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Phylogenetic relationships of wild and cultivated species of Allium section Cepa inferred by nuclear rDNA ITS sequence analysis

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Abstract

Allium section Cepa consists of 12 species most of which are used by humans as condiment, vegetable or medicinal plants. Common onion (Allium cepa) and bunching onion (A. fistulosum) are cultivated species while all others are locally collected from the wild. Although common onion is the most important crop within Allium, its wild progenitor and origin are still not clear. We analyzed the phylogeny of Allium section Cepa using sequences of the nuclear ribosomal DNA internal transcribed spacer (ITS) region of 36 accessions representing eleven species of section Cepa, together with eight outgroup species with phenetic, cladistic, and model-based algorithms. These analyses confirmed section Cepa to be monophyletic and revealed three species groups within the section. These are (i) A. altaicum/A. fistulosum, (ii) A. farctum/A. roylei/A. asarense/A. cepa/A. vavilovii, and (iii) A. galanthum/A. oschaninii/A. praemixtum/A. pskemense. While the first two groups were statistically well supported for the last group support was low, although it resulted in all phylogenetic analyses conducted. Tree and network-based analyses grouped A. cepa within A. vavilovii, indicating the latter to be progenitor of the common onion. However, also an origin of A. cepa through hybridization of A. vavilovii with A. galanthum or A. fistulosum seems possible. We argue that a subdivision of section Cepa in subsections Cepa and Phyllodolon, although possible from our data, as well as the formal description of alliances do not seem reasonable in a small group of species.

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References

  • Álvarez I and Wendel JF (2003). Ribosomal ITS sequences and plant phylogenetic inference. Molec Phylogenet Evol 29: 417–434

    Article  PubMed  Google Scholar 

  • Arnheim N, Krystal M, Schmickel R, Wilson G, Ryder O and Zimmer E (1980). Molecular evidence for genetic exchange among ribosomal genes on nonhomologous chromosomes in man and apes. Proc Natl Acad Sci USA 77: 7323–7327

    Article  PubMed  CAS  Google Scholar 

  • Baldwin BG, Sanderson MJ, Wojciechowski JM, Campbell CS and Donoghue MJ (1995). The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann Missouri Bot Gard 82: 247–277

    Article  Google Scholar 

  • Blattner FR (1999). Direct amplification of the entire ITS region from poorly preserved plant material using recombinant PCR. Biotechniques 29: 1180–1186

    Google Scholar 

  • Blattner FR (2004). Phylogenetic analysis of Hordeum (Poaceae) as inferred by nuclear rDNA ITS sequences. Molec Phylogenet Evol 33: 289–299

    Article  PubMed  CAS  Google Scholar 

  • Blattner FR and Friesen N (2006). Relationship between Chinese chive (Allium tuberosum) and its putative progenitor A. ramosum as assessed by random amplified polymorphic DNA (RAPD). In: Zeder, MA, Bradley, D, Emshwiller, E and Smith, BD (eds) Documenting domestication: new genetic and archaeological paradigms, pp 134–142. Univ California Press, Berkeley

    Google Scholar 

  • Bradeen JM and Havey MJ (1995). Restriction fragment length polymorphisms reveal considerable nuclear divergence within a well-supported maternal clade in Allium section Cepa (Alliaceae). Amer J Bot 82: 1455–1462

    Article  Google Scholar 

  • Clement M, Posada D and Crandall KA (2000). TCS: A computer program to estimate gene genealogies. Molec Ecol 9: 1657–1660

    Article  CAS  Google Scholar 

  • Dubouzet JG, Shinoda K and Murata N (1997). Phylogeny of Allium L. subgenus Rhizirideum (G. Don ex Koch.) Wendelbo according to dot blot hybridization with randomly amplified DNA probes. Theor Appl Genet 95: 1223–1228

    Article  CAS  Google Scholar 

  • Hanelt P (1985). Zur Taxonomie, Chorologie und Ökologie der Wildarten von Allium L. sect. Cepa (Mill.) Prokh. Flora 176: 99–116

    Google Scholar 

  • Hanelt P (1990). Taxonomy, evolution and history. In: Rabinowitch, HD and Brewster, JL (eds) Onions and allied crops, Vol. I. Botany, physiology and genetics, pp 1–26. CRC Press, Boca Raton

    Google Scholar 

  • Havey MJ (1992). Restriction enzyme analysis of the chloroplast and nuclear 45S ribosomal DNA of Allium sections Cepa and Phyllodolon (Alliaceae). Pl Syst Evol 183: 17–31

    Article  CAS  Google Scholar 

  • Friesen N and Klaas M (1998). Origin of some minor propagated Allium crops studied with RAPD und GISH. Genet Res Crop Evol 45: 511–523

    Article  Google Scholar 

  • Friesen N, Pollner S, Bachmann K and Blattner FR (1999). RAPDs and noncoding chloroplast DNA reveal a single origin of the cultivated Allium fistulosum from A. altaicum. Amer J Bot 86: 554–562

    Article  CAS  Google Scholar 

  • Friesen N, Fritsch RM, Blattner FR (2006) Phylogeny and new intrageneric classification of Allium (Alliaceae) based on nuclear rDNA ITS sequences. In: Columbus JT, Friar EA, Hamilton CW, Porter JM, Prince LM, Simpson MG (eds) Monocots: comparative biology and evolution I. Aliso 22: 372–395.

  • Fritsch RM and Friesen N (2002). Evolution, domestication and taxonomy. In: Rabinowitch, HD and Currah, L (eds) Allium crop science: Recent advances, pp 5–30. CABI Publ, Wallingford

    Google Scholar 

  • Jakob SS and Blattner FR (2006). A chloroplast genealogy of Hordeum (Poaceae): long-term persisting haplotypes, incomplete lineage sorting, regional extinction and the consequences for phylogenetic inference. Molec Biol Evol 23: 1602–1612

    Article  PubMed  CAS  Google Scholar 

  • Klaas M and Friesen N (2002). Molecular markers in Allium. In: Rabinowitch, HD and Currah, L (eds) Allium crop science: Recent advances, pp 159–185. CABI Publ, Wallingford

    Google Scholar 

  • Lilly JW and Havey MJ (2001). Sequence analysis of a chloroplast intergenic spacer for phylogenetic estimates in Allium section Cepa and a PCR-based polymorphism detecting mixtures of male-fertile and male-sterile cytoplasmic onion. Theor Appl Genet 102: 78–82

    Article  CAS  Google Scholar 

  • Maas IH (1996). About the origin of the French grey shallot. Genet Res Crop Evol 43: 291–292

    Article  Google Scholar 

  • Posada D and Crandall KA (1998). Modeltest: Testing the model of DNA substitution. Bioinformatics 14: 817–818

    Article  PubMed  CAS  Google Scholar 

  • Posada D and Crandall KA (2001). Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol 16: 37–45

    Article  PubMed  Google Scholar 

  • Prokhanov JI (1930). K poznaniju kul'turnykh lukov i chesnokov Kitaja i Japonii. Trudy prikl bot, genet. Selekcii 24: 123–188

    Google Scholar 

  • Rieseberg LH, Whitton J and Linder CR (1996). Molecular marker incongruence in plant hybrid zones and phylogenetic trees. Acta Bot Neerl 45: 243–262

    CAS  Google Scholar 

  • Ronquist F and Huelsenbeck JP (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574

    Article  PubMed  CAS  Google Scholar 

  • Schubert I and Wobus U (1985). In situ hybridization confirms jumping nucleolus organizing regions in Allium. Chromosoma 92: 143–148

    Article  Google Scholar 

  • Stearn WT (1960). Allium and Milula in the Central and Eastern Himalaya. Bull Br Mus Nat Hist (Bot.), B 2 6: 159–191

    Google Scholar 

  • Swofford DL (2002). Paup*. Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland, MA

    Google Scholar 

  • van Raamsdonk LWD, Wiestma WA and De Vries JN (1992). Crossing experiments in Allium L. section Cepa. Bot J Linn Soc 109: 193–303

    Google Scholar 

  • van Raamsdonk LWD, Vrielink-van Ginkel M and Kik C (2000). Theor Appl Genet 100: 1000–1009

    Article  Google Scholar 

  • van Raamsdonk LWD, Ensink W, van Heusden AW, Vrielink-van Ginkel M and Kik C (2003). Biodiversity assessment based on cpDNA and crossability analysis in selected species of Allium subgenus Rhizirideum. Theor Appl Genet 107: 1048–1058

    Article  PubMed  Google Scholar 

  • Vosa CG (1976). Heterochromatic patterns in Allium. I. The relationships between the species of the Cepa group and its allies. Heredity 36: 383–392

    Google Scholar 

  • Wendel JF and Doyle JJ (1998). Phylogenetic incongruence: window into genome history and molecular evolution. In: Soltis, DE, Soltis, PS and Doyle, JJ (eds) Molecular systematics of plants II: DNA sequencing, pp 265–296. Kluwer, Dordrecht

    Google Scholar 

  • Wendelbo P (1971) Alliaceae. In: Rechinger KH (ed) Flora Iranica. No. 76. Graz, Akademische Druck- und Verlagsanstalt

  • Wissemann V (2003). Hybridization and the evolution of the nrITS spacer region. In: Sharma, AK and Sharma, A (eds) Plant genome, biodiversity and evolution, vol. 1, part A, pp 57–71. Science Publishers, Enfield, New Hampshire

    Google Scholar 

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Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Research (IPK), Gatersleben, Germany

    M. Gurushidze, S. Mashayekhi, F. R. Blattner & R. M. Fritsch

  2. N. Ketskhoveli Institute of Botany, Tbilisi, Georgia

    M. Gurushidze

  3. Botanical Garden, University of Osnabrück, Osnabrück, Germany

    N. Friesen

Authors
  1. M. Gurushidze
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  2. S. Mashayekhi
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  3. F. R. Blattner
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  4. N. Friesen
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  5. R. M. Fritsch
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Correspondence to F. R. Blattner.

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Gurushidze, M., Mashayekhi, S., Blattner, F. et al. Phylogenetic relationships of wild and cultivated species of Allium section Cepa inferred by nuclear rDNA ITS sequence analysis. Plant Syst. Evol. 269, 259–269 (2007). https://doi.org/10.1007/s00606-007-0596-0

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  • DOI: https://doi.org/10.1007/s00606-007-0596-0

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