, Volume 144, Issue 6, pp 627–638 | Cite as

Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers

  • Eleonora Zambrano BlancoEmail author
  • Miklos Maximiliano Bajay
  • Marcos Vinícius Bohrer Monteiro Siqueira
  • Maria Imaculada Zucchi
  • José Baldin Pinheiro


Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species’ genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species’ genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon–Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity’s coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.


Clustering Molecular characterization Population structure AFLP marker Genetic resources Zingiber officinale 



The author Eleonora Zambrano Blanco thanks the Program for Partner Graduate Students (PEC-PG) of Brazilian Federal Agency for Support and Evaluation of graduate education (CAPES) for the scholarship granted. The authors thank the Brazilian National Council for Scientific and Technological Development (CNPq) for the productivity scholarships and to Mrs. Leila Felipini for the translation of this article.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Adaniya S (2001) Optimal pollination environment of tetraploid ginger (Zingiber officinale Roscoe) evaluated by in vitro pollen germination and pollen tube growth in styles. Sci Hortic 90:219–226CrossRefGoogle Scholar
  2. Adaniya S, Shirai D (2001) In vitro induction of tetraploid ginger (Zingiber officinale Roscoe) and its pollen fertility and germinability. Sci Hortic 88:277–287CrossRefGoogle Scholar
  3. Adel S, Prakash J (2010) Chemical composition and antioxidant properties of ginger root (Zingiber officinale). J Med Plants Res 4(24):2674–2679CrossRefGoogle Scholar
  4. Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular markers techniques and their applications in plant sciences. Plant Cell Rep 27:617–631CrossRefPubMedGoogle Scholar
  5. Ali BH, Blunden G, Tanira MO, Nemmar A (2008) Some phytochemical, pharmacological and toxicological properties of ginger (Zingiber officinale Roscoe): a review of recent research. Food Chem Toxicol 46(2):409–420CrossRefPubMedGoogle Scholar
  6. Althoff DM, Gitzendanner MA, Segraves KA (2007) The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. Syst Biol 56:477–484CrossRefPubMedGoogle Scholar
  7. Ashraf K, Ahmad A, Chaudhary A, Mujeeb M, Ahmad S, Amir M, Mallick N (2014) Genetic diversity analysis of Zingiber officinale Roscoe by RAPD collected from subcontinent of India. Saudi J Biol Sci 21(2):159–165CrossRefPubMedGoogle Scholar
  8. Baliga MS, Haniadka R, Pereira MM, D’souza JJ, Pallaty PL, Bhat HP, Popuri S (2011) Update on the chemo preventive effects of ginger and its phytochemicals. Crit Rev Food Sci Nutr 51(6):499–523CrossRefPubMedGoogle Scholar
  9. Benesi IRM, Labuschagne MT, Herselman N, Mahungu N (2010) Ethnobotany, morphology and genotyping of cassava germplasm from malawi. J Biol Sci 10(7):616–623CrossRefGoogle Scholar
  10. Bosetti F, Zucchi MI, Pinheiro JB (2011) Molecular and morphological diversity in Japanese rice germplasm. Plant Genet Resour 9:229–232CrossRefGoogle Scholar
  11. Bua-in S, Paisooksantivatana Y (2010) Study of clonally propagated cassumunar ginger (Zingiber montanum) and its relation of wild Zingiber species from Thailand revealed by RAPD markers. Genet Resour Crop Evol 57(3):405–414CrossRefGoogle Scholar
  12. Butt MS, Sultan MT (2011) Ginger and its health claims: molecular aspects. Crit Rev Food Sci Nutr 51(5):383–393CrossRefPubMedGoogle Scholar
  13. Cavallari MM, Billot C, Bouvet JM, Favreau B, Zucchi MI, Palmieri DA, Gimenes MA (2008) Isolation and characterization of microsatellite markers for Casearia sylvestris Sw. (Salicaceae) a neotropical medicinal tree. Mol Ecol Resour 8(4):802–804CrossRefPubMedGoogle Scholar
  14. Chang JS, Wang KC, Yeh CF, Shieh DE, Chiang LC (2013) Fresh ginger (Zingiber officinale) has anti-viral activity against human respiratory syncytial virus in human respiratory tract cell lines. J Ethnopharmacol 145:146–151CrossRefPubMedGoogle Scholar
  15. Das A, Kesari V, Satyanarayana VM, Parida A, Mitra S, Rangan L (2013) Genetic diversity in ecotypes of the scarce wild medicinal crop Zingiber moran revealed by ISSR and AFLP marker analysis and chromosome number assessment. Plant Biosyst. doi: 10.1080/11263504.2013.795197 Google Scholar
  16. Doyle JJ, Doyle JL (1990) Isolation of plant DNA fresh tissue. Focus 12:13–15Google Scholar
  17. Elpo E, Negrelle R (2004) Zingiber officinale Roscoe: aspectos botânicos e ecológicos. Visão Acad 5(1):27–32Google Scholar
  18. Esfahani ST, Shiran B, Balali G (2009) AFLP markers for the assessment of genetic diversity in european and North American potato varieties cultivated in Iran. Crop Breed Appl Biotechnol 9:75–86CrossRefGoogle Scholar
  19. Evanno G, Regnaut F, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  20. Excoffier L, Lischer HEL (2010) Arlequin suite 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567CrossRefPubMedGoogle Scholar
  21. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedPubMedCentralGoogle Scholar
  22. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7(4):574–578CrossRefPubMedPubMedCentralGoogle Scholar
  23. Geiger J (2005) The essential oil of ginger and anaesthesia. Int J Aromather 15(1):7–14CrossRefGoogle Scholar
  24. Ghosh S, Majumder PB, Mandi S (2011) Species-specific AFLP markers for identification of Zingiber officinale, Z. montanum and Z. zerumbet (Zingiberaceae). Genet Mol Res 10(1):218–229CrossRefPubMedGoogle Scholar
  25. Hangelbroek HH, Ouborg L, Santamaria S, Chwenk E (2002) Clonal diversity and strucuture within a population of the pondweed Potamogeton pectinatus foraged by Bewick’s swans. Mol Ecol 11:2137–2150CrossRefPubMedGoogle Scholar
  26. Ipek M, Ipek A, Simon PW (2006) Sequence homology of polymorphic AFLP markers in garlic (Allium sativum L.). Genome 49:1246–1255CrossRefPubMedGoogle Scholar
  27. Jatoi SA, Kikuchi A, Yi SS, Naing KW, Yamanaka S, Watanabe JA, Watanabe KN (2006) Use of rice SSR markers as RAPD markers for genetic diversity analysis in Zingiberaceae. Breed Sci 56(2):107–111CrossRefGoogle Scholar
  28. Jatoi SA, Kikuchi A, Mimura M, Watanabe KN (2008) Relationships of Zingiber species, and genetic variability assessment in ginger (Zingiber officinale) accessions from ex situ gene bank, on-farm and rural markets. Breed Sci 58(3):261–270CrossRefGoogle Scholar
  29. Jeena K, Liju VB, Kuttan R (2015) Antitumor and cytotoxic activity of ginger essential oil (Zingiber officinale Roscoe). Int J Pharm pharm sci 7(8):341–344Google Scholar
  30. Jiang H, Xie Z, Koo HJ, Mclaughlin SP, Timmermann BN (2006) Gang DR (2006), Metabolic profiling and phylogenetic analysis of medicinal Zingiber species: tools for authentication of ginger (Zingiber officinale Rosc.). Phytochemistry 67(15):1673–1685CrossRefPubMedGoogle Scholar
  31. Kavitha PG, Thomas G (2008) Population genetic structure of the clonal plant Zingiber zerumbet (L.) Smith (Zingiberaceae), a wild relative of cultivated ginger, and its response to Pythium aphanidermatum. Euphytica 160:89–100CrossRefGoogle Scholar
  32. Kavitha PG, Kiran AG, Dinesh RAJ, Sabu M, Thomas G (2010) Amplified fragment length polymorphism analyses unravel a striking difference in the intraspecific genetic diversity of four species of genus Zingiber Boehm. from the Western Ghats, South India. Curr Sci 98(2):242–247Google Scholar
  33. Kizhakkayil J, Sasikumar B (2010) Genetic diversity analysis of ginger (Zingiber officinale Rosc.) germplasm based on RAPD and ISSR markers. Sci Hortic 125:73–76CrossRefGoogle Scholar
  34. Kladmook M, Chidchenchey S, Keeratinijakal V (2010) Assessment of genetic diversity in cassumunar ginger (Zingiber cassumunar Roxb.) in Thailand using AFLP markers. Breed Sci 60(4):412–418CrossRefGoogle Scholar
  35. Kubra IR, Mohan Rao LJ (2012) An impression on current developments in the technology, chemistry, and biological activities of ginger (Zingiber officinale Roscoe). Crit Rev Food Sci Nutr 52(8):651–688CrossRefPubMedGoogle Scholar
  36. Lampasona GS, Martínez L, Burba JL (2003) Genetic diversity among selected Argentinean garlic clones (Allium sativum L.) using AFLP (Amplified Fragment Length Polymorphism). Euphytica 132:115–119CrossRefGoogle Scholar
  37. Lee SY, Fai WK, Zakaria M, Ibrahim H, Othman RY, Gwag JG, Rao VR, Park YJ (2007) Characterization of polymorphic microsatellite markers, isolated from ginger (Zingiber officinale Rosc.). Mol Ecol Notes 7(6):1009–1011CrossRefGoogle Scholar
  38. Ma X, Gang DR (2006) Metabolic profiling of in vitro micropropagated and conventionally greenhouse grown ginger (Zingiber officinale). Phytochemistry 67(20):2239–2255CrossRefPubMedGoogle Scholar
  39. Mohanty S, Panda MK, Acharya L, Nayak S (2014) Genetic diversity and gene differentiation among ten species of Zingiberaceae from Eastern India. Biotech 4:383–390. doi: 10.1007/s13205-013-0166-9 Google Scholar
  40. Morales RGF, Resende JTV, Resende FV, Delatorre CA, Figueiredo AST, Da-Silva PR (2013) Genetic divergence among Brazilian garlic cultivars based on morphological characters and AFLP markers. Genet Mol Res 12(1):270–281CrossRefPubMedGoogle Scholar
  41. Nayak S, Naik PK, Acharya L (2005) Assessment of genetic diversity among 16 promising cultivars of ginger using cytological and molecular markers. Z fur Naturforschung 60:485–492Google Scholar
  42. Nei M (1978) Estimation of average heterozigosity and genetic distance from a small number of individuals. Genetics 89(3):583–590PubMedPubMedCentralGoogle Scholar
  43. Nirmal Babu K, Samsudeen K, Rathnambal MJ (1992) In vitro plant regeneration from leaf derived callus in ginger (Zingiber officinale Rosc.). Plant Cell Tissue 29:71–74CrossRefGoogle Scholar
  44. Palai SK, Rout GR (2007) Identification and genetic variation among eight varieties of ginger by using random amplified polymorphic DNA markers. Plant Biotechnol 24(4):417–420CrossRefGoogle Scholar
  45. Pandotra P, Gupta AP, Husain MK, Gupta S (2013a) Genetic and chemo-divergence in eighteen core collection of Zingiber officinale from North–West Himalayas. Sci Hortic 160:283–291CrossRefGoogle Scholar
  46. Pandotra P, Gupta AP, Husain MK, Gandhiram Gupta S (2013b) Evaluation of genetic diversity and chemical profile of ginger cultivars in north-western Himalayas. Biochem Syst Ecol 48:281–287CrossRefGoogle Scholar
  47. Paradis E, Claude J, Strimmer K (2004) APE: analyses of Phylogenetics and Evolution in R language. Bioinformatics 20:289–290CrossRefPubMedGoogle Scholar
  48. Perrier X, Flor A, Bonno F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publ, Montpellier, pp 43–76Google Scholar
  49. Prem J, Kizhakkayil J, Thomas E, Dhanya K, Syamkumar S, Sasikumar B (2008) Molecular characterization of primitive, elite and exotic ginger genotypes to protect the biowealth of elite ginger accessions. J Spices Aromat Crops 17(2):85–90Google Scholar
  50. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedPubMedCentralGoogle Scholar
  51. Raji AAJ, Fawole I, Gedil M, Dixon AGO (2009) Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markers. Ann Appl Biol 155:187–199CrossRefGoogle Scholar
  52. Ravindran PN, Nirmal Babu K (2005) Botany and crop improvement of ginger. In: Ravindran PN, Nirmal Babu K (eds) Ginger: the genus Zingiber. CRC Press, Washington, pp 15–86Google Scholar
  53. Ravindran P, Sasikumar B, George J, Ratnambal M, Nirmal Babu K, Zachariah J, Nair R (1994) Genetic resources of ginger (Zingiber ofticinale Rosc.) and its conservation in India. Plant Genet Resour 98:1–5Google Scholar
  54. Sajeev S, Roy AR, Iangrai B, Pattanayak A, Deka BC (2011) Genetic diversity analysis in the traditional and improved ginger (Zingiber officinale Rosc.) clones cultivated in North-East India. Sci Hortic 128(3):182–188CrossRefGoogle Scholar
  55. Sharma TR, Sing BM (1995) In vitro microrhizome production in Zingiber officinale rose. Plant Cell Rep 15:274–277PubMedGoogle Scholar
  56. Sharma GJ, Pukhrambam C, Rajkumar K (2011) Gingers of Manipur: diversity and potentials as bioresources. Genet Resour Crop Evol 58(5):753–767CrossRefGoogle Scholar
  57. Singh CB, Nongalleima K, Brojendrosingh S, Ningombam S, Lokendrajit N, Singh LW (2011) Biological and chemical properties of Zingiber zerumbet Smith: a review. Phytochem Rev 11(1):113–125CrossRefGoogle Scholar
  58. Stoilova I, Krastanov A, Stoyanova A, Denev P, Gargova S (2007) Antioxidant activity of a ginger extract (Zingiber officinale). Food Chem 102(3):764–770CrossRefGoogle Scholar
  59. Valenzuela H (2010) Farm and forestry production and marketing profile for ginger (Zingiber officinale). In: ELEVITCH CR (Ed) Specialty crops for Pacific Island agroforestry. Permanent Agriculture Resources Accessed 21June 2015
  60. 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(1):139–151CrossRefPubMedGoogle Scholar
  61. Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fringerprinting. Nucleic Acids Res 23:4407–4414CrossRefPubMedPubMedCentralGoogle Scholar
  62. Wahyuni S, Xu DH, Bermawie N, Tsunematsu H, Ban T (2003) Genetic relationships among ginger accessions based on AFLP marker. J Biotechnol Pertan 8(2):60–68Google Scholar
  63. Wang F, Li F, Wang J, Zhuo Y, Sun H (2011) Genetic diversity of the selected 64 potato germplasms revealed by AFLP markers. Mol Plant Breed 2(4):22–29Google Scholar
  64. Wickham H (2009) ggplot2: elegant graphics for data analysis. Springer, New YorkCrossRefGoogle Scholar
  65. Wright S (1978) Evolution and the genetics of populations: variability within and among natural populations. University of Chicago Press, ChicagoGoogle Scholar
  66. Yeh FC, Boyle T, Rongcai Y et al (1999) Popgene ver 1.31 Accessed 22 June 2015

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.“Luiz de Queiroz” College of Agriculture (ESALQ), Department of GeneticsUniversity of São Paulo (USP)PiracicabaBrazil
  2. 2.Biotechnology and Agricultural Research Center (CIAB)Open and Distance National University (UNAD)DosquebradasColombia
  3. 3.Laboratories Center, Science and Environmental TechnologyUniversity of Sagrado Coração (USC)BauruBrazil
  4. 4.São Paulo Agency for Agribusiness Technology (APTA)PiracicabaBrazil

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