (tuber-bearing wild and cultivated potatoes) are a group of approximately 190 wild species distributed throughout the Americas from the southwestern United States south to Argentina, Chile, and Uruguay. Solanum series Conicibaccata are a group of approximately 40 species within sect. Petota, distributed from central Mexico to central Bolivia, composed of diploids (2n = 2x = 24), tetraploids (2n = 4x = 48) and hexaploids (2n = 6x = 64); the polyploids are thought to be polysomic polyploids. This study initially was designed to address species boundaries of the four Mexican and Central American species of series Conicibaccata with AFLP data with the addition of first germplasm collections of one of these four species, Solanum woodsonii, as a follow-up to prior morphological, chloroplast DNA, and RAPD studies; and additional species of series Conicibaccata from South America. AFLP data from 12 primer combinations (1722 polymorphic bands) are unable to distinguish polyploid species long thought to be distinct. The data suggest a complex reticulate history of the tetraploids or the need for a broad downward reevaluation of the number of species in series Conicibaccata, a trend seen in other series of sect. Petota. Separately, through flow cytometry, we report the first ploidy level of S. woodsonii, as tetraploid (2n = 48). The U.S. Government’s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Hair morphology and the relationships of species inSolanum sect.Basarthrum

The usefulness of features of leaf hairs in distinguishing subgenera and sections is well documented in bothRhododendron andSolanum. In this analysis of the taxa ofSolanum sect.Basarthrum (23 species), and of a sample of closely related taxa from sect.Petota (22 species), it is shown that such features serve to delineate subsectional groups such as series and some species as well. SectionBasarthrum has an unexpected diversity of hair types. Although this group has been characterized by 2-celled bayonet hairs, more than one half of the taxa in the section bear multicellular finger hairs, and 3 species also possess branched hairs. Thus, major rearrangements of the species previously assigned to sect.Basarthrum are indicated or supported by pubescence features. The taxa studied from seriesEtuberosa andJuglandifolia (both of sect.Petota) show hair types that a) are relatively primitive for the section, and b) show linkage between sects.Petota andBasarthrum.     

Two new wild potato species from Bolivia

Two new wild potato species from Bolivia, belonging to Solanum section Petota are described.     

AFLP data support the recognition of a new tuber-bearing Solanum species but are uninformative about its taxonomic relationships

Solanum section Petota, containing the cultivated potato and its wild relatives, is a group of around 200 species. Many of these species are morphologically very variable with unclear boundaries, and the group as a whole appears to be somewhat over-classified. Describing a new species in this group should only be undertaken with caution, and molecular data can be used to test the distinctness of any putative new taxon. AFLP markers have shown the ability to reliably distinguish species in several groups within the genus Solanum. We tested the distinctness of a new tuber-bearing Solanum species using morphological and AFLP data, and tried to establish its affiliation to the series within the section. There was clear support for the species status of the material known as Solanum hannemanii in genebank collections, but the AFLP data were inconclusive about its relationships to the other investigated species. Also, the distinction of the series Tuberosa and Megistacroloba, to which these species belong, was not supported.     

A phylogenetic analysis of Pisum based on morphological characters, and allozyme and RAPD markers

Cladistic analyses of 17 wild and cultivated pea taxa were performed using morphological characters, and allozyme and RAPD (random amplified polymorphic DNA) markers. Both branch-and-bound and bootstrap searches produced cladograms that confirmed the close relationships among the wild species and cultivars of Pisum proposed by a variety of systematic studies. Intraspecific rankings were supported for northern P. humile, southern P. humile, P. elatius and P. sativum, which together comprise a single-species complex. P. fulvum, while clearly the most divergent of the pea taxa, could also be assigned to the same species complex without violating the hierarchial logic of the cladogram. Its inclusion or exclusion depends on whether the level of interfertility it displays with other pea taxa or its overall morphological and chromosomal distinction are emphasized. As suggested by previous studies, northern P. humile was the most likely sister taxon to cultivated P. sativum; although, rigorous phylogenetic evaluation revealed a close genealogical affinity among P. elatius, northern P. humile and P. sativum. Despite their limited number, the 16 morphological characters and allozyme markers used precisely organized the pea taxa into established taxonomic groupings, perhaps in part reflecting the role morphology has played historically in pea classification. The RAPD data also generally supported these same groupings and provided additional information regarding the relationships among the taxa. Given that RAPDs are relatively quick and easy to use, are refractory to many environmental influences, can be generated in large numbers, and can complement traditional characters that may be limited in availability, they provide a valuable new resource for phylogenetic studies.     

Hybrid origins of cultivated potatoes

Solanum section Petota is taxonomically difficult, partly because of interspecific hybridization at both the diploid and polyploid levels. The taxonomy of cultivated potatoes is particularly controversial. Using DNA sequence data of the waxy gene, we here infer relationships among the four species of cultivated potatoes accepted in the latest taxonomic treatment (S. ajanhuiri, S. curtilobum, S. juzepczukii and S. tuberosum, the latter divided into the Andigenum and Chilotanum Cultivar Groups). The data support prior ideas of hybrid origins of S. ajanhuiri from the S. tuberosum Andigenum Group (2x = S. stenotomum) × S. megistacrolobum; S. juzepczukii from the S. tuberosum Andigenum Group (2x = S. stenotomum) × S. acaule; and S. curtilobum from the S. tuberosum Andigenum Group (4x = S. tuberosum subsp. andigenum) × S. juzepczukii. For the tetraploid cultivar-groups of S. tuberosum, hybrid origins are suggested entirely within much more closely related species, except for two of three examined accessions of the S. tuberosum Chilotanum Group that appear to have hybridized with the wild species S. maglia. Hybrid origins of the crop/weed species S. sucrense are more difficult to support and S. vernei is not supported as a wild species progenitor of the S. tuberosum Andigenum Group.     

Comparative Analysis of Phylogenetic Relationships of Grain Amaranths and Their Wild Relatives (Amaranthus; Amaranthaceae) Using Internal Transcribed Spacer, Amplified Fragment Length Polymorphism, and Double-Primer Fluorescent Intersimple Sequence Repeat Markers

The most economically important group of species in the genus Amaranthus is the A. hybridus species complex, including three cultivated grain amaranths, A. cruentus, A. caudatus, and A. hypochondriacus, and their putative wild progenitors, A. hybridus, A. quitensis, and A. powellii. Taxonomic confusion exists among these closely related taxa. Internal transcribed spacer (ITS) of nuclear ribosomal DNA, amplified fragment length polymorphism (AFLP), and double-primer fluorescent intersimple sequence repeat (ISSR) were employed to reexamine the taxonomic status and phylogenetic relationships of grain amaranths and their wild relatives. Low ITS divergence in these taxa resulted in poorly resolved phylogeny. However, extensive polymorphisms exist at AFLP and ISSR loci both within and among species. In phylogenetic trees based on either AFLP or ISSR or the combined data sets, nearly all intraspecific accessions can be placed in their corresponding species clades, indicating that these taxa are well-separated species. The AFLP trees share many features in common with the ISSR trees, both showing a close relationship between A. caudatus and A. quitensis, placing A. hybridus in the same clade as all grain amaranths, and indicating that A. powellii is the most divergent taxon in the A. hybridus species complex. This study has demonstrated that both AFLP and double-primer fluorescent ISSR have a great potential for generating a large number of informative characters for phylogenetic analysis of closely related species, especially when ITS diversity is insufficient.     

Chloroplast DNA variation in the cultivated and wild olive taxa of the genus Olea L.

Polymorphism in the lengths of restriction fragments of the whole cpDNA molecule were studied in 15 taxa (species or subspecies) of the genus Olea. From restriction analysis using nine endonucleases, 28 site mutations and five length polymorphisms were identified, corresponding to 12 distinct chlorotypes. From a phenetic analysis based on a Nei’s dissimilarity matrix and a Dollo parsimony cladistic analysis using, as an outgroup, a species of the genus Phillyrea close to Olea, the ten taxa of section Olea were distinguished clearly from the five taxa of section Ligustroides which appear to posses more ancestral cpDNA variants. Within the section Ligustroides, the tropical species from central-western Africa, Olea hochtetteri, showed a chlorotype which differed substantially from those of the other four Olea taxa growing in southern Africa, supporting a previous assessment according to which O. hochtetteri may have been subjected to a long period of geographical isolation from the other Olea taxa. Within the Olea section, three phyla were identified corresponding to South and East Africa taxa, Asiatic taxa, and a group including Saharan, Macaronesian and Mediteranean taxa, respectively. On the basis of cpDNA variation, the closest Olea taxa to the single Mediterranean species, Olea europaea, represented by its very predominant chlorotype, observed in both wild and cultivated olive, were found to be Olea laperrinei (from the Sahara), Olea maroccana (from Maroccan High Atlas) and Olea cerasiformis (from Macaronesia). These three taxa, which all share the same chlorotype, may have a common maternal origin. Received: 5 December 1999 / Accepted: 30 December 1999     

The potential of AFLPs in biosystematics: A first application inSolanum taxonomy(Solanaceae)

Using the AFLP technique highly informative DNA fingerprints were generated from 19 taxa ofSolanum sect.Petota (potatoes) and three taxa ofSolanum sect.Lycopersicum (tomatoes). Both phenetic and cladistic analyses were conducted from the individual genotypic level to the species level. An AFLP fingerprint, using a combination of suitable AFLP primers, generated 12 to 71 scorable fragments per genotype which was sufficient for taxonomic interpretation. The classifications based on the molecular markers were generally in agreement with current taxonomic opinions. Unexpectedly,S. microdontum was associated with ser.Megistacroloba rather than with ser.Tuberosa, andS. demissum (ser.Demissa) and species of ser.Acaulia appeared closely affiliated. AFLP is an efficient and reliable technique to generate biosystematic data and therefore a promising tool for evolutionary studies.     

Genetic relationships among subspecies of Vigna unguiculata (L.) Walp. based on allozyme variation

 The cowpea [Vigna unguiculata (L.) Walp.] is a morphologically and genetically variable species composed of wild perennial, wild annual, and cultivated forms that are mainly used for edible seeds and pods. In this study, genetic variation in 199 germplasm accessions of wild and cultivated cowpea was evaluated using an allozyme analysis. The results from this survey showed that wild cowpea exhibits genetic variation perfectly fitted with the existing morphological classification. The cowpea gene-pool is characterized by its unusually large size. It encompasses taxa (ranked as subspecies) that could be considered as different species considering the high genetic distances observed between accessions belonging to different taxa. These subspecies can be classified into three groups characterized by their breeding systems: perennial outcrossers, perennial out-inbreds, and inbred annuals. Allozyme data confirm this grouping. Perennial outcrossers look primitive and are more remote from each other and from perennial out-inbreds. Within this large gene-pool, mainly made of perennial taxa, cultivated cowpeas (ssp. unguiculata var. unguiculata) form a genetically coherent group and are closely related to annual cowpeas (ssp. unguiculata var. spontanea) which may include the most likely progenitor of cultivated cowpeas. Received: 15 June 1998 / Accepted: 29 September 1998     

AFLP analysis of relationships among cassava and other Manihot species

 Despite the worldwide importance of cultivated cassava (M. esculenta Crantz) its origin and taxonomic relationships with other species in the genus have not been clearly established. We evaluated a representative sample of the crop’s diversity and six wild taxa with AFLPs to estimate genetic relationships within the genus. Groupings of accessions of each species by data analysis corresponded largely with their previous taxonomic classifications. A mixed group, consisting of Manihot esculenta subsp. flabellifolia and M. esculenta subsp. peruviana, was most similar to cassava, while M. aesculifolia, M. brachyloba, and M. carthaginensis were more distant. Species-specific markers, which may be useful in germ-plasm classification or introgression studies, were suggested by the unique presence of AFLP products in samples of each of the three wild species. Heterogeneity of similarities among individuals of certain species suggested the existence of intraspecific gene pools, a hypothesis that was supported by morphological or ecogeographic evidence with varying degrees of success. Quantitative assessment of genetic diversity revealed greater homogeneity among cassava accessions than among itsclosest wild relatives. The demonstration of unique genetic diversity in the two M. esculenta subspecies and their genetic similarity to the crop supports the hypothesis that these materials may be the ancestors of cassava. Received: 4 November 1996 / Accepted: 20 December 1996     

The discovery and phylogenetic implications of a novel 41 bp plastid DNA deletion in wild potatoes

Insertions and deletions (indels) are common in intergenic spacer regions of plastid DNA and can provide important phylogenetic characters for closely related species. For example, a 241-bp plastid DNA deletion in the trnV-UAC/ndhC intergenic spacer region has been shown to have major phylogenetic importance in determining the origin of the cultivated potato. As part of a phylogenetic study of the wild potato Solanum series Piurana group we screened 199 accessions of 38 wild potato species in nine of the 19 tuber-bearing (Solanum section Petota) series that have not been examined before for indels in the trnV-UAC/ndhC intergenic spacer region. A novel 41 bp deletion (but no 241 bp deletion) was discovered for 30 accessions of three species: S. chiquidenum (5 of 10 accessions), S. chomatophilum (19 of 28), and S. jalcae (6 of 6). Accessions with and without this deletion are found throughout much of the north-south range of all three species in northern and central Peru, but not east of the Marañón River. Multivariate morphological analyses of these 44 accessions showed no morphological associations to the deletion. The results suggest extensive interspecific gene flow among these three species, or a common evolutionary history among species that have never been suggested to be interrelated.     

CHROMOSOME NUMBERS IN SPHAERALCEA SECTION FENDLERIANAE

Chromosome numbers are reported for ten taxa in Sphaeralcea section Fendlerianae (Malvaceae). New ploidy levels are reported for six taxa, with one species not previously reported, and extensive polyploidy at all taxonomic levels is documented. The geographic and taxonomic distribution of polyploids suggests that polyploidy arose many times in the taxa of Sphaeralcea. Sphaeralcea fendleri var. venusta, S. polychroma, and S. wrightii populations have yielded exclusively tetraploid counts. Tetraploidy is correlated with taxa having lavender petals. Polyploidy has also allowed the taxa to expand their distributions without resulting in speciation.     

Genomic amplification of the <Emphasis Type="Italic">Gret1</Emphasis> retroelement in white-fruited accessions of wild <Emphasis Type="Italic">Vitis</Emphasis> and interspecific hybrids

Retrotransposons are retrovirus-related mobile sequences that have the potential to replicate via RNA intermediates and increase the genome size by insertion into new sites. The retroelement, Gret1, has been identified as playing a key role in generating fruit color variation in cultivated grape (Vitis vinifera L.) due to its insertion into the promoter of VvMybA1. Fruit color variation is an important distinguishing feature of cultivated grapes and virtually no fruit color variation is observed in wild grape species. The presence and relative copy number of Gret1 was assessed using quantitative PCR on 22 different Vitis species, only four of which (plus interspecific hybrids) are known to contain white accessions. Gret1 copy number was observed to vary by species as well as by color within species and was significantly higher in white-fruited accessions across all taxa tested. Additionally, genomic regions surrounding Gret1 insertion were sequenced in white V. vinifera, hybrid, V. labrusca, V. aestivalis, and V. riparia accessions.