Skip to main content
SpringerLink
Log in

Analysis of ITS of the rDNA to infer phylogenetic relationships among Vietnamese Citrus accessions

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

This study focused on clarifying phylogenetic relationships among Citrus accessions from Vietnam. Our phylogenetic analysis based on nucleotide sequences from the ITS of the ribosomal DNA included 69 accessions belonging to Citrus and related (sub)genera. Maximum parsimony and Bayesian analysis confirmed a clear separation of the three ‘true’ Citrus species (C. medica, C. maxima and C. reticulata). Confirming recent taxonomic revisions, Fortunella, Poncirus trifoliata and Citrus hystrix are clustered among the accessions of subgenus Citrus. C. × sinensis accessions revealed a close evolutionary relationship to either C. maxima or C. reticulata, thereby confirming their involvement in its hybrid origin. Also, some other hybrid taxa and their proposed parental species were investigated and their origin could in some cases be confirmed using the ITS sequence data.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing genetic diversity and population structure in a Citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531

    Article  CAS  PubMed  Google Scholar 

  • Barrett HC, Rhodes AM (1976) A numerical taxonomic study of the affinity relationships in cultivated Citrus and its close relatives. Syst Bot 1:105–136

    Article  Google Scholar 

  • Bretó MP, Ruiz C, Pina JA, Asins MJ (2001) The diversification of Citrus clementina Hort. Ex Tan., a vegetatively propagated crop species. Mol Phyl Evol 21:285–293

    Article  Google Scholar 

  • Fang DQ, Roose ML (1997) Identification of closely related Citrus cultivars with inter-simple sequence repeats markers. Theor Appl Genet 95:408–417

    Article  CAS  Google Scholar 

  • Fang DQ, Roose ML, Krueger RR, Federici CT (1997) Fingerprinting trifoliate orange germplasm accessions with isozymes, RFLPs, and inter-simple sequence repeat markers. Theor Appl Genet 95:211–219

    Article  CAS  Google Scholar 

  • Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 94:812–822

    Article  Google Scholar 

  • Gmitter FG Jr (1995) Origin, evolution and breeding of the grapefruit. Plant Breed Rev 13:345–363

    Google Scholar 

  • Green RM, Vardi A, Galune E (1986) The plastome of Citrus. Physical map, variation among Citrus cultivars and species and comparison with related genera. Theor Appl Genet 72:170–177

    Article  CAS  Google Scholar 

  • Gulsen O, Roose ML (2001) Lemons: diversity and relationships with selected Citrus genotypes as measured with nuclear genome markers. J Amer Soc Hort Sci 126:309–317

    CAS  Google Scholar 

  • Herrero R, Asins MJ, Carbonell EA, Navarro L (1996) Genetic diversity in the orange subfamily Aurantioideae. I. Intraspecies and intragenus genetic variability. Theor Appl Genet 92:599–609

    Article  CAS  Google Scholar 

  • Hodgson RW (1965) Taxonomy and nomenclature in the Citrus fruits. In: Krishnamurthi S (ed) Advances in agriculture sciences and their applications. Agric. Coll. Res. Inst., Coimbatore, pp 317–331

    Google Scholar 

  • Hodgson RW (1967) Horticultural varieties of Citrus. In: Reuther W, Webber HJ, Batchelor LD (eds) The Citrus industry. Vol. I. history world distribution, botany, and varieties. Univ of California, Div of Agricultural Sci, Berkeley, pp 431–591

    Google Scholar 

  • Hooker JD (1875) Rutaceae. In: Reeve L (ed) The flora of British India. London, pp 484–517

  • Jena SN, Kumar S, Nair NK (2009) Molecular phylogeny in Indian Citrus L. (Rutaceae) inferred through PCR-RFLP and trnL-trnF sequence data of chloroplast DNA. Scientia Hort 119:403–416. doi:10.1016/j.scienta.2008.08.030

    Article  CAS  Google Scholar 

  • Linnaeus C (1753) Species plantarum, exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominibus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale digestas. Holmiae

  • Mabberley DJ (2008a) 21. CITRUS Linnaeus, Sp. Pl. 2: 782. 1753. Flora China 11:90–96

    Google Scholar 

  • Mabberley DJ (2008b) Mabberley’s plant book: a portable dictionary of plants, 3rd edn. Cambridge University Press, Avon

    Google Scholar 

  • Moore GF (2001) Orange and lemons: clues to the taxonomy of Citrus from molecular markers. Trends Genet 17:536–540

    Article  CAS  PubMed  Google Scholar 

  • Nicolosi E, Deng ZN, Gentile A, La Malfa S, Continella G, Tribulato E (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100:1155–1166

    Article  CAS  Google Scholar 

  • Pang XM, Hu DG, Deng XX (2003) Phylogenetic relationships among Citrus and its relatives as revealed by SSR markers. Acta Genet Sin 30:81–87

    CAS  PubMed  Google Scholar 

  • Pang XM, Hu CG, Deng XX (2007) Phylogenetic relationships within Citrus and its related genera as inferred from AFLP markers. Genet Resour Crop Evol 54:429–436

    Article  CAS  Google Scholar 

  • Rogers SO, Bendich AJB (1988) Extraction of DNA from plant tissues Plant molecular Biology Manual, vol A6. Kluwer Academic Publishers, Dordrecht, pp 1–10 printed in Belgium

    Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 12:1572–1574

    Article  Google Scholar 

  • Scora RW (1975) On the history and origin of Citrus. Bull Torrey Bot Club 102:369–375

    Article  Google Scholar 

  • Singh R, Nath N (1969) Practical approach to the classification of Citrus. Proceedings of 1st international Citrus symposium, pp 435–440

  • Swingle WT, Reece PC (1967) The botany of Citrus and its wild relatives. In: Reuther W, Webber HJ, Batchelor LD (eds) The Citrus industry. Vol. I. History, world distribution, botany, and varieties. Univ of California, Div of Agricultural Sci, Berkeley, pp 190–430

    Google Scholar 

  • Swofford DL (2002) PAUP. Phylogenetic analysis using parsimony (* and other methods). Version 4.0. Sinauer Associates, Boston

    Google Scholar 

  • Tanaka T (1954) Species problem in Citrus. A critical study of wild and cultivated units of Citrus, based upon field studies in their native homes. Japanese Society for the Promotion of Science, Ueno

    Google Scholar 

  • Tanaka T (1977) Fundamental discussion of Citrus classification. Stud Citrol 14:1–6

    Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  Google Scholar 

  • Torres AM, Soost RK, Diedenhofen U (1978) Leaf isozymes as genetic markers in Citrus. Am J Bot 65:869–881

    Article  Google Scholar 

  • Webber HJ (1967) History and development of the Citrus industry. In: Reuther W, Webber HJ, Batchelor LD (eds) The Citrus industry. Vol. I. history world distribution, botany, and varieties. Univ of California, Div of Agricultural Sci, Berkeley, pp 1–39

    Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Shinsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322

    Google Scholar 

Download references

Acknowledgments

Special thanks are given to colleagues and institutions for providing Citrus accessions and technical assistance: Dr. Do Dinh Ca-Research Institute for Fruits and Vegetables (RIFAV) (Ha Noi), Ms Vo Thi Tuyet-Phu Qui’s Fruit Tree Center, (PQFC), Dr. Pham Van Chuong-Agricultural Science Institute of North-Central Vietnam (ASINC), MSc Doan Nhan Ai- Fruit Tree Research & Development Center of ThuaThien-Hue (FRDC-Hue), Dr. Nguyen Minh Chau, Dr. Nguyen Thi Thu Hong, Ir Pham Ngoc Lieu-Institute of Southern Fruit Research Institute (SOFRI).

Author information

Authors and Affiliations

  1. Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University (UGent), Coupure Links 653, 9000, Ghent, Belgium

    Tina Kyndt & Godelieve Gheysen

  2. Biotechnology Research and Development Institute, Can Tho University, Campus II, 3-2 Street, Can Tho City, Vietnam

    Tran Nhan Dung & Ha Thanh Toan

  3. Department of Biology, Faculty of Sciences, UGent, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium

    Paul Goetghebeur

Authors
  1. Tina Kyndt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tran Nhan Dung
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paul Goetghebeur
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ha Thanh Toan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Godelieve Gheysen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Godelieve Gheysen.

Additional information

Tina Kyndt and Tran Nhan Dung equally contributed to this work.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kyndt, T., Dung, T.N., Goetghebeur, P. et al. Analysis of ITS of the rDNA to infer phylogenetic relationships among Vietnamese Citrus accessions. Genet Resour Crop Evol 57, 183–192 (2010). https://doi.org/10.1007/s10722-009-9460-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-009-9460-0

Keywords

Search

Navigation