Genetic Resources and Crop Evolution

, Volume 64, Issue 2, pp 291–305 | Cite as

Morphological, SSR and ploidy analysis of water yam (Dioscorea alata L.) accessions for utilization of aerial tubers as planting materials

  • Gezahegn Girma
  • Melaku Gedil
  • Charles Spillane
Research Article


The high cost and supply shortage of seed yam propagules for planting are major constraints in yam production. In the water yam (Dioscorea alata L.), aerial tubers have potential as alternative sources of planting material. In this study, we investigated morphological, molecular and ploidy variation across multiple aerial tuber producing accessions of Dioscorea alata. Initial screening of over 800 accessions from the International Institute of Tropical Agriculture germplasm collection for aerial tuber production identified a subset (15 %) of accessions, which produced aerial tubers. The aerial tuber producing accessions (along with 18 non-aerial tuber accessions) were further characterized for phenotypic and ploidy variation. In addition, using SSR markers we characterized the genetic diversity amongst all of the aerial tuber producing accessions, along with six non-aerial tuber producing accessions. Multiple Correspondence Analysis (MCA) using morphological data grouped the accessions according to their aerial tuber production. The aerial tuber production characteristics of accessions were associated with phenotypic variables and ploidy levels. The MCA analysis revealed three main groups consisting of; Group 1) all non aerial tuber producing accessions (n = 15), hastate leaf shape, less or no anthocyanin pigmentation and diploid (2n = 2x = 40), Group 2) group with some aerial tuber producing accessions, different extent of anthocyanin pigmentation, sagittate leaf shape, mainly diploid (n = 44) and three triploid (2n = 3x = 60) and 3) a group where all individuals bear aerial tuber, cordate leaf shape, intermediate anthocyanin pigmentation and majority (n = 74) tetraploid (2n = 4x = 80) and three triploid individuals. Aerial tuber production may be subject to a genome dosage effect as an increase in aerial tuber production was associated with increased ploidy level. For instance, tetraploid plants produce more aerial tubers per sprout than either triploids or diploids. Principal coordinate analysis based on SSR markers using Jaccard’s coefficient also revealed distinct groups associated with the pattern of aerial tuber formation, leaf shape and anthocyanin pigmentation. Overall our study indicates the usefulness of combining SSR markers, ploidy level and phenotypic data for identification and classification of Dioscorea alata accessions according to their extent of aerial tuber production.


Aerial tuber Dioscorea alata Genome dosage effect Ploidy SSR Vegetative propagation Water yam 



The study was carried out at the International Institute of Tropical Agriculture (IITA), Ibadan Nigeria. The CGIAR Research Program on Roots, Tubers and Bananas funded this work. The first author acknowledges support from the Netherlands Ministry of Foreign Affairs, and PhD fee waiver from the National University of Ireland Galway.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Acha I, Shiwachi H, Asiedu R, Akoroda M (2004) Effect of auxins on root development in yam (Dioscorea rotundata) vine. Trop Sci 44:80–84CrossRefGoogle Scholar
  2. Aighewi BA, Asiedu R, Maroya N, Balogun M (2015) Improved propagation methods to raise the productivity of yam (Dioscorea rotundata Poir.). Food Sec 7:823–834CrossRefGoogle Scholar
  3. Allario T, Brumos J, Colmenero-Flores JM, Tadeo F, Froelicher Y, Talon M, Navarro L, Ollitrault P, Morillon R (2011) Large changes in anatomy and physiology between diploid Rangpur lime (Citrus limonia) and its autotetraploid are not associated with large changes in leaf gene expression. J Exp Bot 62:2507–2519CrossRefPubMedGoogle Scholar
  4. Arnau G, Nemorin A, Maledon E, Abraham K (2009) Revision of ploidy status of Dioscorea alata L. (Dioscoreaceae) by cytogenetic and microsatellite segregation analysis. Theor Appl Genet 118:1239–1249CrossRefPubMedGoogle Scholar
  5. Asante BO, Otoo E, Wiredu AN, Acheampong P, Osei-Adu J, Frimpong BN (2011) Willingness to dopt the vine multiplication technique in seed yam production in the forest savanna transition agro-ecological zone, Ghana. J Dev Agric Econ 3:710–719Google Scholar
  6. Babil PK, Irie K, Shiwachi H, Tun Y, Toyohara H, Fujimaki H (2010) Ploidy variation and their effects on Leaf and stoma traits of water yam (Dioscorea alata L.) collected in Myanmar. Trop Agr Develop 54:132–139Google Scholar
  7. Babil PK, Funayama C, Iijima K, Irie K, Shiwachi H, Toyohara H, Fujimaki H (2011) Effective induction of polyploidy by in vitro treatment with colchicine and characterization of induced polyploid variants in water yam (Dioscorea alata L.). Trop Agr Develop 55:142–147Google Scholar
  8. Bradshaw JE, Bonierbale M (2010) Potatoes. In: Bradshaw JE (ed) Handbook of plant breeding. Springer, New York, pp 1–52Google Scholar
  9. Dansi A, Dantsey-Barry H, Dossou-Aminon I, N’Kpenu E, Agre A, Sunu Y, Kombate K, Loko Y, Dansi M, Assogba P, Vodouhe R (2013) Varietal diversity and genetic erosion of cultivated yams (Dioscorea cayenensis Poir - D. roundata Lam complex and D. alata L.) in Togo. Int J Biodivers Conserv 5:223–239Google Scholar
  10. Dumet D, Ogunsola D (2008) Regeneration guidelines: yams, crop specific regeneration guidelines. In: Dulloo ME, Thormann I, Jorge MA, Hanson J (eds) CGIAR System-wide Genetic Resource Programme, RomeGoogle Scholar
  11. Duszynska D, McKeown PC, Juenger TE, Pietraszewska-Bogiel A, Geelen D, Spillane C (2013) Gamete fertility and ovule number variation in selfed reciprocal F1 hybrid triploid plants are heritable and display epigenetic parent-of-origin effects. New Phytol 198:71–81CrossRefPubMedGoogle Scholar
  12. Egesi CN, Pillay M, Asiedu R, Egunjobi JK (2002) Ploidy analysis in water yam, Dioscorea alata L. germplasm. Euphytica 128:225–230CrossRefGoogle Scholar
  13. Egesi CN, Asiedu R, Ude G, Ogunyemi S, Egunjobi JK (2006) AFLP marker diversity in water yam (Dioscorea alata L.). Plant Genet Resour 4:181–187CrossRefGoogle Scholar
  14. Fort A, Ryder P, McKeown PC, Wijnen C, Aarts MG, Sulpice R, Spillane C (2015) Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. New Phytol. doi: 10.1111/nph.13650 Google Scholar
  15. Hammer O, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9Google Scholar
  16. Hasan SMZ, Ngadin AA, Shah RM, Mohamad N (2008) Morphological variability of greater yam (Dioscorea alata L.) in Malaysia. Plant Genet Resour 6:52–61CrossRefGoogle Scholar
  17. IPGRI/IITA (1997) Descriptors for Yam (Dioscorea spp.). International Institute of Tropical Agriculture, Ibadan, Nigeria/International Plant Genetic Resources Institute, Rome, ItalyGoogle Scholar
  18. Jaccard P (1908) Nouvelles recherches Sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270Google Scholar
  19. Jan CC, Chandler JM, Wagner SA (1988) Induced tetraploidy and trisomic production of Helianthus annuus L. Genome 30:647–651CrossRefGoogle Scholar
  20. Kabeya MJ, Kabeya UC, Bekele BD, Kikuno H (2013) Vine cuttings technology in food yam (Discorea rotundata) production. Asian J Plant Sci Res 3:107–111Google Scholar
  21. Kikuno H, Matsumoto R, Shiwachi H, Toyohara H, Asiedu R (2007) Comparative effects of explants sources and age of plant on rooting, shooting and tuber formation of vine cuttings from yams (Dioscorea spp.). Trop Agr Develop 51 Extra issue 2Google Scholar
  22. Lê S, Josse J, Husson F (2008) FactoMineR: an R Package for multivariate analysis. J Stat Softw 25:1–18CrossRefGoogle Scholar
  23. Lebart L (2006) Validation techniques in multiple correspondence analysis. In: Greenacre MJ, Blasius J (eds) Multiple correspondence analysis and related methods. Chapman & Hal, London, pp 179–195CrossRefGoogle Scholar
  24. Lebot V (2009) Tropical root and tuber crops: cassava, sweet potato, yams and aroids. CABI Publishers, Wallingford, p 414Google Scholar
  25. Lebot V, Trilles B, Noyer JL, Modesto J (1998) Genetic relationships between Dioscorea alata L. cultivars. Genet Resour Crop Evol 45:499–509CrossRefGoogle Scholar
  26. Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398CrossRefGoogle Scholar
  27. Malapa R, Arnau G, Noyer JL, Lebot V (2005) Genetic Diversity of the greater yam (Dioscorea alata L.) and relatedness to D. nummularia Lam. and D. transversa Br. as revealed with AFLP Markers. Genet Resour Crop Evol 52:919–929CrossRefGoogle Scholar
  28. Matsumoto R, Shiwachi H, Kikuno H, Irie R, Toyohara H, Komamine A, Fujimaki H (2010) Characterization of sprouting and shoot formation processes of rooted cuttings of water yam (Dioscorea alata L.). Trop Agr Develop 54:107–112Google Scholar
  29. Mignouna HD, Abang MM, Fagbemi SA (2003) A comparative assessment of molecular marker assays (AFLP, RAPD and SSR) for white yam (Dioscorea rotundata) germplasm characterization. Ann Appl Biol 142:269–276CrossRefGoogle Scholar
  30. Morgante M, Hanafey H, Powell W (2002) Microsatellites are preferntially associated with nonrepetitive DNA in plant genome. Nat Genet 30:194–200CrossRefPubMedGoogle Scholar
  31. Nemorin A, David J, Maledon E, Nudol E, Dalon J, Arnau G (2013) Microsatellite and flow cytometry analysis to help understand the origin of Dioscorea alata polyploids. Ann Bot 112(5):811–819CrossRefPubMedPubMedCentralGoogle Scholar
  32. Obidiegwu JE, Asiedu R, Ene-Obong EE, Mouneke CO, Kolesnikova-Allen M (2009a) Genetic characterization of some water yam (Dioscorea alata L.) in West Africa with simple sequence repeats. J Food Agri Environ 7:132–136Google Scholar
  33. Obidiegwu JE, Kolesnikova-Allen M, Muoneke CO, Asiedu R (2009b) SSR markers reveal diversity in guinea yam (Dioscorea cayenensis/D. rotundata) core set. Afr J Biotechnol 8:2730–2739Google Scholar
  34. Okagami N, Tanno N (1991) Dormancy in Dioscorea: comparison of dormant characters in bulbils of a northern species (D. opposita) and a southern species (D. bulbifera var. vera). J Plant Physiol 138:559–565CrossRefGoogle Scholar
  35. Paál D, Kopernický J, Gasper J, Vašíček D, Vašíčková K, Bauerová M, Bauer M (2013) Microsatellite analysis of the Slovak carniolan honey bee (Apis mellifera Carnica). J Microb Biotech Food Sci 2:1517–1525Google Scholar
  36. Perrier J, Jacquemoud-Collet J (2006) DARwin software.
  37. Petro D, Onyeka T, Etienne S, Rubens S (2011) An interspecific genetic map of water yam (Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance. Euphytica 179:405–416CrossRefGoogle Scholar
  38. R Core Team (2013) R: a language and environment for statistical computing. R foundation for statistical computing Vienna, Austria.
  39. Raz, Lauren/Flora of North America Editorial Committee (eds) (2002) Dioscoreaceae R. Brown: Yam family. Flora of North America North of Mexico, Magnoliophyta: Liliidae: Liliales and Orchidales, pp 479–485Google Scholar
  40. Roldán-Ruiz I, Dendauw J, Van Bockstaele E, Depicker A, De Loose M (2000) AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breed 6:125–134CrossRefGoogle Scholar
  41. Shiwachi H, Kikuno H, Asiedu R (2006) Mini tuber production using yam (Dioscorea rotundata) vines. Trop Sci 45(4):163–169CrossRefGoogle Scholar
  42. Siqueira MVBM, Dequigiovanni G, Corazon-Guivin MA, Feltran JC, Veasey EA (2012) DNA fingerprinting of water yam (Dioscorea alata) cultivars in Brazil based on microsatellite markers. Horti Bras 30:653–659CrossRefGoogle Scholar
  43. Sitther V, Zhang D, Dhekney SA, Harris DL, Yadav AK, Okie WR (2012) Cultivar identification, pedigree verification, and diversity analysis among peach cultivars based on simple sequence repeat markers. J Am Soc Hort Sci 137(2):114–121Google Scholar
  44. Statistica Stat Soft I (2001) STATISTICA (data analysis software system) Version 6.0.
  45. Tay D (2013) Tropical and subtropical root and tuber crops. In: Normah MN, Chin HF, Reed BM (eds) Conservation of tropical plant species. Springer, New York, pp 249–292CrossRefGoogle Scholar
  46. Walck JL, Cofer MS, Hidayati SN (2010) Understanding the germination of bulbils from an ecological perspective: a case study on Chinese yam (Dioscorea polystachya). Ann Bot 106:945–955CrossRefPubMedPubMedCentralGoogle Scholar
  47. Wright S (1978) Evolution and the genetics of populations.Variability within and among natural populations. University of Chicago Press, Chicago, p 580Google Scholar
  48. Yeh FC, Yang RC, Boyle T (1997) Population genetic analysis of codominant markers and qualitative traits. Belgian J Bot 129:157Google Scholar
  49. Yildiz M (2013) Plant responses at different ploidy levels. In: Silva-Opps M (ed) Current progress in biological research. InTech, Rijeka, pp 363–385Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Gezahegn Girma
    • 1
    • 2
  • Melaku Gedil
    • 1
  • Charles Spillane
    • 2
  1. 1.International Institute of Tropical Agriculture (IITA)IbadanNigeria
  2. 2.Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), School of Natural SciencesNational University of Ireland GalwayGalwayIreland

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