Abstract
As part of the development of a molecular toolkit for the study of diversity within large plant germplasm collections, RAPD technology has been applied to accessions of rice (Oryza sativa) obtained from the major world collection held at IRRI (the International Rice Research Institute) which supplies germplasm to breeders. Methods for the speedy extraction of DNA representative of a rice accession, its amplification by PCR to reveal reproducible products, and the analysis of the banding data using numerical techniques have been established. The biological meaningfulness of RAPD data has also been demonstrated by reference to previous work on classification and crossability.
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Andersen, W R, and Fairbanks, D J. 1990. Molecular markers: important tools for plant genetic resource characterization. Diversity, 6, 51–53.
Brown, A D H. 1989a. The case for core collections. In: Brown, A. D. H., Marshall, D. R., Frankel, O. H. and Williams, J. T. (eds) The Use of Plant Genetic Resources, pp. 136–151. Cambridge University Press, Cambridge.
Brown, A D H. 1989b. Core collections: a practical approach to genetic resources management. Genome, 31, 818–824.
Butany, W T. 1957. Natural crossing in rice. Rice News Teller, 5, 18–21.
Caetano-Anolles, G. 1993. Amplifying DNA with arbitrary oligonucleotide primers. PCR Methods Applic, 3, 85–94.
Demeke, T, Adams, R P, and Chibbar, R. 1992. Potential taxonomic use of Random Amplified Polymorphic DNA (RAPD)- a case study in Brassica. Theor Appl Genet, 84, 990–994.
Edwards, K, Johnstone, C, and Thompson, C. 1991. A Simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucl Acids Res, 19, 1349.
Francisco-Ortega, J, Newbury, H J, and Ford-Lloyd, B V. 1993. Numerical analyses of RAPD data highlight the origin of cultivated tagasaste (Chamaecytisus proliferus ssp. palmensis) in the Canary Islands. Theor Appl Genet, 87, 264–270.
Frankel, O H. 1984. Genetic perspectives of plant germplasm conservation. In: Arber, W., Llimensee, K., Peacock, W. J. and Starlinger, P. (eds) Genetic Manipulation: Impact on Man and Society, pp. 161–170. Cambridge University Press, Cambridge.
Frankel, O H, and Brown, A D H. 1984. Current plant genetic resources- a critical appraisal. In: Genetics: New Frontiers, vol. IV, pp 1–11. Oxford and IBH Publishing Co., New Delhi.
Fukuoka, S, Hosaka, K, and Kamijima, O. 1992. Use of random amplified polymorphic DNAs (RAPDs) for identification of rice accessions. Jap J Genet, 67, 243–252.
Gawel, N J, and Jarret, R L. 1991. A modified CTAB DNA extraction procedure for Musa and Ipomoea. Pl Mol Biol Rep, 9, 262–266.
Glaszmann, J C. 1987. Isozymes and the classification of Asian rice varieties. Theor Appl Genet, 74, 21–30.
Glaszmann, J C. 1988. Geographic pattern of variation among Asian rice cultivars (Oryza sativa L.) based on 15 isozyme loci. Genome, 30, 782–792.
Helentjaris, T, King, G, Slocum, M, Siedenstrang, C, and Wegman, S. 1985. Restriction fragment polymorphisms as probes for plant diversity and their development as tools for applied plant breeding. Plant Mol Biol, 5, 109–118.
Hill, M O. 1979. TWINSPAN- a Fortran Program for Arranging Multivariate Data in an Ordered Two-way Table by Classification of the Individuals and Attributes. Cornell University, Ithaca, New York.
Howell, E C, Newbury, H J, Swennen, R L, Withers, L A, and Ford-Lloyd, B V. 1994. The use of RAPD for identifying and classifying Musa germplasm. Genome, 37, 328–332.
Kato, H, and Namai, H. 1987. Floral characteristics and environmental factors for increasing natural outcrossing rate for F1 hybrid seed production of rice (Oryza sativa L.). Jap J Breed, 37, 318–330.
Kazan, K, Manners, J M, and Cameron, D F. 1993. Genetic variation in agronomically important species of Stylosanthes determined using random amplified polymorphic DNA markers. Theor Appl Genet, 85, 882–888.
Macpherson, J M, Eckstein, P E, Scoles, G J, and Gajadhar, A A. 1993. Variability of the random amplified polymorphic DNA assay among thermal cyclers, and effects of primer and DNA concentration. Mol Cell Probes, 7, 289–293.
Munthali, M, Ford-Lloyd, B V, and Newbury, H J. 1992. The random amplification of polymorphic DNA for fingerprinting plants. PCR Methods and Applications, 1, 274–276.
Nei, M, and Li, W H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA, 74, 5267–5273.
Newbury, H J, and Ford-Lloyd, B V. 1993. The use of RAPD for assessing variation in plants. Plant Growth Reg, 12, 43–51.
Oka, H I. 1983. The indica-japonica differentiation of rice cultivars- a review. Proc 4th Int SABRAO Congress, pp. 117–128.
Sambrook, J, Fritsch, E F, and Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York.
SAS. 1990. SAS/STAT User's Guide. Version 6, 4th edn, vol. 1. SAS Institute, Cary, NC.
Tanksley, S D, Young, N D, Paterson, A H, and Bonierbale, M W. 1989. RFLP mapping in plant breeding: new tools for an old science. Bio/Technology, 7, 258–264.
Vaughan, D A, and Jackson, M T. 1994. The core as a guide to the whole collection. In: Hodkin, T. and Brown, A. D. H. (eds) Proceedings of the International Workshop on Core Collections IBPGR/CGN/CENARGEN Workshop, Brasilia, 23–28, August, 1992. John Wiley (in press).
Wang, Z Y, and Tanksley, S D. 1989. Restriction fragment length polymorphism in Oryza sativa L. Genome, 32, 1113–1118.
Wang, Z Y, Second, G, and Tanksley, S D. 1992. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet, 83, 565–581.
Williams, J G K, Kubelik, A R, Livak, K J, Rafalski, J A, and Tingey, S V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res, 18, 6531–6535.
Williams, J G K, Hanafey, M K, Rafalski, J A, and Tingey, S V. 1993. Genetic analysis using random amplified polymorphic DNA markers. Methods Enzymol, 218, 704–740.
Wilkie, S N, Isaac, P G, and Slater, R J. 1993. Random amplified polymorphic DNA (RAPD) markers for genetic analysis in Allium. Theor Appl Genet, 86, 497–504.
Yu, L-X, and Nguyen, H T. 1994. Genetic variation detected with RAPD markers among upland and lowland rice cultivars (Oryza sativa L.). Theor Appl Genet, 87, 668–672.
Zhang, Q, Saghai Maroof, M A, Lu, T Y, and Shen, B Z. 1992. Genetic diversity and differentiation of indica and japonica rice detected by RFLP analysis. Theor Appl Genet, 83, 495–459.
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Virk, P., Ford-Lloyd, B., Jackson, M. et al. Use of RAPD for the study of diversity within plant germplasm collections. Heredity 74, 170–179 (1995). https://doi.org/10.1038/hdy.1995.25
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