SolRgene

Phylogen of Solanum

The secondary genepool of our modern cultivated potato (Solanum tuberosum L.) consists of a large number of tuber-bearing wild Solanum species which grow in various habitats from the southern states of the USA to the most southern parts of Chile and Argentina. These wild species are important as a resource for valuable traits that can be used to improve the quality of the cultivars, including resistance against important diseases like Phytophthora infestans and potato cyst nematodes (Globodera spp.). Therefore it is no surprise that the wild relatives of the cultivated potato have since long drawn the attention of many plant breeders and botanists. To benefit most from the possibilities that the secondary genepool has to offer, it is necessary to have a good insight in the taxonomy. The classical treatments of potato taxonomy are from Correll [1], and Hawkes [2], later followed by reviews from Spooner and Hijmans [3], Spooner and Salas [4], and van den Berg and Jacobs [5].

There are two major taxonomic problems in the section Petota. First, many described species are extremely similar to each other and section Petota seems to be overclassified [5]. In many cases, potato species can only be distinguished by means of multivariate analysis of quantitative characters and/or on the basis of geographic origin [6-9].

The main cause for these difficulties is the ability of many species in section Petota to hybridize easily with other species [4]. Many species have been suspected to arise from hybrid speciation. Other causes are high morphological similarity among species, and phenotypic plasticity in different environments [3]. In recent reviews the number of species is reduced due to increased insights in potato taxonomy. Hawkes [2] recognized 227 tuber bearing species (7 cultivated species included) and 9 non-tuber-bearing species within section Petota. Spooner and Hijmans [3] recognized 203 tuber-bearing species including 7 cultivated species. Finally, Spooner and Salas [4], reduced the number further to 189 species (including 1 cultivated species) in section Petota.

The second taxonomic problem is the series classification. Hawkes [2] classified section Petota into 19 tuber bearing series plus two non-tuber bearing series that vary considerably in the number of species included. The boundaries between some series are unclear. As outlined earlier by Spooner et al. [10], the series classification of Hawkes and previous authors has received only partial cladistic support in any molecular study to date. The cpDNA RFLP data from Spooner and Sytsma [11], Castillo and Spooner [12], Rodriguez and Spooner [13], and Spooner and Castillo [14] could only find support for a classification in 4 clades.

The aim of the present study is to focus on the second problem and to describe the structure within section Petota. In the present study the largest number of species and accessions to date are examined in one simultaneous AFLP analysis. The obtained data are used for evaluation of the hypothesis put forward by Hawkes [2] that section Petota can be divided in 21 series and the hypothesis of Spooner and Castillo [14], that the section consists of 4 clades only.

AFLP has proven to be a useful method to solve phylogenetic relationships at a low taxonomic level [15-17]. The application of AFLP has many advantages. It produces highly reproducible data [18], it does not need a priori sequence information and it has the ability of high resolution [17]. Because AFLP generates fragments at random over the whole genome it avoids the problem that many sequence data based phylogeny reconstructions have, e.g. the generation of a gene tree instead of a species tree [15].

Results

We constructed a NJ tree for 4929 genotypes. For the other analyses, due to practical reasons, a condensed dataset was created consisting of one representative genotype from each available accession. We show a NJ jackknife and a MP jackknife tree. A large part of both trees consists of a polytomy. Some structure is still visible in both trees, supported by jackknife values above 69. We use these branches with > 69 jackknife support in the NJ jackknife tree as a basis for informal species groups. The informal species groups recognized are: Mexican diploids, Acaulia, Iopetala, Longipedicellata, polyploid Conicibaccata, diploid Conicibaccata, Circaeifolia, diploid Piurana and tetraploid Piurana.

Conclusion

Most of the series that Hawkes and his predecessors designated can not be accepted as natural groups, based on our study. Neither do we find proof for the 4 clades proposed by Spooner and co-workers. A few species groups have high support and their inner structure displays also supported subdivisions, while a large part of the species cannot be structured at all. We believe that the lack of structure is not due to any methodological problem but represents the real biological situation within section Petota.

Interactive Phylogenetic tree

In this resource, we offer the interactive, searchable version of the NJ tree for 4929 genotypes. The different groups, in the tree, can be highlighted using the three letter coded species codes.

References

  1. Correll DS: The potato and its wild relatives. In Contributions from the Texas Research Foundation 4. Texas Research Foundation, Renner, Texas; 1962.
  2. Hawkes JG: The Potato, Evolution, Biodiversity and Genetic Resources. London: Belhaven Press; 1990.
  3. Spooner DM, Hijmans RJ: Potato systematics and germplasm collecting, 1989–2000. Amer J of Potato Res 2001, 78:237-268.
  4. Spooner DM, Salas A: Structure, biosystematics and genetic resources. In Handbook of Potato, production, improvement and postharvest management. Edited by: Gopal J, Khurana SMP. New York: The Haworth Press; 2006:1-39.

  5. Berg RG, Jacobs MMJ: Molecular Taxonomy.

    In Potato Biology and Biotechnology Edited by: Vreugdehil D, Elsevier. 2007, 55-76.

  6. Giannattasio RG, Spooner DM: A reexamination of species boundaries and hypotheses concerning Solanum megistacrolobum and S. toralapanum (Solanum sect. Petota series Megistacroloba): Molecular data.

    Syst Bot 1994, 19:106-115. Publisher Full Text

  7. Berg RG, Miller JI, Ugarte ML, Kardolus JP, Villand J, Nienhuis J, Spooner DM: Collapse of morphological species in the wild potato Solanum brevicaule complex (Solanaceae: sect. Petota).

    Am J Bot 1998, 85:92-109. Publisher Full Text
  8. Berg RG, Groendijk-Wilders N: Numerical analysis of the taxa of series Circaeifolia (Solanum sect. Petota). In Proceedings of the International Conference Solanaceae IV: July 1994, Adelaide. Edited by: Nee M, Symon DE, Lester RN, Jessop JP. The Royal Botanical gardens, Kew; 1999:213-226.
  9. Kardolus JP: A biosystematic analysis of Solanum acaule. In PhD Thesis. Wageningen University; 1998.
  10. Spooner DM, Berg RG, Rodríguez A, Bamberg J, Hijmans RJ, Lara-Cabrera SI: Wild Potatoes (Solanum section Petota; Solanaceae) of North and Central America. In Systematic Botany Monographs. Edited by: McPherson GD, Prather LA, Ranker TA, Reznicek AA. USA: The American Society of Plant Taxonomists; 2004.

  11. Spooner DM, Sytsma KJ: Reexamination of Series Relationships of Mexican and Central-American Wild Potatoes (Solanum Sect Petota) – Evidence from Chloroplast DNA Restriction Site Variation.

    Syst Bot 1992, 17:432-448. Publisher Full Text

  12. Castillo RO, Spooner DM: Phylogenetic relationships of wild potatoes, Solanum series Conicibaccata (Sect. Petota).

    Syst Bot 1997, 22:45-83. Publisher Full Text

  13. Rodríguez A, Spooner DM: Chloroplast DNA analysis of Solanum bulbocastanum and S. cardiophyllum, and evidence for the distinctiveness of S. cardiophyllum subsp. ehrenbergii (sect. Petota).

    Syst Bot 1997, 22:31-43. Publisher Full Text

  14. Spooner DM, Castillo RT: Reexamination of series relationships of South American wild potatoes (Solanaceae : Solanum Sect. Petota): Evidence from chloroplast DNA restriction site variation.

    Am J B 1997, 84:671-685. Publisher Full Text

  15. Despres L, Gielly L, Redoutet W, Taberlet P: Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability.

    Mol Phylogenet Evol 2003, 27:185-196. Publisher Full Text

  16. Koopman WJM: Phylogenetic signal in AFLP Data Sets.

    Syst Biol 2005, 54:197-217. Publisher Full Text

  17. Meudt HM, Clarke AC: Almost Forgotten or latest Practice? AFLP applications, analyses and advances.

    Trends in Plant Science 2007, 12:106-117. Publisher Full Text

  18. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert E, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A: Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories.

    Mol Breed 1997, 3:381-390. Publisher Full Text