AFLP analysis of genetic relationships among the cultivated eggplant, Solanummelongena L., and wild relatives (Solanaceae)

The AFLP technique of DNA analysis was evaluated as a tool for assessing genetic relationships among the cultivated eggplant, S. melongena, and related species [Solanum L. subgenus Leptostemonum (Dunal) Bitter, section Melongena (Mill.) Dunal, series Incaniformia Bitter]. Genetic distances based on the AFLP data were estimated for 49 samples of 36 distinct accessions. Phenetic trees were constructed using Jaccard’s coefficient and UPGMA, and other clustering methods: they all had very high co-phenetic correlation values, and were found to be consistent with previous trees based on other data types, in particular ITS-1 sequences, isozymes and morphology, carried out on the same accessions. These results indicated that the AFLP technique is both an efficient and effective tool for determining genetic relationships among species of Solanum. A new classification is proposed for series Incaniformia. Received: 11 January 1999 / Accepted: 30 January 1999     

What's in a name; Genetic structure in Solanum section Petota studied using population-genetic tools

Background  

The taxonomy and systematic relationships among species of Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species.     

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.     

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.     

Epidermal hair morphology in Solanum L. section Solanum

Scanning electron microscopy was used to examine stem, leaf, staminal and stylar hairs on species belonging to Solanum L. section Solanum. The surface morphology of these hairs is illustrated. Simple, uniseriate hairs characterize the section Solanum, and these may have eglandular or glandular heads; they are usually multicellular, but in some species the stylar hairs appear to be unicellular. In addition, stalked glands, described here as spherical, four-celled glands, are universally present in species belonging to the section Solanum.     

The phylogenetic relationship of Solanum flavonols

Flavonoid profiles of Solanum sections Petota, Basarthrum, Solanum and Androceras have all proved to be useful in the delineation of species and series boundaries. A total of sixty-four flavonols have been isolated from these four sections, forty of which have been fully characterized. Flavonol glycosides of kaempferol and quercetin are confirmed as the flavonoids characteristic of this genus but in addition methylated and acylated compounds have also been isolated. By combining existing data, it is possible to develop a phylogenetic scheme illustrating the relationship between each section on the basis of the biosynthetic complexity of their flavonol substitution patterns. Sections Petota and Basarthrum appear to be more ‘primitive’ than sections Solanum and Androceras.     

Phylogeny of firs (genus <Emphasis Type="Italic">Abies</Emphasis>, Pinaceae) based on multilocus nuclear markers (AFLP)

To study the phylogenetic relationships, evolutionary history, and molecular systematics of firs (genus Abies), the phylogenetic reconstruction, based on nuclear multilocus markers—amplified fragment length polymorphism (AFLP)—was conducted. Using seven combinations of selective primers, 84 samples of 39 taxa were genotyped for 553 polymorphic AFLP loci. A comparison with our earlier chloroplast and mitochondrial phylogenies of the genus (in 2014) shows that the nuclear phylogeny generally is more congruent to the chloroplast tree. Most of the clades resolved by the chloroplast phylogeny were supported also in the AFLP tree. Employing the nuclear DNA-based tree, we revealed the presence of new groups and the differences in the topology of several clades. AFLP confirmed the monophyly of Asian species of section Balsamea and their sister position in relation to the American group of species of this section. As shown by the tree of chloroplast DNA, Asian species of section Balsamea do not form a monophyletic group, but belong to the clade comprising the majority of Asian species. Phylogenetically mitochondrial DNA data to a large extent are not congruent to the nuclear and chloroplast DNA trees, and are more in line with geographical distribution of species. Conflicts between nuclear and cytoplasmic phylogeny were analyzed. Taking them into account, we consider the hypothesis of a hybrid origin of particular groups of firs, including ancient hybridization in section Balsamea. A comparison of molecular data with traditional taxonomy of the genus is discussed.     

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.     

Meiosis and pollen germinability in small-flowered anemone type chrysanthemum cultivars

The potatoes, Solanum L. section Petota Dumortier, are a group of species that possess a very broad range of biological diversity, and a wide geographical distribution in the Americas. These species constitute euploid series with somatic chromosome numbers ranging from 2n = 2x = 24 to 2n = 6x = 72. Although special attention has been given to the origin of polyploid potato species, principally the cultivated forms, that are major food crops, and hybridization has been accepted as an important evolutionary force in the section, the mechanisms involved in the origin and evolution of the diploid species have not been elucidated. Herein, we propose that homoploid hybridization is the main mechanism involved in the origin and evolution of the diploid potato species, and discuss the evidences that support our proposal.     

Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum

Interspecific hybridization is known for triggering genetic and epigenetic changes, such as modifications on DNA methylation patterns and impact on phenotypic plasticity and ecological adaptation. Wild potatoes (Solanum, section Petota) are adapted to multiple habitats along the Andes, and natural hybridizations have proven to be a common feature among species of this group. Solanum × rechei, a recently formed hybrid that grows sympatrically with the parental species S. kurtzianum and S. microdontum, represents an ideal model for studying the ecologically and evolutionary importance of hybridization in generating of epigenetic variability. Genetic and epigenetic variability and their correlation with morphological variation were investigated in wild and ex situ conserved populations of these three wild potato species using amplified fragment length polymorphism (AFLP) and methylation‐sensitive amplified polymorphism (MSAP) techniques. We observed that novel methylation patterns doubled the number of novel genetic patterns in the hybrid and that the morphological variability measured on 30 characters had a higher correlation with the epigenetic than with the genetic variability. Statistical comparison of methylation levels suggested that the interspecific hybridization induces genome demethylation in the hybrids. A Bayesian analysis of the genetic data reveled the hybrid nature of S. × rechei, with genotypes displaying high levels of admixture with the parental species, while the epigenetic information assigned S. × rechei to its own cluster with low admixture. These findings suggested that after the hybridization event, a novel epigenetic pattern was rapidly established, which might influence the phenotypic plasticity and adaptation of the hybrid to new environments.     

Musa Genetic Diversity Revealed by SRAP and AFLP

The sequence-related amplified polymorphism (SRAP) technique, aimed for the amplification of open reading frames (ORFs), vis-â-vis that of the amplified fragment length polymorphisms (AFLP) were used to analyze the genetic variation and relationships among forty Musa accessions; which include commercial cultivars and wild species of interest for the genetic enhancement of Musa. A total of 403 SRAP and 837 AFLP amplicons were generated by 10 SRAP and 15 AFLP primer combinations, of which 353 and 787 bands were polymorphic, respectively. Both cluster analysis of unweighted pair-grouping method with arithmetic averages (UPGMA) and principal coordinate (PCO) analysis separated the forty accessions into their recognized sections (Eumusa, Australimusa, Callimusa and Rhodochlamys) and species. The percentage of polymorphism amongst sections and species and the relationships within Eumusa species and subspecies varied between the two marker systems. In addition to its practical simplicity, SRAP exhibited approximately threefold more specific and unique bands than AFLP, 37 and 13%, respectively. SRAP markers are demonstrated here to be proficient tools for discriminating amongst M. acuminata, M. balbisiana and M. schizocarpa in the Eumusa section, as well as between plantains and cooking bananas within triploid cultivars.     

Chemophenetics of Solanum based on steroidal alkaloids

Steroidal alkaloids (SA) are nitrogen-containing specialized metabolites applied as chemophenetic markers in Solanum L. (Solanaceae). Over time, Solanum has been the focus of several molecular phylogenetic studies in an attempt to resolve its infrageneric classification and the relationship among species belonging to this genus. Here we aimed to study SA chemodiversity to identify chemical patterns and to perform a chemophenetic characterization of the Solanum genus and its major clades. Chemical literature data about Solanum steroidal alkaloids was assessed and structural variability of this biogenetic group was used in the chemometric analysis, by applying a Principal Component Analysis and Hierarchical Cluster Analysis. The results demonstrate that the SA chemodiversity in Solanum is represented by the occurrence of nine SA subtypes. The biosynthetic predominance of the spirosolane-type in Solanum clades was observed, except for the preference of the Potato clade in producing the solanidane-type. The Geminata clade displayed low SA glycosylation patterns, containing 3-oxy groups. In addition, low SA production in the Cyphomandra clade was observed. Chemical similarities between the Archaesolanum, Dulcamaroid and Morelloid clades were observed by chemometric analyses. In sum, chemophenetics was proven a reliable and additional tool to describe the array of specialized metabolites in Solanum clades, showing chemical information suitable to corroborate molecular phylogenetic studies.     

Analysis of eggplant (<Emphasis Type="Italic">Solanum melongena</Emphasis>)-related germplasm: morphological and AFLP data contribute to phylogenetic interpretations and germplasm utilization

A total of 94 Solanum accessions, including eggplants and related species, were morphologically characterized based on greenhouse observations, and molecularly analysed by the AFLP technique. Morphological parameters were helpful in assessing similarities or differences among accessions, and molecular data were used to support morphological conclusions. A dendrogram was computed based on the Dice genetic distances using the neighbour-joining method. The analysis was efficient in the assignment of a species name for eight out of nine accessions that were not previously classified, and revealed that 14 further accessions were misnamed in the collection originally received. The results indicate that the taxonomy of Solanum sections and subgenera including several species should be reconsidered. The AFLP technique was revealed as an efficient tool in determining genetic relationships among species. In general, morphological observations were consistent with molecular data, indicating that both approaches complemented to define the phylogenetic status of a large genus like Solanum. In terms of eggplant breeding, the molecular analysis of the Melongena complex, and of the other sections of the subgenus Leptostemonum, establishes useful germplasm relationships in the gene pool available for the genetic improvement of the cultivated species. The results we have provided highlight an urgent necessity to include molecular parameters in handling and characterizing the genebank-deposited germplasm related to cultivated crops.Communicated by F. Salamini     

Karyotype and AFLP data reveal the phylogenetic position of the Brazilian endemic Hypochaeris catharinensis (Asteraceae)

The genus Hypochaeris offers an excellent model for studies of recent adaptive radiation in the South American continent. We used karyotype analysis with chromomycin?A₃ (CMA₃)/4??,6-diamidino-2-phenylindole (DAPI) banding and fluorescence in?situ hybridization (FISH), and amplified fragment length polymorphism (AFLP) fingerprinting to investigate for the first time the Brazilian endemic H.?catharinensis and define its position within the South American group of species. Strong CMA-positive signals were seen at the end of both arms of chromosome?3 and at the end of the long arm of chromosome?4. DAPI bands were only detected in subterminal position on short arm of chromosome?4. FISH with 5S and 35S ribosomal DNA (rDNA) probes revealed a single 5S rDNA locus on short arm of chromosome?2, typical for all other South American Hypochaeris taxa analyzed to date. The 35S rDNA locus was identified at subterminal position on the short arm of chromosome?3, as reported so far for only two of the known species (H.?lutea and H.?patagonica). The AFLP study included 55 individuals, comprising nine species of the South American Hypochaeris plus their putative ancestor H.?angustifolia. Eleven AFLP primer combinations generated a total of 401 fragments, of which 388 (96.7%) were polymorphic. High genetic similarities were observed among taxa, with all South American Hypochaeris species falling into one main cluster [100% bootstrap (BS)]. Hypochaeris catharinensis is closely related to H.?lutea (82% BS), forming a well-separated subcluster within the South American species. Taken together, the karyological and AFLP data contribute to the placement of H.?catharinensis within the phylogenetic framework of South American species of Hypochaeris and allow the definition of a novel and well-resolved phylogenetic group (the Lutea group).     

Genetic diversity and relationships in Solanum subg. Archaesolanum (Solanaceae) based on RAPD and chloroplast PCR-RFLP analyses

The subgenus Archaesolanum is a group composed of eight species with a characteristic chromosome number based on n?=?x?=?23 and an area restricted to the South Pacific. This subgenus is an isolated group of Solanum for which extensive information about phylogenetic relationships based on molecular genetic methods is lacking. This study represents an approach to analyze genetic relationships within this group. In this context, seven species were examined using random amplified polymorphic DNA (RAPD) markers. In further analysis, the amplification products of two chloroplast regions (trnS-trnG and rbcL) were studied with polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) method. Screening for the presence of unique mitochondrial rearrangements was also carried out using universal mitochondrial primers for the detection of fragment length polymorphisms. We identified two major groups within the subgenus; one was composed of the members of ser. Avicularia and Laciniata, while the other was formed by species belonging to ser. Similia. It is suggested that the taxonomic status of series within the Archaesolanum clade should be revised. The hybrid origin of S.?laciniatum was also tested, and two hypotheses regarding its phylogeny are assumed.     

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.     

AFLP analysis of genetic relationships in the tribe Datureae (Solanaceae)

The AFLP technique was evaluated as a tool for assessing species relationships within the tribe Datureae and genetic distances were estimated for 47 accessions of over 12 species. The phenetic trees from various analyses of the AFLP data gave very high co-phenetic correlation values, and were found to be consistent with previous trees based on the analysis of different data types, in particular ITS-1 sequences, isozymes and morphology, carried out on the same accessions. These results indicated that the AFLP technique is both an efficient and effective tool for determining genetic relationships among taxa in the Solanaceae. A new classification is proposed for the tribe Datureae, which maintains the arborescent species as a separate genus, Brugmansia, and recognises three sections within the genus Datura; Stramonium, Dutra and Ceratocaulis. D. discolor, previously placed in section Dutra, was found to be intermediate between sections Dutra and Stramonium. Received: 11 January 1999 / Accepted: 1 February 1999     

Can taxonomic distinctness assess anthropogenic impacts in inland waters? A case study from a Mediterranean river basin

1. It is increasingly recognised that adequate measures of biodiversity should include information on the ‘relatedness’ of species within ecological assemblages, or the phylogenetic levels at which diversity is expressed. Taxonomic distinctness measures provide a series of indices to achieve this, which are independent of sample size. Taxonomic distinctness has been employed widely in marine systems, where it has been suggested that this index can provide a reliable measure of anthropogenic impact. 2. We tested the behaviour of three related taxonomic distinctiveness indices (Average Taxonomic Distinctness, Δ⁺; Variation in Taxonomic Distinctness, Λ⁺; and Total Taxonomic Distinctness, sΔ⁺) in relation to putative levels of anthropogenic impact in inland waters and their potential utility in environmental monitoring, using an extensive data set for aquatic beetles from the south‐east of the Iberian Peninsula. 3. Taxonomic distinctness measures were not able to identify human disturbance effects and there were no clear relationships between these new biodiversity measures and the disturbance level recorded at individual localities. Furthermore, the taxonomic distinctness measures used were apparently less sensitive to the effects of anthropogenic impact than other diversity metrics, such as species richness and rarity. 4. We conclude that taxonomic distinctness indices may not always perform as well as other metrics in the assessment of environmental quality. In addition, taxonomic distinctness measure should be interpreted with caution, as their performance and ability to detect anthropogenic disturbance may depend on the phylogenetic structure of sampled taxa within a region, and their evolutionary and ecological history.     

Species-Specific Identification from Incomplete Sampling: Applying DNA Barcodes to Monitoring Invasive Solanum Plants

Comprehensive sampling is crucial to DNA barcoding, but it is rarely performed because materials are usually unavailable. In practice, only a few rather than all species of a genus are required to be identified. Thus identification of a given species using a limited sample is of great importance in current application of DNA barcodes. Here, we selected 70 individuals representing 48 species from each major lineage of Solanum, one of the most species-rich genera of seed plants, to explore whether DNA barcodes can provide reliable specific-species discrimination in the context of incomplete sampling. Chloroplast genes ndhF and trnS-trnG and the nuclear gene waxy, the commonly used markers in Solanum phylogeny, were selected as the supplementary barcodes. The tree-building and modified barcode gap methods were employed to assess species resolution. The results showed that four Solanum species of quarantine concern could be successfully identified through the two-step barcoding sampling strategy. In addition, discrepancies between nuclear and cpDNA barcodes in some samples demonstrated the ability to discriminate hybrid species, and highlights the necessity of using barcode regions with different modes of inheritance. We conclude that efficient phylogenetic markers are good candidates as the supplementary barcodes in a given taxonomic group. Critically, we hypothesized that a specific-species could be identified from a phylogenetic framework using incomplete sampling–through this, DNA barcoding will greatly benefit the current fields of its application.