Pen Academic Publishing   |  e-ISSN: 2602-4772

International Journal of Innovative Approaches in Agricultural Research 2017, Vol. 1(1) 51-70

RFLP- Based Gel Electrophoregram of DNA Primers for Acha (Fonio) Characterisation From Nigeria

Nyam D.D., Kwon-Ndung E.H. & Wuyep A. P.

pp. 51 - 70   |  DOI:   |  Manu. Number: MANU-1712-02-0003

Published online: December 19, 2017  |   Number of Views: 116  |  Number of Download: 115


The evaluation of the molecular diversity of Acha (Digitaria sp.) was carried out using Microsatelite primer combinations specially designed forDigitaria exilis. The amplifiedmicrosatellite fragments were also used in the other species of Digitaria namely; Digitaria barbinodis and Digitaria iburua.DNA extraction was carried and Agarose Gel Electrophoresis was conducted on the restricted amplified DNA extracts using microsatellite primers developed for Digitaria exilis. RFLPs clearly suggest a distinct separation of the three species of Acha at the molecular level (D. iburua, D. exilis and D. barbinodis) demonstrating the extent of their genetic differences at the DNA level.

Keywords: Gel, electrophoresis, RFLP, Acha

How to Cite this Article?

APA 6th edition
D.D., N., E.H., K. & P., W.A. (2017). RFLP- Based Gel Electrophoregram of DNA Primers for Acha (Fonio) Characterisation From Nigeria. International Journal of Innovative Approaches in Agricultural Research, 1(1), 51-70. doi: 10.29329/ijiaar.2017.100.6

D.D., N., E.H., K. and P., W. (2017). RFLP- Based Gel Electrophoregram of DNA Primers for Acha (Fonio) Characterisation From Nigeria. International Journal of Innovative Approaches in Agricultural Research, 1(1), pp. 51-70.

Chicago 16th edition
D.D., Nyam, Kwon-Ndung E.H. and Wuyep A. P. (2017). "RFLP- Based Gel Electrophoregram of DNA Primers for Acha (Fonio) Characterisation From Nigeria". International Journal of Innovative Approaches in Agricultural Research 1 (1):51-70. doi:10.29329/ijiaar.2017.100.6.

  1. Adoukonou-Sagbadja, H. (2010). Genetic characterization of traditional fonio millets (Digitaria exilis, D. iburua STAPF) landraces from West-Africa: Implications for conservation and breeding. Phd Dissertation. Justus-Liebig University Giessen.
  2. Adoukonou-Sagbadja, H., Schubert, V., Dansi, A., Jovtchev, G., Meister, A., Pistrick, K., Akpagana, K. & Friedt, W. (2007). Flow cytometric analysis reveals different nuclear DNA contents in cultivated fonio (Digitaria sp.) and some wild relatives. Plant Systematics and Evolution, 267: 163-176.
  3. Agrama, H. A. & Tuinstra, M. R. (2003). Phylogenetic diversity and relationships among sorghum accessions using SSRs and RAPDs. African Journal of Biotechnology, 2: 334 – 340.
  4. Akkaya, M. S., Bhagwat, A. A. & Gregan, P. B. (1992). Length polymorphism of simple sequence repeat DNA in soybean. Genetics, 132: 1131-1139. 
  5. Aldrich, P. R., Doebley, J., Schertz, K. F. & Stec, A. (1992). Patterns of allozyme variation in cultivated and wild Sorghum bicolor. Theoretical and Applied genetics, 85: 293-302. 
  6. Anand, P., Samit, R. & Amit, R. (2014). Molecular markers in phylogenetic studies-A review. Retrieved June 25, 2016, from
  7. Archak, S., Gaikwad, A. B., Gautam, D., Rao, E. V. V. B., Swamy, K. R. M & Karihaloo, J. L. (2003). Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India. Genome, 46: 362-369.
  8. Arumuganathan, K. & Earle, E. D. (1991). Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter, 9: 208–218.
  9. Avise, J. C. (2004). Molecular markers, natural history and evolution. (2nd Edition) Chapman & Hall Inc., New York, 541 p..
  10. Ayana, A., Bryngelsson, T. & Bekele, E. (2000). Genetic variation of Ethiopian and Eritrean sorghum [Sorghum bicolor (L.) Moench.] germplasm assessed by random amplified polymorphic DNA (RAPD). Genetic Resources and Crop Evolution, 47: 471-482. 
  11. Bänfer, G., Fiala, B., Weising, K. (2004). AFLP analysis of phylogenetic relationships among myrmecophytic of Macaranga (Euphorbiaceae) and their allies. Plant Systematics and Evolution, 249: 213-231.
  12. Banjo, A. (1988). Keynote address delivered at the Proceeding of an International Conference on crop Genetic Resources of Africa. 11th - 20th October.  Genetics, 4, 237-24.
  13. Barnaud, A., Vignes, H., Risterucci, A., Noyer, J., Pham, J., Blay, C., Buiron, M., Vigouroux, Y. & Billot, C. (2012). Development of Nuclear Microsatellite Markers for the Fonio, Digitaria exilis (Poaceae), an understudied West African Cereal. Retrieved February 16, 2014, from e105-e107 doi:10.3732/ajb.1100423.
  14. Barow, M. & Meister, A. (2002). Lack of correlation between AT frequency & genome size in higher plants and the effect of nonrandomness of basesequences on dye binding. Cytometry, 47: 1–7.
  15. Barrett, B. A. & Kidwell, K. K. (1998). AFLP-based genetic diversity assessment among wheat cultivars from the Pacific Northwest. Crop Science, 38: 1261-1271. 
  16. Bonin, A., Pompanon, F. & Taberlet, P. (2005).Use of Amplified Fragment Length Polymorphism (AFLP) markers in surveys of vertebrate diversity. Methods in Enzymology, 395: 145-161.
  17. Borlaug, N. E. (1968). Proceedings of 3rd International Wheat genetics Symposium. Canberra, 1-36.
  18. Broun, P. & Tanksley, S. D. (1996). Characterization and genetic mapping of simple repeat sequences in the tomato genome. Molecular Genetics, 250: 39-49. 
  19. Brown, S. M., Hopkins, M. S., Mitchell, S. E., Senior, M. L., Wang, T. Y., Duncan, R. R., Gonzalez-Candelas, F. & Kresovich, S. (1996). Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench]. Theoretical and Apllied genetics 93: 190-198. 
  20. Burr, B. (1994). Some concepts and new methods for molecular mapping in plants. In: Philips, R. L. & Vasil, I. K. (eds.) DNA-based Markers in Plants. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 1-7. 
  21. Busch, R. H. & Rauchi, T. L. (1993). Agronomic performance of tall versus short semi dwarf lines of spring wheat. Crop Science, 33: 941-943.
  22. Cao, W., Scoles, G., Hucl, P. & Chibbar, R. N. (1999). The use of RAPD analysis to classify Triticum accessions. Theoretical and Applied Genetics, 98: 602-607. 
  23. Caponio, I. & Rua, G. H. (2003). Reproductive biology of Digitaria bicornis, a common weed of northeastern Argentina. Revista Científica Agropecuaria, 2: 21-27.
  24. Carr, J., Xu, M., Dudley, J. W. & Korban, S. S. (2003). AFLP analysis of genetic variability in New Guinea impatiens. Theoretical and Applied Genetics,106: 1509-1516.
  25. Cervera, M. T., Cabezas, J. A., Sancha, J. C., Martínez de Toda, F. & Martínez-Zapater, J. M. (1998). Application of AFLPs to the characterization of grape vine (Vitis vinifera L.) genetic resources. A case study with accessions from Rioja (Spain). Theoretical and Applied Genetics, 97: 51-59. 
  26. Chandler, R. F. Jr. (1968). Science for better living. U.S. Department of Agriculture Handbook.
  27. Chowdari, K. V., Davierwala, A. P., Gupta, V. S., Ranjekar, P. K. & Govila, O. P. (1998a). Genotype identification and assessment of genetic relationships in pearl millet [Pennisetum glaucum (L.) R. Br.] using microsatellites and RAPDs. Theoretical and Applied Genetics, 97, 154-162. 
  28. Chowdari, K. V., Venkatachalam, S. R., Davierwala, A. P., Gupta, V. S., Ranjekar, P. K. & Govila, O. P. (1998b). Hybrid performance and genetic distance as revealed by the GATA microsatellite and RAPD markers in pearl millet. Theoretical and Applied Genetics, 97: 163-169. 
  29. Danna, K. & Nathans, D. (1971). Specific changes of simian virus 40 DNA by restriction endonuclease of Hemophilus influenza. Proceedings of National Academy of  Science, 68: 2913-2917.
  30. Dauda, A. & Luka, D. (2003). Status of Acha (Digitaria exilis) production in Bauchi State, Nigeria. In: proceedings of the first National Acha stakeholders workshop at PADP, Jos (9-11th March 2003). Kwon-Ndung, E. H., Bright, E. O. & Vodouhe, R. (eds). 
  31. de Oliveira, A. C., Richter, T. & Bennetzen, J. L. (1996). Regional and racial specifications in sorghum germplasm assessed with DNA markers. Genome,39, 579-587. 
  32. Dean, R. E., Dahlberg, J. A., Hopkins, M. S., Mitchell, S.E., & Kresovich, S. (1999). Genetic Redundancy and diversity among ‘Orange’ accessions in the U.S. national sorghum collection as assessed with simple sequence repeat (SSR) markers. Crop Science, 39, 1215-1221. 
  33. De-Bustos, A., Soler, C. & Jouve, N. (1999). Analysis by PCR-based markers using designed primers to study relationships between species of Hordeum (Poaceae). Genome, 42, 129-138. 
  34. Edna, S. & Victor, H. A. (2008). History, objectivity, and the construction of molecular phylogenies. Stud. Hist. Phil. Biol. and Biomedical Science, 39, 451 – 468.
  35. Excoffier, L., Smouse, P. E. & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
  36. Fahima, T., Sun, G.L., Beharav, A., Krugman, T., Beiles, A. & Nevo, E. (1999). RAPD polymorphism of wild emmer wheat populations, Triticum dicoccoides, in Israel. Theoretical and Applied genetics,98, 434-447. 
  37. Feuk, L., Carson,  A. R. & Scherer, S. W. (2006). Structural variation in the human genome. Nature Review of Genetics,7, (2).85–97
  38. Gao, L. Z. & Hong, S. G. D. (2000). Allozyme variation and population genetic structure of common wild rice Oryza rufipogon Griff. in China. Theoretical and Applied genetics,101, 494-502.
  39. Gerber, S., Mariette, S., Streiff, R. & Kremer, A. (2000). Comparison of microsatellites and AFLP markers for parental analysis. Molecular Ecology,9, 1037-1048.
  40. Haq, N. & Ogbe, F. D. (1995). Fonio (Digitaria exilis and Digitaria iburua). In: Cereals and pseudocereals, boundary row, Chapman & Hall, London, Chap 5, 2–6.
  41. Hayward, M. D. & Hacker, J. B. (1980). Genetic control of some esterase isozymes of Digitaria species, and their utility in the identification of hybrids. Euphytica,29, 347-356.
  42. Henrard, J. T. (1950). Monograph of the genus Digitaria. Leiden Univ. Press, Leiden.
  43. Hilu, K. W. (1995). Evolution of finger millet: evidence from random amplified polymorphic DNA. Genome,38, 232-238.
  44. Hongtrakul, V., Huestis, G. M., & Knapp, S.  J. (1997). Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: Genetic diversity among oilseed inbred lines.  95, 400-407. 
  45. Ibrahim, A. (2001). Hungry rice (Fonio): A neglected cereal crop. NAQAS Newsletter, Vol. No. 4 – 5.
  46. Jideani, I. A. (1999). Traditional and possible technological uses of Digitaria exilis (Acha) and Digitaria iburua (iburu): a review. Plant Foods for Human Nutrition,54, 363-374.
  47. Jones, C. J., Edwards, K. J., Castiglione, S., Winfield, M. O., Sala, F., Van-der-Weil, C., Vosman, B. L., Matthes, M., Daly, A., Brettschneider, R., Bettini, P., Buiatti, M., Maestri, E., Marmiroli, N., Aert, R. L., Volckaert, G., Rueda, J., Vazquez, A. & Karp, A. (1998). Reproducibility testing of RAPDs by a network of European laboratories. In: Karp A, Isaac P. G., Ingram, D. S. (eds.) Molecular tools for screening biodiversity, Chapman & Hall, London, UK, pp 176-179. 
  48. Kimberling, D. N., Ferreira, A. R., Shuster, S. M. & Keim, P. (1996). RAPD marker estimation of genetic structure among isolated northern leopard frog populations in southwestern USA. Molecular Ecology, 5, 521-529.
  49. Kuta, D. D., Kwon-Ndung, E., Dachi, S., Bakare, O. & Ogunkanmi, L. A. (2005). Optimization of protocols for DNA extraction and RAPD analysis in West-African fonio (Digitaria exilis and Digitaria iburua) germplasm characterization. African Journal of Biotechnology,4, 1368-1371.
  50. Kuta, D. D., Kwon-Ndung, E., Dachi, S., Ukwungwu, M. & Imolehin, E. D. (2003). Potential role of biotechnology tools for genetic improvement of lost crops of Africa: the case of fonio (Digitaria exilis and Digitaria iburua). African Journal of Biotechnology,2, 580-585.
  51. Kwon-Ndung, E. H. & Misari, S. M. (1999). Overview of research and development of fonio (Digitaria exilis Kippist Stapf) and prospect for improvement in Nigeria. In: Genetics and food security in Nigeria. GSN Publication, Nigeria, P. 71 – 76.
  52. Kwon-Ndung, E. H., Misari, S. M. & Dachi, S. N. (1998). Collecting germplasm of Acha, Digitaria exilis (Kipp.) Stapf, accessions in Nigeria. Plant Genetic Resources Newsletter,116, 30–31.
  53. Morden, C. W., Doebley, J. F. & Schertz, K. F. (1989). Allozyme variation in old world races of Sorghum bicolor (Poaceae). American Journal of Botany,76, 247-255. 
  54. Morgante, M. & Olivieri, A. M. (1993). PCR-amplified microsatellites as markers in plant genetics. Plant Journal, 3, 175-182. 
  55. Mullis, K. B., Faloona, F., Scharf, S., Saiki, R., Horn, G. & Erlich, H. A. (1986). Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symp. Quantitative Biology 51: 263-273
  56. NRC. (1996). Lost crops of Africa volume 1: Grains national Research Council. National Academy Press. Washington, DC, pp 59-75.
  57. Portères, R. (1946). L’aire culturale du Digitaria iburua Stapf, cereal mineure de l’ouest-Africain.L’Agronomie Tropicale 1:589–592.
  58. Portères, R. (1955). African Cereals: Eleucine, Fonio, Black Fonio, Teff, Brachiaria,Paspalum, Pennisetum and African Rice. In: Harlan JR, de Wet JMJ, Stemler ABL (eds) Origins of African plant domestication. Mouton Publishers, The Hague, pp 498.
  59. Russell, J. R., Fuller, J. D., Macaulay, M., Hatz, B. G., Jahoor, A., Powell, W. & Waugh, R. (1997). Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied genetics,95, 714-722. 
  60. Saghai-Maroof, M. A., Biyashev, R. M., Yang, G. P., Zhang, Q. & Allard, R. W. (1994). Extraordinarily polymorphic  microsatellite DNA in barley: Species diversity, chromosomal locations, and population dynamics. Proceedings of National Academy of Science, (USA) 91, 5466-5470. 
  61. Semagn, K., Bjørnstad, Å. & Ndjiondjop, M. N. (2006). An overview of molecular marker methods for plants. African Journal of Biotechnology,5, 2540-2568.
  62. Smith, S. & Helentjaris, T. (1996). DNA fingerprinting and plant variety protection. In: Paterson, A. H. (Ed.) Genome mapping in plants, Academic Press, San Diego, CA USA, pp 95-110. 
  63. Stankiewicz, P. &  Lupski, J. R. (2002). Genome architecture, rearrangements and genomic disorders. Trends in Genetics 18, (2). 74–82.
  64. Stapf, O. (1915). Iburu and Fundi, two cereals of Upper Guinea (Digitaria iburua, D. exilis). Kew Bulletin, 8, 381-386.
  65. Struss, D. & Plieske, J. (1998). The use of microsatellite markers for detection of genetic diversity in barley populations. Theoretical and Applied genetics,97, 308-315. 
  66. Temple, V. J. & Bassa, J. D. (1991). Proximate chemical composition of fonio (Digitaria exilis) grain. Journal of Science, Food and Agriculture,56, 561-564.
  67. Zhang, Q., Liu, K. D., Yang, G. P., Saghai-Maroof, M. A., Xu, C. G. & Zhou, Z. Q. (1997). Molecular marker diversity and hybrid sterility in indica-japonica rice crosses. Theoretical and Apllied genetics,95, 112-118. 
  68. Zhu, J., Gale, M. D., Quarrie, S., Jackson, M. T. & Bryan, G. J. (1998). AFLP markers for the study of rice biodiversity. Theoretical and Applied genetics,96, 602-61.