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Molecular Biology Reports

, Volume 42, Issue 1, pp 159–166 | Cite as

Genetic analysis of litchi (Litchi chinensis Sonn.) in southern China by improved random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR)

  • Yan Long
  • Jingliang Cheng
  • Zhiqiang Mei
  • Ling Zhao
  • Chunli Wei
  • Shelly Fu
  • Md. Asaduzzaman Khan
  • Junjiang Fu
Article

Abstract

Litchi (Litchi chinensis Sonn., L. chinensis), a type of tree growing in most areas of southern China, produces an edible fruit that is also a source of traditional medicine. Genetic identification of litchi species or cultivars using molecular markers is very important. In this study, a total of six litchi samples from Fujian, Hainan, Guangdong, Guangxi and Sichuan province, as well as one wild Dimocarpus confinis (D. confinis) sample from Guangxi province were collected for genetic analysis. The cluster dendrograms were constructed for genetic analysis on the basis of DNA amplification results by RAPD and ISSR. The improved RAPD amplified DNA with consistent and clear banding patterns. A total of 176 bands were found, indicating a 72.7 % polymorphism in L. chinensis DNA samples. Significant genetic distances were found among the different species or cultivars, with an index of similarity coefficient ranging from 0.59 to 0.87. Similar to RAPD results, ISSR analysis of the L. chinensis DNA samples showed a range of 0.70–0.93 similarity coefficients. The genetic distance between Hainan sample and Sichuan samples was the farthest, which is consistent with their geographic distance. Furthermore, the index of similarity coefficient between D. confinis and L. chinensis was 0.35–0.41 by RAPD and 0.38–0.48 by ISSR, indicating that these two species have significant genetic difference. This study reveals the high level of genetic differences between different litchi species or cultivars, and confirms the significance of the improved RAPD method in genetic characterization of organisms. Taken together, the improved RAPD combined with ISSR analysis can be used frequently for the genetic diversity, germplasm resources preservation, molecular-assisted breeding, and genetic characterization of various organisms.

Keywords

Litchi chinensis Sonn. Genetic authentication RAMP Random amplified polymorphic DNA Inter-simple sequence repeat Dimocarpus confinis Genetic distance 

Notes

Acknowledgments

This work was supported in part by the National Natural Science Foundation of China (81172049), Science and Technology Innovation Team of Colleges and Universities of Sichuan Province (13TD0032), Applied Basic Research Program of Science and Technology Department of Sichuan Province (14JC0797) and Luzhou City Special Foundation (2013LZLY-J10). The authors thank all individuals who provided plant leaves or DNAs.

Conflict of interest

None.

References

  1. 1.
    Wang X, Yuan S, Wang J, Lin P, Liu G, Lu Y, Zhang J, Wang W, Wei Y (2006) Anticancer activity of litchi fruit pericarp extract against human breast cancer in vitro and in vivo. Toxicol Appl Pharmacol 215:168–178PubMedCrossRefGoogle Scholar
  2. 2.
    Hsu CP, Lin CC, Huang CC, Lin YH, Chou JC, Tsia YT, Su JR, Chung YC (2012) Induction of apoptosis and cell cycle arrest in human colorectal carcinoma by Litchi seed extract. J Biomed Biotechnol 2012:341479PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Huang F, Zhang R, Yi Y, Tang X, Zhang M, Su D, Deng Y, Wei Z (2014) Comparison of physicochemical properties and immunomodulatory activity of polysaccharides from fresh and dried litchi pulp. Molecules 19:3909–3925PubMedCrossRefGoogle Scholar
  4. 4.
    Xu L, Xue J, Wu P, Wang D, Lin L, Jiang Y, Duan X, Wei X (2013) Antifungal activity of hypothemycin against Peronophythora litchii in vitro and in vivo. J Agric Food Chem 61:10091–10095PubMedCrossRefGoogle Scholar
  5. 5.
    Ichinose T, Musyoka TM, Watanabe K, Kobayashi N (2013) Evaluation of antiviral activity of Oligonol, an extract of Litchi chinensis, against betanodavirus. Drug Discov Ther 7:254–260PubMedCrossRefGoogle Scholar
  6. 6.
    Yang B, Wang J, Zhao M, Liu Y, Wang W, Jiang Y (2006) Identification of polysaccharides from pericarp tissues of litchi (Litchi chinensis Sonn.) fruit in relation to their antioxidant activities. Carbohydr Res 341:634–638PubMedCrossRefGoogle Scholar
  7. 7.
    Duan X, Wu G, Jiang Y (2007) Evaluation of the antioxidant properties of litchi fruit phenolics in relation to pericarp browning prevention. Molecules 12:759–771PubMedCrossRefGoogle Scholar
  8. 8.
    Kong F, Zhang M, Liao S, Yu S, Chi J, Wei Z (2010) Antioxidant activity of polysaccharide-enriched fractions extracted from pulp tissue of Litchi Chinensis Sonn. Molecules 15:2152–2165PubMedCrossRefGoogle Scholar
  9. 9.
    Yang DJ, Chang YZ, Chen YC, Liu SC, Hsu CH, Lin JT (2012) Antioxidant effect and active components of litchi (Litchi chinensis Sonn.) flower. Food Chem Toxicol 50:3056–3061PubMedCrossRefGoogle Scholar
  10. 10.
    Zhang R, Zeng Q, Deng Y, Zhang M, Wei Z, Zhang Y, Tang X (2013) Phenolic profiles and antioxidant activity of litchi pulp of different cultivars cultivated in Southern China. Food Chem 136:1169–1176PubMedCrossRefGoogle Scholar
  11. 11.
    Su D, Zhang R, Hou F, Zhang M, Guo J, Huang F, Deng Y, Wei Z (2014) Comparison of the free and bound phenolic profiles and cellular antioxidant activities of litchi pulp extracts from different solvents. BMC Complement Altern Med 14:9PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Sung YY, Yang WK, Kim HK (2012) Antiplatelet, anticoagulant and fibrinolytic effects of Litchi chinensis Sonn. extract. Mol Med Rep 5:721–724PubMedGoogle Scholar
  13. 13.
    Guo J, Li L, Pan J, Qiu G, Li A, Huang G, Xu L (2004) Pharmacological mechanism of Semen Litchi on antagonizing insulin resistance in rats with type 2 diabetes. Zhong Yao Cai 27:435–438PubMedGoogle Scholar
  14. 14.
    Noh JS, Kim HY, Park CH, Fujii H, Yokozawa T (2010) Hypolipidaemic and antioxidative effects of oligonol, a low-molecular-weight polyphenol derived from lychee fruit, on renal damage in type 2 diabetic mice. Br J Nutr 104:1120–1128PubMedCrossRefGoogle Scholar
  15. 15.
    Noh JS, Park CH, Yokozawa T (2011) Treatment with oligonol, a low-molecular polyphenol derived from lychee fruit, attenuates diabetes-induced hepatic damage through regulation of oxidative stress and lipid metabolism. Br J Nutr 106:1013–1022PubMedCrossRefGoogle Scholar
  16. 16.
    Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Hess J, Kadereit JW, Vargas P (2000) The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Mol Ecol 9:857–868PubMedCrossRefGoogle Scholar
  18. 18.
    Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631PubMedCrossRefGoogle Scholar
  19. 19.
    Varela ES, Lima JP, Galdino AS, Pinto Lda S, Bezerra WM, Nunes EP, Alves MA, Grangeiro TB (2004) Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from internal transcribed spacer sequences from nuclear ribosomal DNA. Phytochemistry 65:59–69PubMedCrossRefGoogle Scholar
  20. 20.
    Noormohammadi Z, Hasheminejad-Ahangarani Farahani Y, Sheidai M, Ghasemzadeh-Baraki Alishah S, Alishah O (2013) Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers. Genet Mol Res 12:256–269PubMedCrossRefGoogle Scholar
  21. 21.
    Pachuau L, Atom AD, Thangjam R (2014) Genome classification of Musa cultivars from Northeast India as revealed by ITS and IRAP markers. Appl Biochem Biotechnol 172:3939–3948PubMedCrossRefGoogle Scholar
  22. 22.
    Khadivi-Khub A, Soorni A (2014) Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers. Mol Biol Rep 41:4007–4016PubMedCrossRefGoogle Scholar
  23. 23.
    Fu J, Li L, Xu X, Wang Z, Tang G, Yin C, Lu G (2000) An improved method for increasing the efficiency of the technique of random amplified polymorphic DNA (RAPD). Hereditas 22:251–252Google Scholar
  24. 24.
    Fu J, Yang L, Khan MA, Mei Z (2013) Genetic characterization and authentication of Lonicera japonica Thunb. by using improved RAPD analysis. Mol Biol Rep 40:5993–5999PubMedCrossRefGoogle Scholar
  25. 25.
    Ding XD, Lu LX, Chen XJ (2001) Segregation patterns of RAPD markers in an F1 population of Litchi chinensis Sonn. Acta Hort 558:167–172Google Scholar
  26. 26.
    Liu LS, Pan DM, Zhong FL, Wang JB (2010) POD isoenzyme and RAPD analysis on litchi in Fuqing. The Third international conference symposium on Longan, Lychee and other fruit trees in Sapindaceae family. Acta Hort 863:189–194Google Scholar
  27. 27.
    Zhou J, Fu JX, Wu ZX, Huang SS, Zhao YH, Zhang B, Hu YL, Hu GB, Liu CM (2012) Construction of two high density genetic linkage maps in litchi. Acta Hort 929:207–213Google Scholar
  28. 28.
    Mei ZQ, Fu SY, Yu HQ, Yang LQ, Duan CG, Liu XY, Gong S, Fu JJ (2014) Genetic characterization and authentication of Dimocarpus longan Lour. using an improved RAPD technique. Genet Mol Res 13:1447–1455PubMedCrossRefGoogle Scholar
  29. 29.
    Mei Z, Yang L, Khan MA, Yang M, Wei C, Yang W, Peng X, Tania M, Zhan Hg, Li X, Fu J (2014) Genotyping of ganoderma species by improved random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analysis. Biochem Syst Ecol 56:40–48CrossRefGoogle Scholar
  30. 30.
    Yang L, Khan MA, Mei Z, Yang M, Zhang T, Wei C, Yang W, Zhu L, Long Y, Fu J (2014) Development of RAPD-SCAR markers for Lonicera japonica Thunb. (Caprifolicaceae) variety authentication by improved RAPD and DNA cloning. Rev Biol Trop 62:(in press)Google Scholar
  31. 31.
    Yang L, Fu S, Khan MA, Zeng W, Fu J (2013) Molecular cloning and development of RAPD-SCAR markers for Dimocarpus longan variety authentication. SpringerPlus 2:501PubMedCentralPubMedCrossRefGoogle Scholar
  32. 32.
    Sharma P, Joshi N, Sharma A (2010) Isolation of genomic DNA from medicinal plants without liquid nitrogen. Indian J Exp Biol 48:610–614PubMedGoogle Scholar
  33. 33.
    Fu JJ (2012) Short protocols in medical molecular biology. China Medical Science Press, BeijingGoogle Scholar
  34. 34.
    Rohlf FJ (2002) NTSYS-pc: numerical taxonomy system ver.2.1. Exeter Pub Ltd, Setauket, New York. http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html. Accessed 6 June 2014

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Yan Long
    • 1
  • Jingliang Cheng
    • 1
  • Zhiqiang Mei
    • 1
  • Ling Zhao
    • 2
  • Chunli Wei
    • 1
  • Shelly Fu
    • 3
  • Md. Asaduzzaman Khan
    • 1
  • Junjiang Fu
    • 4
    • 1
  1. 1.The Research Center for Preclinical MedicineLuzhou Medical CollegeLuzhouChina
  2. 2.The Department of PharmacyLuzhou Medical CollegeLuzhouChina
  3. 3.Michael E. DeBakey High School for Health ProfessionsHoustonUSA
  4. 4.Forensic CenterLuzhou Medical CollegeLuzhouChina

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