Molecular evolution of 35S rDNA and taxonomic status of Lycopersicon within Solanum sect. Petota

To clarify the taxonomic status of tomatoes (“Lycopersicon”) and their relationship to the members of sect. Petota of genus Solanum L., organization of the rDNA external transcribed spacer (5′ ETS) was studied in 33 Solanum and “Lycopersicon” species. Phylogenetic reconstruction revealed that three major groups can be distinguished. Non-tuber-bearing species of ser. Etuberosa as well as tuber-bearing Central American diploids appeared as a paraphyletic group. The first of two well-defined clades embraced all tuber-bearing South American species and Central American polyploids. The other clade (named “tomato clade”) contains non-tuber-bearing species of ser. Juglandifolia and tomato species of ser. Neolycopersicon, which appears to be imbedded in sect. Petota. The new 5′ ETS variant D characterized by a cluster of downstream subrepeats is characteristic for the tomato clade. The variant D originated directly from the most ancestral variant A found in ser. Etuberosa and the Central American diploids, whereas variants B and C specific for the tuber-bearing South American species and Central American polyploids represent a parallel lineage of molecular evolution. The sequence analysis demonstrates the existence of an evolutionary trend of parallel multiplication of specific motifs in 5′ ETS in different groups of sect. Petota.     

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.     

Polymorphism of the KPI-A gene sequence in the potato subgenera Potatoe (Sect. Petota, Esolonifera, and Lycopersicum) and Solanum

Group A Kunitz-type protease inhibitors (KPI-A) are involved in protecting potato plants from microorganisms and pests. While the nucleotide sequence is known for many KPI-A genes of various potato cultivars (Solanum tuberosum subsp. tuberosum) and a few genes of tomato (Solanum lycopersicum), there are no data on their allelic diversity in other species of the genus Solanum. KPI-A fragments were cloned, amplified, sequenced, and analyzed from plants of the subgenera Potatoe sect. Petota (five genes from S. tuberosum ssp. andigenum and two genes from S. stoloniferum) and Solanum (five genes from S. nugrum), and their consensus sequences were established. An identity of 97–100% was observed among these sequences and the KPI-A sequences of the sections Petota (cultivated potato Solanum tuberosum ssp. tuberosum) and Etuberosum (S. palustre) The interspecific variation of KPI-A did not exceed its intraspecific variation for all but one species (S. lycopersicum). The distribution of highly variable and conserved sequences in the mature protein-coding region was the same in all of the above species. The same primers failed to amplify the homologous genes from Solanum dulcamara, S. lycopersicum, and Mandragora officinarum. Phylogenetic analysis of the KPI-A sequences showed that S. lycopersicum clustered separately from all of the other species examined, that S. nigrum clustered together with species of the sections Etuberosum and Petota, and that these species produced no species-specific clusters. Although S. nigrum is resistant to all known races of the oomycete Phytophthora infestans, which causes one of the most economically important diseases of Solanaceae, the amino acid sequences encoded by S. nigrum KPI-A differed slightly, if at all, from their counterparts of cultivated potato, which is susceptible to P. infestans infection.     

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.     

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.     

Comparison of four molecular markers in measuring relationships among the wild potato relatives Solanum section Etuberosum (subgenus Potatoe)

We evaluated chloroplast DNA (cpDNA), isozymes, single to low-copy nuclear DNA (RFLPs), and random amplified polymorphic DNAs (RAPDs) in terms of concordance for genetic distance of 15 accessions each of Solanum etuberosum and S. palustre, and 4 accessions of S. fernandezianum. These self-compatible, diploid (2n=24), and morphologically very similar taxa constitute all species in Solanum sect. Etuberosum, a group of non-tuber-bearing species closely related to Solanum sect. Petota (the potato and its wild relatives). Genetic distance and multidimentional scaling results show general concordance of isozymes, RFLPs and RAPDs between all three taxa; cpDNA shows S. etuberosum and S. palustre to be more similar to each other than to S. fernandezianum. Interspecific sampling variance shows a gradation of resolution from allozyme (low) to RAPD to RFLP (high); while intraspecific comparisons graded from RFLPs (low) to RAPDs (high; lack of sufficient allozyme variability within species precluded comparisons for allozymes). Experimental error was low in RFLPs and RAPDs.Names are necessary to report factually and available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable     

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.     

Reexamination of series relationships of South American wild potatoes (Solanaceae: Solanum sect. Petota): evidence from chloroplast DNA restriction site variation

Chloroplast DNA (cpDNA) restriction enzyme site analysis was used to test hypotheses of series and superseries affiliations of 76 taxa, representing 11 of the 13 South American series (material unavailable for two series) of wild potatoes (Solanum sect. Petota) recognized in the latest classification by Hawkes. The cladistic results, combined with those from earlier cpDNA studies of 30 taxa of the Mexican and Central American species (representing eight series; ser. Conicibaccata and ser. Tuberosa have representatives in Mexico and in South America), support four main clades for 17 of the 19 series examined in sect. Petota: (1) the Mexican and Central American diploid species, exclusive of S. bulbocastanum, S. cardiophyllum, and S. verrucosum, (2) S. bulbocastanum and S. cardiophyllum (ser. Bulbocastana, ser. Pinnatisecta), (3) South American diploid species constituting all of ser. Piurana, but also members of ser. Conicibaccata, ser. Megistacroloba, ser. Tuberosa, and ser. Yungasensia, (4) all Mexican and Central American polyploid species (ser. Longipedicellata, ser. Demissa), S. verrucosum (diploid Mexican species in ser. Tuberosa), and South American diploid and polyploid members of ser. Acaulia, ser. Circaeifolia, ser. Commersoniana, ser. Conicibaccata, ser. Cuneoalata, ser. Lignicaulia, ser. Maglia, ser. Megistacroloba, ser. Tuberosa, and ser. Yungasensia. Each of these clades contains morphologically and reproductively very diverse species, and there are no evident morphological features that unite members within a clade to therefore distinguish them. These results strongly suggest a need for a reevaluation of the series and superseries classifications of sect. Petota.     

Molecular evolution of rDNA external transcribed spacer and phylogeny of sect. Petota (genus Solanum)

The 5(') external transcribed spacer (ETS) region of ribosomal DNA of 30 species of Solanum sect. Petota and the European Solanum dulcamara were compared. Two structural elements can be distinguished in the ETS: (i). a variable region (VR), demonstrating significant structural rearrangements and (ii). a conservative region (CR), evolving mainly by base substitutions. In VR, a conservative element (CE) with similarity to the ETS of distantly related Nicotiana is present. The ancestral organization of ETS (variant A) was found for non-tuber-bearing species of ser. Etuberosa, tuber-bearing wild potatoes of Central American ser. Bulbocastana, Pinnatisecta, and Polyadenia and S. dulcamara. Duplication of CE took place in the ETS of species from ser. Commersoniana and Circaeifolia (variant B). South American diploids and Mexican polyploids from superser. Rotata also possess two CE, and additionally two duplications around CE1 are present in VR (variant C). Three major lineages could be distinguished: non-tuber-bearing species of ser. Etuberosa, tuber-bearing Central American diploids and all South American species radiated from a common ancestor at early stages of evolution, indicating a South American origin of the tuber-bearing species. Later, Central and South American diploids evolved further as independent lineages. South American species form a monophyletic group composed of series with both stellata and rotata flower morphology. Solanum commersonii represents a sister taxon for all rotata species, whereas ser. Circaeifolia diverged earlier. Two main groups, C1 and C2, may be distinguished for species possessing ETS variant C. C1 contains ser. Megistacroloba, Conicibaccata, Maglia, and Acaulia, whereas all diploids of ser. Tuberosa are combined into C2. A closer relationship of Solanum chacoense (ser. Yungasensa) to the C2 group was found. The origin of polyploid species Solanum maglia, Solanum acaule, Solanum tuberosum, Solanum iopetalum, and Solanum demissum is discussed.     

CHLOROPLAST DNA EVIDENCE FOR THE INTERRELATIONSHIPS OF TOMATOES,POTATOES, AND PEPINOS (SOLANACEAE)

We used chloroplast DNA restriction site analysis to test hypotheses of relationships of Solarium subgenus Potatoe (including potatoes and pepinos), two other Solanum, Cyphomandra (the tree tomatoes), and Lycopersicon (the tomatoes). Capsicum and Datura were used as outgroups. The results support two main clades among the taxa we studied: 1) Solanum subgenus Potatoe and Lycopersicon; and 2) other Solanum and Cyphomandra. Within the first clade, the following groups were supported: a) sect. Basarthrum and sect. Anarrhichomenum; b) sect. Etuberosum; c) sect. Petota; d) sect. Juglandifolium, including subsect. Lycopersicoides; and e) the genus Lycopersicon. These results, in combination with an analysis of morphological data, advocate the controversial, but previously suggested, treatment of Lycopersicon as congeneric with Solanum in subgenus Potatoe. Thus, the cultivated tomato will be recognized as Solanum lycopersicum L. Solanum chmielewskii and Solanum lycopersicum var. cerasiforme are proposed as new combinations; Solanum neorickii is proposed as a new name for Lycopersicon parviflorum. Our data also suggest that Cyphomandra should be included within Solanum.     

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.     

Stomatal Response of some Cultivated and Wild Tuber-bearing Potatoes in Warm Tropics as Influenced by Water Deficits

Leaf resistances of 14 cultivated potato genotypes (Solanumspp) and three tuber-bearing wild Solanum species were comparedwhen plants were grown under water stress at two tropical sitesFactors investigated were diurnal changes in leaf resistance,the effect of plant age, transient drought versus well-wateredconditions of potted and field-grown plants These measurementswere carried out in order to determine the stomatal behaviourof tuber-bearing genotypes and species Significant genotypic differences in leaf resistances were notedwithin the cultivated genotypes All genotypes had higher resistanceswhen water-stressed, but LT-7 appeared to have the lowest leafresistances Genetic differences in stomatal behaviour of tuber-bearingSolanum species were confirmed Abaxial stomatal resistancesof water-stressed plants of the species ranged between 1 74and 13 8 s cm^–1 Stomata of S chacoense were less affectedby drought (three-fold) than S tuberosum (four-fold) The greatesteffect was on S jungasense (five-fold) and on S raphanifoliumThese data show that stomata behaviour among tuber-bearing Solanumspecies is sufficiently different to warrant investigationsof drought-resistance in potato species under dry hot conditions Solanum tuberosum L., Solanum raphanifolium, Solanum chacoense, Solanum jungasense, leaf resistance     

Somatic hybridization in the genus Solanum: S. tuberosum and S. brevidens

Somatic hybrid plants were regenerated from fused mesophyll protoplasts of an albino potato (Solanum tuberosum spp. tuberosum) variant and Solanum brevidens, a non-tuber bearing species which is sexually incompatible with S. tuberosum. These somatic hybrid plants represent the first example of direct hybridization between potato and members of the taxonomic group Etuberosa, and offer the potential for introgressing valuable germplasm from Solanum species outside the sexually compatible range into a worldwide crop species.     

New species of <Emphasis Type="Italic">Euphorbia</Emphasis> (Euphorbiaceae) from eastern Ethiopia

The new species Solanum pronum Thulin, from Acacia-Commiphora bushland in eastern Ethiopia and central Somalia, is described and illustrated. It is a member of Solanum sect. Somalanum and is compared with S. benadirense, S. jubae and S. pampaninii.     

Structure and expression of a hybrid proline-rich protein gene in the solanaceous species,Solanum brevidens, Solanum tuberosum, andLycopersicum esculentum

The full-length cDNA of a previously identified Solanum brevidens gene was isolated and characterised. DNA sequence analysis revealed an open reading frame that encodes a hybrid proline-rich cell wall protein of 407 amino acids. The putative protein was designated SbrPRP. The SbrPRP harbours three parts, an N-terminal signal peptide followed by a repetitive proline-rich domain and a cysteine-rich C-terminus resembling non-specific lipid-transfer proteins. The repetitive proline-rich domain contains two repeated motifs, PPHVKPPSTPK and PTPPIVSPP extended with TPKYP and TPKPPS motifs, respectively, at their N- or C-terminal. The SbrPRP gene of the non-tuberising Solanum species, Solanum brevidens, possesses highly homologous counterparts in the tuberising species, Solanum tuberosum (StPRP) and in the related species, Lycopersicum esculentum (TFM7). All three genes are present in single- or low copy number in the corresponding genome. Organ-specific expression of the genes, however, is different in the three solanaceous species.     

Molecular analysis of highly repeated genome fractions in Solanum and their use as markers for the characterization of species and cultivars

Summary Highly repeated DNA of potato (Solanum sp.) was characterized by cloning various major repeated elements of the nuclear genome. The percentage of the nuclear genome of the specific fractions and the restriction enzyme patterns were determined in order to show the distribution and organization of the respective repeats in the genome of Solanum tuberosum cultivars, dihaploid breeding lines and in wild species of Solanum. Several of the clones obtained were represented in a high copy number but showed no informative RFLP patterns. More information was gained from restriction satellite repeats. The clone pR1T320 was found to contain satellite repeats (360 bp in length) that are proportionally present in the genome of all Solanum species at frequencies, between 0.5% and 2.6% and which are differently organized. This repeat was also found in the genera Lycopersicon, Datura and Nicotiana. With various restriction enzymes characteristic RFLP patterns were detected. A more or less genus-specific element for Solanum was the 183-bp repeat (clone pSA287; between 0.2–0.4% of the nuclear genome) that was present in the majority of the Solanum species analyzed except S. kurtzianum, S. bulbocastanum and S. pinnatisectum. In a few wild species (prominently in S. kurtzianum, S. demissum and S. acaule) a specific repeat type was detected (clone pSDT382; repeat length approximately 370 bp) that could be used to trace the wild species introduced into S. tuberosum cultivars. The repeats analyzed together with the 18S, 5.8S and 25S ribosomal DNA (1.9–5.2%, corresponding to 1800-5500 rDNA copies) comprised approximately 4–7% of the Solanum genome.     

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.     

ALLOZYME VARIATION WITHIN SOLANUM SECT. PETOTA,SER. ETUBEROSA (SOLANACEAE)

Enzyme electrophoresis was employed to measure genetic variation within and divergence among 32 populations of three species in Solanum sect. Petota (S. brevidens, S. etuberosum, and S. fernandezianum). These species are self-compatible, diploid (2n = 2x = 24), and members of the monophyletic series Etuberosa. Solanum etuberosum is distributed in southern Chile, S. brevidens occurs in southern Chile and adjacent southern Argentina, and S. fernandezianum is endemic to Masatierra Island in the Juan Fernández Archipelago, 650 km west of continental Chile. Very low levels of observed heterozygosity (0.00–0.04) are found within populations of all three species. Interspecific mean genetic identities between S. brevidens and S. etuberosum (0.854) were similar to their intraspecific values (0.923, 0.865, respectively), with both species monomorphic for alleles at nine of the 12 loci examined. Solanum fernandezianum shows no heterozygosity and is more divergent to both S. brevidens (0.780) and S. etuberosum (0.698) than either is to each other. The divergence of S. fernandezianum to S. brevidens and S. etuberosum results from novel alleles at two of the 12 isozyme loci; in addition, it possesses only a subset of the variability found in S. brevidens and S. etuberosum at three other loci.     

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.     

Novel inter-series hybrids in Solanum, section Petota

Sexual hybrids between distantly related Solanum species can undergo endosperm failure, a post-zygotic barrier in inter-species hybridizations. This barrier is explained by the endosperm balance number (EBN) hypothesis, which states that parents must have corresponding EBNs for viable seed formation. Tests for inter-crossability were made involving the Mexican species Solanum pinnatisectum Dunal. (series Pinnatisecta, A^piA^pi, 1EBN), autotetraploids of this species, Solanum verrucosum Schlechtd. (series Tuberosa, AA, 2EBN), haploids (2x, 2EBN) of the South American S. tuberosum L. (series Tuberosa, A₁A₁A₂A₂, 4EBN), and F₂ haploid-species hybrids with South American species (AA, 2EBN) S. berthaultii Hawkes, S. sparsipilum (Bitter.) Juz. and Bukasov and S. chacoense Bitter. The development of hybrid endosperms was investigated for these combinations by confocal microscopy with regard to cell-division timing and tissue collapse. Novel sexual diploid (AA^pi) and triploid (AA^piA^pi) inter-series hybrids were generated from S. verrucosum × S. pinnatisectum crosses by using post-pollination applications of auxin. F₁ embryos were rescued in vitro. The hybrid status of recovered plants was verified by microsatellite marker analysis, and the ploidy was determined by chromosome counting. The application of phytohormones in inter-ploidy S. pinnatisectum × S. tuberosum crosses, however, did not delay endosperm collapse, and embryos were not formed. Other diploid, 1EBN species tested in remote hybridizations with Group Tuberosum were S. cardiophyllum Lindl., S. trifidum Correll, and S. tarnii Hawkes and Hjert., series Pinnatisecta, and S. bulbocastanum Dunal., series Bulbocastana. Based on the analysis of post-zygotic reproductive barriers among isolated species of section Petota, we propose strategies to overcome such incompatibilities.