Genetic Resources and Crop Evolution

, Volume 61, Issue 3, pp 639–650 | Cite as

Genetic diversity analysis of yams (Dioscorea spp.) cultivated in China using ISSR and SRAP markers

  • Zhi Gang Wu
  • Xiao Xia Li
  • Xin Chun Lin
  • Wu Jiang
  • Zheng Ming Tao
  • Nitin Mantri
  • Chuan Yin Fan
  • Xiao Qing Bao
Research Article


Yam (Dioscorea spp.) is widely cultivated in China and many landraces are maintained by local farmers. However, there is little information available about their diversity and species identity. In this study, inter simple sequence repeat (ISSR) and sequence related amplified polymorphism (SRAP) techniques were used to assess genetic diversity within 21 yam landraces from seven cultivated populations. We observed high level of polymorphism among these landraces, specifically, 95.3 % for ISSR and 93.5 % for SRAP. Analysis of molecular variance revealed a significantly greater variation among the four yam species (40.39 %) and their populations (35.78 %) than within the populations (23.83 %). The unweighted pair group method arithmetic averages clusters and principal component analysis for 21 landraces formed four well-separated groups containing landraces of each of the four species, namely, Dioscorea opposita Thunb., Dioscorea alata L., Dioscorea persimilis Prain et Burkill, and Dioscorea fordii Prain et Burkill. The ISSR and SRAP primers were highly discriminatory among the 21 landraces; all 21 landraces could be easily differentiated using these primers. The average mean of gene flow (Nm = 0.1081) estimated from high genetic differentiation (Gst = 0.8222) suggested that gene flow among the populations was relatively restricted. The lack of genetic diversity within individual yam species suggests that it is critical to develop long-term strategies for enhancing genetic diversity within various yam species.


China Dioscorea Genetic diversity ISSR SRAP Yam 



The present study was supported by the Agricultural Science and Technology Program of Wenzhou in China (Grant No. N20100003), Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants (Grant No. 2011E10015). We are grateful to RuiAn Agriculture and Foresty Bureau (Ruian city, Zhejiang Province), Sanming Agricultural Science Institute (Sanming city, Fujian Province), Wenxian Agricultural Science Institute (Wenxian City, Henan Province), for positive help with sampling yam landraces. Many thanks to Pro. Xin-Chun Lin and Xiao-Xia Li, for their help with PCR experiments.

Supplementary material

10722_2013_65_MOESM1_ESM.doc (2.2 mb)
Supplementary material 1 (DOC 2288 kb)


  1. Asemota HN, Ramer J, Lopéz-Peralta C, Weising K, Kahl G (1996) Genetic variation and cultivar identification of Jamaican yam germplasm by random amplified polymorphic DNA analysis. Euphytica 92:341–351CrossRefGoogle Scholar
  2. Bahieldin A, Ahmed IA, Gad El-Karim GA, Eissa HF, Mahfouz HT, Saleh OM (2006) DGGE-RAPD analysis as a useful tool for cultivar identification. Afr J Biotechnol 5:566–569Google Scholar
  3. Board of pharmacopoeia of PR China (2010) Pharmacopoeia of the People’s Republic of China, part I. Board of pharmacopoeia of PR China, Beijing, p 27Google Scholar
  4. Budak H, Shearman RC, Parmaksiz I, Dweikat I (2004) Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogentic relationship using ISSRs, SSRs, RAPDs, and SRAPs. Theor Appl Genet 109:280–288PubMedCrossRefGoogle Scholar
  5. Burkill IH (1960) The organography and evolution of Dioscoreaceae, the family of yams. J Linn Soc Lond Bot 56:319–412CrossRefGoogle Scholar
  6. Cai JH, Yan JZ, Huang XH, Ye SJ, Jiang LW, Gu ZZ (1999) A taxonomical study on varietal resource of Dioscorea species. Acta Jiangxi Agric Univ 21:53–57Google Scholar
  7. Coursey DG (1967) Yams: an account of the nature, origins, cultivation and utilization of the useful members of the Dioscoreaceae. Longmans, Green, LondonGoogle Scholar
  8. Dansi A, Mignouna HD, Zoundjihékpon J, Sangare A, Ahoussou N, Asiedu R (2000a) Identification of some Benin Republic’s Guinea yams (Dioscorea cayenenis/Dioscorea rotundata complex) cultivars using randomly amplified polymorphic DNA. Genet Resour Crop Evol 47:619–625Google Scholar
  9. Dansi A, Mignouna HD, Zoundjihékpon J, Sangare A, Asiedu R, Ahoussou N (2000b) Using isozyme polymorphism to assess genetic variation within cultivated yams (Dioscorea cayenenis/Dioscorea rotundata complex) of the Republic of Benin. Genet Resour Crop Evol 47:371–383Google Scholar
  10. De Carvalho VM, Marochio CA, Mangolin CA, Da Silva Machado MDFP (2011) The use of esterase polymorphism for analysis of the genetic diversity and structure of stevia (Stevia rebaudiana (Bert.) Bertoni) populations. Biochem Syst Ecol 39:594–599Google Scholar
  11. Ding Z, Gilbert MG (2000) Flora of China, vol 24 (Dioscoreacea). In: Wu Z, Raven PH (eds) Flagellariaceae through Marantaceae. Missouri Botanical Garden, St. Louis, pp 276–296Google Scholar
  12. Dumont R, Vernier P (2000) Domestication of yams (Dioscorea cayenensis-rotundata) within the Bariba ethnic group in Benin. Outlook Agric 6:137–142CrossRefGoogle Scholar
  13. Ellstrand N (1992) Gene flow by pollen: implications for plant conversation genetics. Oikos 63:77–86CrossRefGoogle Scholar
  14. Excoffier L (1993) Analysis of molecular variance. Version 1.5. Genetics and Biometry Laboratory, University of Geneva, GenevaGoogle Scholar
  15. Gilbert JE, Lewis RV, Wilkinson MJ, Galigari PDS (1999) Developing and appropriate strategy to assess genetic variability in plant germplasm collections. Theor Appl Genet 98:1125–1131CrossRefGoogle Scholar
  16. Gucker CL (2009) Dioscorea spp. In: Fire Effects Information System, [Online]. Department of Agriculture, Forest Service, Rocky Mountain Research Station, Fire Sciences Laboratory (Producer). Accessed 9 Dec 2011
  17. Hahn SK (1995) Yams: Dioscorea spp. (Dioscoreaceae). In: Smartt J, Simmonds NW (eds) Evolution of crop plants. B. Longman, Essex, pp 112–120Google Scholar
  18. Hamrick JL, Nason JD (1996) Consequence of dispersal in plants. In: Rhodes OE, Ronald KC, Smith MH (eds) Population dynamics in ecological space and time. Chicago, pp 203–235Google Scholar
  19. Hua SM, Tu QC, Lei FG (2009) Genetic diversity of Dioscorea polystachya Turcz. revealed by RAPD markers. J Plant Resour Environ 10:1995–2000Google Scholar
  20. Huang WH (2005) Non-pollution and standardization cultivation for yam. Beijing, pp 16–44Google Scholar
  21. Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP) a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Gent 103:455–461CrossRefGoogle Scholar
  22. Li MJ, Xu X, Zhang XL, Liu YK (2007) Isolation of genomic DNA and optimization of RAPD conditions of Dioscorea opposita Thunb. J Henan Norm Univ 35:140–143Google Scholar
  23. Liu P, Guo SL, Lu HF, Xie XW, Wu XY (1993) A summary on of the study on Chinese Dioscorea spp. J Zhejiang Norm Univ 16:100–106Google Scholar
  24. Loveless MD, Hamrick JL (1984) Ecological determinants of genetic structure in plant populations. Ann Rev Ecol Syst 15:65–95CrossRefGoogle Scholar
  25. Mengesha WA, Demissew S, Fay MF, Smith RJ, Nordal I, Wilkin P (2013) Genetic diversity and population structure of Guinea yams and their wild relatives in South and South West Ethiopia as revealed by microsatellite markers. Genet Resour Crop Evol 60:529–541CrossRefGoogle Scholar
  26. Mignouna HD, Dansi A (2003) Yam (Dioscorea spp.) domestication by the Nago and Fon ethnic groups in Benin. Genet Resour Crop Evol 50:519–528CrossRefGoogle Scholar
  27. Mignouna HD, Mank RA, Ellis THN, Van Den Bosch N, Asiedu R, Abang MM, Peleman J (2002) A genetic linkage map of water yam (Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance. Theor Appl Genet 105:726–735PubMedCrossRefGoogle Scholar
  28. Nascimento WF, Rodrigues JF, Koehler S, Gepts P, Veasey EA (2013) Spatially structured genetic diversity of the Amerindian yam (Dioscorea trifida L.) assessed by SSR and ISSR markers in Southern Brazil. Genet Resour Crop Evol. 60:2405–2420Google Scholar
  29. Ngu MS, Sabu KK, Lim LS, Abdullah MZ, Wickneswari R (2010) Genetic structure of Oryza rufipogon Griff. natural populations in Malaysia: implications for conservation and genetic introgression of cultivated Rice. Trop Plant Biol 3:227–239CrossRefGoogle Scholar
  30. Okoli OO (1991) Yam germplasm diversity, use and prospects for crop improvement in Africa. In: Crop genetic resources of Africa, vol 2. IITA/IBPGR/UNER/CNR, Ibadan, Nigeria, pp 109–117Google Scholar
  31. Pei J, Ding ZZ (1985) Flora of China, vol. 16 (Dioscoreacea). Beijing, pp 103–119Google Scholar
  32. Pelsy F, Hocquigny S, Moncada X, Barbeau G, Forget D, Hinrichsen P, Merdinoglu D (2010) An extensive study of the genetic diversity within seven French wine grape variety collections. Theor Appl Genet 120:1219–1231PubMedCrossRefGoogle Scholar
  33. Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112CrossRefGoogle Scholar
  34. Qin HZ, Zhang MZ, Ling PP, Ding ZZ, Dou FP (1985) A cytotaxonomic study on Chinese Dioscorea L.—the chromosome numbers and their relation to the origin and evolution of the genus. Acta Phytotax Sin 23:11–18Google Scholar
  35. Ramser J, Weising K, Lopez-peralta C, Terhalle W, Terauchi R, Kahl G (1997) Molecular marker based taxonomy and phylogeny of Guinea yam (Dioscorea rotundataD. cayenensis). Genome 40:903–915PubMedCrossRefGoogle Scholar
  36. Rohlf FJ (2000) NTSYSpc: numerical taxonomy and multivariate analysis system. Exeter Software, New YorkGoogle Scholar
  37. Rubatzky VE, Yamaguchi M (1997) World vegetables: principles, production, and nutritive values (2nd edn). New York, pp 162–182Google Scholar
  38. Sartie A, Asiedu R, Franco J (2012) Genetic and phenotypic diversity in a germplasm working collection of cultivated tropical yams (Dioscorea spp.). Genet Resour Crop Evol 59:1753–1765CrossRefGoogle Scholar
  39. Scarcelli N, Tostain S, Mariac C, Agbangla C, Da O, Berthaud J, Pham JL (2006) Genetic nature of yams (Dioscorea spp.) domesticated by farmers in Benin (West Africa). Genet Resour Crop Evol 53:121–130CrossRefGoogle Scholar
  40. Shao QS, Guo QS, Deng YM, Guo HP (2010) A comparative analysis of genetic diversity in medicinal Chrysanthemum morifolium based on morphology, ISSR and SRAP markers. Biochem Syst Ecol 38:1160–1169Google Scholar
  41. Shu P (1987) Study on pollen morphology from Dioscorea genus in China. Acta Phytotax Sin 25:357–365Google Scholar
  42. Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 36:1349–1368CrossRefGoogle Scholar
  43. Tamiru M, Becker HC, Maass BL (2007) Genetic diversity in yam germplasm from Ethiopia and their relatedness to the main cultivated Dioscorea species assessed by AFLP markers. Crop Sci 47:144–153CrossRefGoogle Scholar
  44. Tostain S, Agbangla C, Scarcelli N, Mariac C, Daïnou O, Berthaud J, Pham JL (2007) Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir.) in Benin using simple sequence repeat (SSR) markers. Plant Genet Resour 5:71–81Google Scholar
  45. Valbuena-Carabana M, Gonzalez-Martinez SC, Gil L (2008) A case study in Quercus pyrenaica Willd. from central Spain. For Ecol Manag 254:225–232CrossRefGoogle Scholar
  46. Wilkin P, Schols P, Chase M, Chayamarit K, Furness CA, Huysmans S, Rakotonasolo F, Smets E, Thapyai C (2005) A plastid gene phylogeny of the yam genus, Dioscorea: roots, fruits and Madagascar. Syst Bot 30:736–749Google Scholar
  47. Wu ZG, Leng CH, Tao ZM, Wei YH, Jiang CX (2009) Genetic diversity of Dioscorea alata L. based on ISSR analysis. J Chin Mater Med 34:3017–3019Google Scholar
  48. Xia CX, Gao SL, Zhang CY, Huang XS (2004) Analysis of the chemical components and isomorphic amylase among different local cultivars of Diocorea opposita. J Plant Resour Environ 13:21–24Google Scholar
  49. Xiao PG (2002) Modern Chinese Materia Medica, vol I. Beijing, p 740Google Scholar
  50. Xu GJ, Xu LS (1997) Species systematization and quality evaluation of commonly used Chinese traditional drugs, South-China, vol II. Fuzhou, pp 449–471Google Scholar
  51. Zhou YQ, Jing JZ, Li ZY, Hao J, Jia JF, Zhang BH, Hao JG (2005) Genetic diversity of yam (Dioscorea opposita Thunb.) detected by ISSR markers. Acta Bioe Exp Sin 38:324–329Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Zhi Gang Wu
    • 1
  • Xiao Xia Li
    • 1
    • 2
  • Xin Chun Lin
    • 3
  • Wu Jiang
    • 1
  • Zheng Ming Tao
    • 1
  • Nitin Mantri
    • 4
  • Chuan Yin Fan
    • 1
    • 2
  • Xiao Qing Bao
    • 1
    • 2
  1. 1.Zhejiang Institute of the Subtropical CropsWenzhouPeople’s Republic of China
  2. 2.Wenzhou Medical CollegeWenzhouPeople’s Republic of China
  3. 3.Key Lab for Modern Silvicultural Technology of ZhejiangZhejiang Forestry UniversityLinanPeople’s Republic of China
  4. 4.School of Applied Sciences, Health Innovations Research InstituteRMIT UniversityMelbourneAustralia

Personalised recommendations