Skip to main content

Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers

Molecular Biology Reports volume 39, pages 3637–3647 (2012)Cite this article

Abstract

The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

References

  1. Han YC, Teng CZ, Chang FH, Robert GW, Zhou MQ, Hu ZL, Song YC (2007) Analysis of genetic relationships in Nelumbo nucifera using nuclear ribosomal ITS sequence data, ISSR and RAPD markers. Aquat Bot 87:141–146

    Article  CAS  Google Scholar 

  2. Pan L, Xia QJ, Quan ZW, Liu HG, Ke WD, Ding Y (2010) Development of novel EST–SSRs from sacred lotus (Nelumbo nucifera Gaertn) and their utilization for the genetic diversity analysis of N. nucifera. J Hered 101(1):71–82

    PubMed  Article  CAS  Google Scholar 

  3. Hu M, Skibsted LH (2002) Antioxidative capacity of rhizome extract and rhizome knot extract of edible lotus (Nelumbo nucifera). Food Chem 76:327–333

    Article  CAS  Google Scholar 

  4. Kashiwada Y, Aoshima A, Ikeshiro Y, Chen YP, Furukawa H, Itoigawa M, Fujioka T, Mihashi K, Cosentino LM, Morris-Natschke SL, Lee KH (2005) Anti-HIV benzylisoquinoline alkaloids and flavonoids from the leaves of Nelumbo nucifera, and structure-activity correlations with related alkaloids. Bioorgan Med Chem 13:443–448

    Article  CAS  Google Scholar 

  5. Lee HK, Choi YM, Noh DO, Suh HJ (2005) Antioxidant effect of Korean traditional lotus liquor (Yunyupju). Int J Food Sci Tech 40:709–715

    Article  CAS  Google Scholar 

  6. Ling ZQ, Xie BJ, Yang EL (2005) Isolation, characterization, and determination of antioxidative activity of oligomeric procyanidins from the seedpot of Nelumbo nucifera Gaertn. J Agric Food Chem 53:2441–2445

    PubMed  Article  CAS  Google Scholar 

  7. An N, Guo HB, Ke WD (2009) Genetic variation in rhizome lotus (Nelumbo nucifera Gaertn. ssp. nucifera) germplasms from China assessed by RAPD markers. Agric Sci China 8(1):31–39

    Article  CAS  Google Scholar 

  8. Wang Q, Zhang X (2004) Illustrations of lotus cultivars in China. China Forestry Press, Beijing

    Google Scholar 

  9. Guo HB (2009) Cultivation of lotus (Nelumbo nucifera Gaertn. ssp. nucifera) and its utilization in China. Genet Resour Crop Evol 56:323–330

    Article  Google Scholar 

  10. Xue J, Zhuo L, Zhou S (2006) Genetic diversity and geographic pattern of wild lotus (Nelumbo nucifera) in Heilongjiang Province. Chin Sci Bull 51:421–432

    Article  CAS  Google Scholar 

  11. Guo HB, Li SM, Ke WD (2007) Genetic diversity of Nelumbo accessions revealed by RAPD. Genet Resour Crop Evol 54:741–748

    Article  Google Scholar 

  12. Han YC, Teng CZ, Zhong S, Zhou MQ, Hu ZL, Song YC (2007) Genetic variation and clonal diversity in populations of Nelumbo nucifera (Nelumbonaceae) in central China detected by ISSR markers. Aquat Bot 86:69–75

    Article  Google Scholar 

  13. Chen YY, Zhou RC, Lin XD, Wu KQ, Qian X, Huang SZ (2008) ISSR analysis of genetic diversity in sacred lotus cultivars. Aquat Bot 89:311–316

    Article  CAS  Google Scholar 

  14. Tian HL, Xue JH, Wen J, Mitchell G, Zhou SL (2008) Genetic diversity and relationships of lotus (Nelumbo) cultivars based on allozyme and ISSR markers. Sci Hortic 116:421–429

    Article  CAS  Google Scholar 

  15. Li Z, Liu XQ, Robert GW, Juntawong N, Zhou MQ, Chen LQ (2010) Genetic diversity and classification of Nelumbo germplasm of different origins by RAPD and ISSR analysis. Sci Hortic 125:724–732

    Article  CAS  Google Scholar 

  16. Sun QB, Li LF, Li Y, Wu GJ, Ge XJ (2008) SSR and AFLP markers reveal low genetic diversity in the biofuel plant Jatropha curcas in China. Crop Sci 48:1865–1871

    Article  CAS  Google Scholar 

  17. Gaudeul M, Till-Bottraud I, Barjon F, Manel S (2004) Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers. Heredity 92:508–518

    PubMed  Article  CAS  Google Scholar 

  18. Maguire TL, Peakall R, Saenger P (2002) Comparative analysis of genetic diversity in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae) detected by AFLPs and SSRs. Theor Appl Genet 104:388–398

    PubMed  Article  CAS  Google Scholar 

  19. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acid Res 21:4407–4414

    Article  Google Scholar 

  20. Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Catiglioni P, Taramino G et al (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97:1248–1255

    Article  CAS  Google Scholar 

  21. Teulat B, Aldam C, Trehin R, Lebrun P, Barker JHA, Arnold GM et al (2000) An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs. Theor Appl Genet 100:764–771

    Article  CAS  Google Scholar 

  22. Sudheer PDVN, Singh S, Mastan SG, Patel J, Reddy MP (2009) Molecular characterization and identification of markers for toxic and non-toxic varieties of Jatropha curcas L using RAPD, AFLP and SSR markers. Mol Biol Rep 36(6):1357–1364

    Article  Google Scholar 

  23. Pan L, Quan ZW, Li SM, Liu HG, Huang XF, Ke WD, Ding Y (2007) Isolation and characterization of microsatellite markers in the sacred lotus (Nelumbo nucifera Gaertn.). Mol Ecol Notes 7:1054–1056

    Article  CAS  Google Scholar 

  24. Tian HL, Chen XQ, Wang JX, Xue JH, Wen J, Mitchell G, Zhou SL (2008) Development and characterization of microsatellite loci for lotus (Nelumbo nucifera). Conserv Genet 9:1385–1388

    Article  CAS  Google Scholar 

  25. Kubo N, Hirai M, Kaneko A, Tanaka D, Kasumi K (2009) Development and characterization of simple sequence repeat (SSR) markers in the water lotus (Nelumbo nucifera). Aquat Bot 90:191–194

    Article  CAS  Google Scholar 

  26. Kubo N, Hirai M, Kaneko A, Tanaka D, Kasumi K (2009) Classification and diversity of sacred and American Nelumbo species: the genetic relationships of flowering lotus cultivars in Japan using SSR markers. Plant Genet Resour 7(3):260–270

    Article  CAS  Google Scholar 

  27. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  28. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.01): an integrated software package for population genetics data analysis. Computational and Molecular Population Genetics Lab (CMPG), Berne

  29. Van Ooseterhaut C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECHER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  Google Scholar 

  30. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap evolution. Int J Org Evol 39:779–783

    Google Scholar 

  31. Mantel M (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  32. Rohlf FJ (2008) NTSYSpc: numerical taxonomy and multivariate analysis system, ver. 2.21. Exeter Software, Setauket

    Google Scholar 

  33. Weir BS (1990) Genetic data analysis: Methods for discrete population genetic data. Sinauer Associates, Sunderland

    Google Scholar 

  34. Menkir A, Kling JG, Badu-Apraku B, Ingelbrecht I (2005) Molecular marker-based genetic diversity assessment of Striga-resistant maize inbred lines. Theor Appl Genet 110:1145–1153

    PubMed  Article  CAS  Google Scholar 

  35. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11:139–151

    PubMed  Article  CAS  Google Scholar 

  36. Sudheer PDVN, Pandya N, Reddy MP, Krishnan TR (2009) Comparative study of interspecific genetic divergence and phylogenic analysis of genus Jatropha by RAPD and AFLP. Mol Biol Rep 36:901–907

    Article  Google Scholar 

  37. Sudheer PDVN, Mastan SG, Rahman H, Prakash CR, Singh S, Reddy MP (2011) Cross species amplification ability of novel microsatellites isolated from Jatropha curcas and genetic relationship with sister taxa. Mol Biol Rep 38:1383–1388

    PubMed  Article  CAS  Google Scholar 

  38. Tahernezhad Z, Zamani MJ, Solouki M, Zahravi M, Imamjomeh AA, Jafaraghaei M, Bihamta MR (2010) Genetic diversity of Iranian Aegilops tauschii Coss. using microsatellite molecular markers and morphological traits. Mol Biol Rep 37:3413–3420

    PubMed  Article  CAS  Google Scholar 

  39. Wu ZH, Wang SZ, Hu JH, Li F, Ke WD, Ding Y (2011) Development and characterization of microsatellite markers for Sagittaria trifolia var. sinensis (Alismataceae). Am J Bot 98:e36–e38

    PubMed  Article  CAS  Google Scholar 

  40. Li JK, Zhou EX, Li DX, Huang SQ (2010) Multiple northern refugia for Asian sacred lotus, an aquatic plant with characteristics of ice-age endurance. Aust J Bot 58:463–472

    Article  Google Scholar 

Download references

Acknowledgments

We are grateful to Dr. F. James Rohlf (Department of Ecology and Evolution, Stony Brook University, USA) and Dr. Sudheer Pamidimarri (Shree M. and N. Virani Science College, Saurashtra University, India) for their help with bootstrap analysis). This work was supported by National Nature Science Foundation of China (Grant no. 30771152).

Author information

Affiliations

  1. State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, People’s Republic of China

    Jihong Hu, Lei Pan, Honggao Liu, Shuzhen Wang, Zhihua Wu & Yi Ding

  2. Wuhan National Germplasm Repository for Aquatic Vegetables, Wuhan, 430065, People’s Republic of China

    Weidong Ke & Yi Ding

Authors
  1. Jihong Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lei Pan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Honggao Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shuzhen Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhihua Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Weidong Ke
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yi Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yi Ding.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Hu, J., Pan, L., Liu, H. et al. Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers. Mol Biol Rep 39, 3637–3647 (2012). https://doi.org/10.1007/s11033-011-1138-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-011-1138-y

Keywords

  • AFLP (amplified fragment length polymorphism)
  • Genetic diversity
  • Nelumbo nucifera
  • SSR (simple sequence repeat)