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Plant Systematics and Evolution

, Volume 301, Issue 2, pp 737–747 | Cite as

Genetic diversity of Opuntia spp. varieties assessed by classical marker tools (RAPD and ISSR)

  • Ernestina Valadez-MoctezumaEmail author
  • Samir Samah
  • Arturo Luna-Paez
Original Article

Abstract

Opuntia, commonly named “nopal” in Mexico, is an important crop for its agronomical, economical, ecological and cultural value. Furthermore, it is known for its taxonomic complexity. In this paper, we report the genetic variability of 52 Opuntia cultivars with agronomic and economic importance, classified into 12 different species using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) markers. Ten primers, five for each marker type, were selected to assess their ability to detect polymorphisms in this plant accesions/varieties. Both marker systems generated a total of 307 bands, of which 50.8 % were polymorphic with an average of 15.6 polymorphic bands per primer. Thus, we assume that Mexican Opuntia varieties present broad genetic variation. Based on percentage of polymorphic bands; resolving power; polymorphic information content; and Marker Index, the K-12 (RAPD) and IS-06 (ISSR) primers were the most informative ones. Clusters obtained from RAPD, ISSR and a combination of both data sets did not match the actual taxonomic classification. On the other hand, the putative varieties currently classified in the same species were not located in the same cluster. Besides, the varieties included in O. ficus-indica, O. albicarpa and O. megacantha showed broad variation but were not well defined into separate clades; these cultivars possibly have common ancestry. The results presented here support our hypothesis about the existence of a smaller number of Opuntia species in accordance with those currently described, but with high intraspecific genetic variation.

Keywords

Nopal RAPD ISSR Genetic variability Taxonomy 

Abbreviations

DNA

Deoxyribonucleic acid

ISSR

Inter-simple sequence repeats

RAPD

Random amplified polymorphic DNA

UPGMA

Unweighted pair group method with the arithmetic averaging

AMOVA

Analysis of molecular variance

PIC

Polymorphic information content

MI

Marker index

Rp

Resolving power

Notes

Acknowledgments

We are grateful for the support obtained by the UACH and the SNICS–UACH agreement, and by the “Red Nacional de Nopal” for giving us the study materials. The authors especially acknowledge the anonymous referees for their comments on this paper.

References

  1. Anderson EF (2001) The cactus family. Timber, PortlandGoogle Scholar
  2. Archak S, Gaikwad AB, Gautam D, Rao EVVB, Swamy KRM, Karihaloo JL (2003) Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India. Genome 46:362–369PubMedCrossRefGoogle Scholar
  3. Aswathi AK, Nagaraja GM, Naik GV, Kanginakudru S, Thangavelu K, Nagaraju J (2004) Genetic diversity and relationships in mulberry (genus Morus) as revealed by RAPD and ISSR marker assays. BMC Genet 5:1. doi: 10.1186/1471-2156-5-1 CrossRefGoogle Scholar
  4. Bandyopadhyay (Biswas) B, Sharma A (2000) The use of multivariate analysis of karyotypes to determine relationships between species of Opuntia (Cactaceae). Caryologia 53(2):121–126Google Scholar
  5. Behera TK, Singh AK, Staub JE (2008) Comparative analysis of genetic diversity in Indian bitter gourd (Momordica charantia L.) using RAPD and ISSR markers for developing crop improvement strategies. Sci Hortic 115:209–217CrossRefGoogle Scholar
  6. Belaj A, Satovic Z, Cipriani G, Baldoni L, Testolin R, Rallo L, Trujillo I (2003) Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor Appl Genet 107:736–744PubMedCrossRefGoogle Scholar
  7. Bendhifi M, Baraket G, Zourgui L, Souid S, Salhi-Hannachi A (2013) Assessment of genetic diversity of Tunisian Barbary fig (Opuntia ficus indica) cultivars by RAPD markers and morphological traits. Sci Hortic 158:1–7CrossRefGoogle Scholar
  8. Biswas MK, Xu Q, Deng XX (2010) Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Sci Hortic 124:254–261CrossRefGoogle Scholar
  9. Bravo HH (1978) Las cactáceas de México 1. Universidad Nacional Autónoma de México, D.F. MéxicoGoogle Scholar
  10. Britton NL, Rose JN (1963) The Cactaceae, vol 1. Dover, New YorkGoogle Scholar
  11. Caruso M, Currò S, Las Casas G, La Malfa S, Gentile A (2010) Microsatellite markers help to assess genetic diversity among O. ficus indica cultivated genotypes and their relation with related species. Plant Syst Evol 290:85–97CrossRefGoogle Scholar
  12. De Riek J, Calsyn E, Everaert I, Van Bocksteal E, De Loose M (2001) AFLP based alternative for the assessment of the distinctness, uniformity and stability of sugar beat varieties. Theor Appl Genet 103:1254–1256CrossRefGoogle Scholar
  13. Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedCentralPubMedGoogle Scholar
  14. Fang DQ, Roose ML (1997) Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theor App Genet 95:408–417CrossRefGoogle Scholar
  15. Felker P, Paterson A, Jenderek MM (2006) Forage potential of Opuntia clones maintained by the USDA National Plant Germplasm System (NPGS) collection. Crop Sci 46:2161–2168CrossRefGoogle Scholar
  16. Gilbert JE, Lewis RV, Wilkinson MJ (1999) Developing an appropriate strategy to assess genetic variability in plant germplasm collections. Theor Appl Genet 98:1125–1131CrossRefGoogle Scholar
  17. Griffith MP (2004) The origins of an important cactus crop, Opuntia ficus-indica (Cactaceae): new molecular evidence. Am J Bot 91(11):1915–1921PubMedCrossRefGoogle Scholar
  18. Gupta S, Srivastava M, Mishra GP, Naik PK, Chauhan RS, Tiwari SK, Kumar M, Singh R (2008) Analogy of ISSR and RAPD markers for comparative analysis of genetic diversity among different Jatropha curcas genotypes. Afr J Biotechnol 7(23):4230–4243Google Scholar
  19. Guzmán U, Arias S, Dávila P (2003) Catálogo de cactáceas mexicanas. UNAM and CNCUB, D.F. MéxicoGoogle Scholar
  20. Helsen P, Verdyck P, Tye A, Van Dongen S (2009) Low levels of genetic differentiation between O. echios varieties on Santa Cruz (Galapagos). Plant Syst Evol 279:1–10CrossRefGoogle Scholar
  21. Hunt D (2002) Alphabetical list of currently accepted species. In: Hunt D, Taylor N (eds) Studies in the Opuntioideae. Sherborne, England, pp 250–255Google Scholar
  22. Jana S, Pietrzak LN (1988) Comparative assessment of genetic diversity in wild and primitive cultivated barley in a center of diversity. Genetics 119:981–990PubMedCentralPubMedGoogle Scholar
  23. Kalpana D, Choi SH, Choi TK, Senthil K, Lee YS (2012) Assessment of genetic diversity among varieties of mulberry using RAPD and ISSR fingerprinting. Sci Hortic 134:79–87CrossRefGoogle Scholar
  24. Labra M, Grassi F, Bardini M, Imazio S, Guiggi A, Citterio S, Banfi E, Sgorbati S (2003) Relationships in Opuntia Mill. Genus (Cactaceae) detected by molecular marker. Plant Sci 165:1129–1136CrossRefGoogle Scholar
  25. Loarce Y, Gallego R, Ferrer E (1996) A comparative analysis of genetic relationships between rye cultivars using RFLP and RAPD markers. Euphytica 88:107–115CrossRefGoogle Scholar
  26. Lu X, Lu L, Gong Y, Zhao L, Song X, Zhu X (2009) Cultivar identification and genetic diversity analysis of broccoli and its related species with RAPD and ISSR markers. Sci Hortic 122:645–648CrossRefGoogle Scholar
  27. Luna-Paez A, Valadez-Moctezuma E, Barrientos-Priego AF, Gallegos-Vázquez C (2007) Characterization of Opuntia spp. by means of seed with RAPD and ISSR markers and its possible use for differentiation. J PACD 9:43–59Google Scholar
  28. Majure LC, Puente R, Griffith MP, Judd WS, Soltis PS, Soltis DE (2012) Phylogeny of Opuntia s.s. (cactaceae): clade delineation, geographic origins, and reticulate evolution. Am J Bot 99(5):847–864PubMedCrossRefGoogle Scholar
  29. Mihalte L, Sestras RE, Gyorgy-Feszt G, Tamas E (2011) Assessment of genetic variation on four genera of Cactaceae using taxonomic, cytological and molecular markers methods. Plants Omics J 4(3):142–148Google Scholar
  30. Miller JC, Tanksley SD (1990) Effects of different restriction enzymes, probe source, and probe length on detecting restriction fragment length polymorphism in tomato. Theor App Genet 80(3):385–389CrossRefGoogle Scholar
  31. Mondragón JC, Bordelon BB (2002) Presencia de apomixis en cruzas de nopales mexicanos y su identificación molecular preliminar. Rev Fitot Mex 25(3):247–252Google Scholar
  32. Mondragón-Jacobo C (2003) Molecular characterization using RAPDs of a cactus (Opuntia spp. Cactaceae) collection from central México as a basis for plant breeding. Rev Chap Ser Hortic 9(1):97–114Google Scholar
  33. Montiel D, Valadez-Moctezuma E, Palomino G, Bermúdez MA, Fernández FJ (2012) DNA extraction from roots of xoconostle. J PACD 14:35–40Google Scholar
  34. Nieddu G, Chessa I (1997) Distribution of phenotypic characters within a seedling population from Opuntia ficus-indica (cv. ‘‘Gialla’’). Acta Hortic 438:37–43Google Scholar
  35. Nieddu G, Chessa I, Barberis A (2006) Characterization of seedlings obtained from open pollinated ‘Gialla’ cactus pear (Opuntia ficus-indica). Acta Hortic 728:105–110Google Scholar
  36. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539PubMedCentralPubMedCrossRefGoogle Scholar
  37. Powell AM, Weedin JF (2001) Chromosome numbers in Chihuahuan desert Cactaceae. III. Trans-Pecos Texas. Am J Bot 88(3):481–485CrossRefGoogle Scholar
  38. Rebman JP, Pinkava DJ (2001) Opuntia cacti of North America-an overview. Flor Ent 84(4):474–483CrossRefGoogle Scholar
  39. Reyes-Agüero JA, Aguirre JR, Hernández HM (2005) Systematic notes and a detailed description of Opuntia ficus-indica (L.) Mill. (Cactaceae). Agrociencia 39:395–408Google Scholar
  40. Roldán-Ruiz I, Dendauw J, Van Bockstaele E, Depicker A, De Loose M (2000) AFLP Markers reveal high polymorphic rates in Ryegrasses (Loium spp.). Mol Breed 6:125–135CrossRefGoogle Scholar
  41. Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722CrossRefGoogle Scholar
  42. Scheinvar L (1995) Taxonomy of utilized opuntias. In: Barbera G, Inglese P, Pimienta-Barrios E (eds) Agroecology, cultivation and uses of cactus pear. FAO plant production and protection paper 132. FAO, Rome, pp 20–27Google Scholar
  43. Segura S, Scheinvar L, Olalde G, Leblanc O, Filardo S, Muratalla A, Gallegos C, Flores C (2007) Genome sizes and ploidy levels in Mexican cactus pear species Opuntia (Tourn.) Mill. Series Streptacanthae Britton et Rose, Leucotrichae DC, Heliabravoanae Scheinvar and Robustae Britton et Rose. Genet Resour Crop Evol 54:1033–1041CrossRefGoogle Scholar
  44. Shilpha J, Silambarasan T, Pandian SK, Ramesh M (2013) Assessment of genetic diversity in Solanum trilobatum L., an important medicinal plant from South India using RAPD and ISSR markers. Genet Resour Crop Evol 60:807–818CrossRefGoogle Scholar
  45. Souto-Alves T, Vanusa da Silva M, Alves de Almeida CM, Oliveira Jordão do Amaral D, Cordeiro dos Santos D, Farias I, Tenório Sabino Donato VM, da Costa AF (2009) Genetic diversity in cactus clones using ISSR markers. Acta Hortic 811:55–58Google Scholar
  46. Taylor CL, Barker NP (2012) Species limits in Vachellia (Acacia) karroo (Mimosoideae: Leguminoseae): Evidence from automated ISSR DNA “fingerprinting”. South Afr J Bot 83:36–43CrossRefGoogle Scholar
  47. Valadez-Moctezuma E, Kahl G, Ramser J, Hüttel B, Rubluo-Islas A (2001) Técnicas moleculares para la caracterización de genomas vegetales (garbanzo) y algunas aplicaciones potenciales. Rev Fitotec Mex 24(1):103–120Google Scholar
  48. Valdéz-Cepeda RD, Blanco-Macías F, Gallegos-Vázquez C (2003) Ordenación y clasificación numérica en nopal tunero mediante atributos de fruto. Rev Chap Ser Hortic 9(2):81–95Google Scholar
  49. Vos P, Hogers R, Bleeker M, Reijans M, Lee TV, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabea M (1995) AFLP: a new technique for DNA Fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCentralPubMedCrossRefGoogle Scholar
  50. Wang ZY, Second G, Tanksley SD (1992) Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet 83(5):565–581PubMedCrossRefGoogle Scholar
  51. Wang X, Felker PD, Burow M, Paterson HA (1998) Comparison of RAPD marker patterns to morphological and physiological data in the classification of Opuntia accessions. J PACD 3:3–14Google Scholar
  52. Waugh R, Powell W (1992) Using RAPD markers for crop improvement. Trends Biotechnol 10:186–191CrossRefGoogle Scholar
  53. Xiao LQ, Ge XJ, Gong X, Hao G, Zheng SI (2004) ISSR Variation in the Endemic and Endangered Plant Cycas guizhouensis (Cycadaceae). Ann Bot 94:133–138PubMedCentralPubMedCrossRefGoogle Scholar
  54. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183PubMedCrossRefGoogle Scholar
  55. Zoghlami N, Chrita I, Bouamama B, Gargouri M, Zemni H, Ghorbel A, Mliki A (2007) Molecular based assessment of genetic diversity within Barbary fig (Opuntia ficus indica (L.) Mill. in Tunisia. Sci Hortic 113:134–141CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2014

Authors and Affiliations

  • Ernestina Valadez-Moctezuma
    • 1
    Email author
  • Samir Samah
    • 1
  • Arturo Luna-Paez
    • 1
  1. 1.Laboratorio de Biología Molecular, Departamento de FitotecniaUniversidad Autónoma ChapingoChapingo Edo. MéxicoMexico

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