Abstract
Microsatellites consisting of AT repeats are highly polymorphic in rice genomes and can be used to distinguish between even closely related japonica cultivars in Japan. Polymorphisms of 20 microsatellite loci were determined using 59 japonica cultivars, including both domestic and modern Japanese cultivars. Although the polymorphisms of these 20 microsatellite loci indicated that the Japanese cultivars were genetically quite similar, microsatellites consisting of AT repeats showed high gene diversity even among such closely related cultivars. Combinations of these hypervariable microsatellites can be employed to classify individual cultivars, since the microsatellites were stable within each cultivar. An identification system based on these highly polymorphic microsatellites could be used to maintain the purity of rice seeds by eliminating contamination. A parentage diagnosis using 17 polymorphic microsatellite loci clearly demonstrated that plants which carried desired chromosome regions had been selected in breeding programs. Thus, these hypervariable microsatellites consisting of AT repeats should promote the selection of plants which carry desired chromosomes from genetically similar parents. Backcrossing could also help to eliminate unnecessary chromosome regions with microsatellite polymorphisms at an early stage in breeding programs.
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References
Akagi H, Nakamura A, Sawada R, Oka M, Fujimura T (1995) Genetic diagnosis of cytoplasmic male-sterile cybrid plants of rice. Theor Appl Genet 90:948–951
Akagi H, Yokozeki Y, Inagaki A, Fujimura T (1996) Microsatellite DNA markers for rice chromosomes. Theor Appl Genet (in press)
Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131–1139
Becker J, Heum M (1995) Barley microsatellites: allele variation and mapping. Plant Mol Biol 27:835–845
Dib C, Fauré S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Sebourn E, Lathrop M, Gyapay G, Morissette J, Weissenbach (1996) A comprehensive genetic map of the human genome based on 5264 microsatellites. Nature 380:152–154
Edwards K, Johnstone C, Thompson C (1991) A simple and rapid method for the preparation of plant genome DNA for PCR analysis. Nucleic Acids Res 19:1349
Glaszmann JC, Arraudeau M (1986) Rice plant type variation: “Japonica”-“Javanica” relationships. Rice Genet Newslett 3:41–43
Lagercrantz U, Ellegren H, Anderson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115
Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401
McCouch, SR, Tanksley SD (1991) Development and use of restriction fragment length polymorphism in rice breeding and genetics. In: Khush GS, Toenniessen GN (eds) Rice biotechnology. CAB International, Wallingford, pp 109–133
McCouch S, Chen X, Panaud O, Xu Y, Cho YG, Harrington S, Yanagihara S, Xiao J, Moekpojawiro S, Ahn N, Koh HJ, Olufowote J (1995) New dimensions of map development and application to rice improvement. 3rd Int Rice Genet Symp pp. 19
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323
Oka HI (1991) Genetic diversity of wild and cultivated rice. In: Khush GS, Toenniessen GN (eds) Rice biotechnology. CAB International, Wallingford, pp 55–81
Plaschke J, Ganal MW, Röder MS (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet 91:1001–1007
Röder MS, Plaschke J, König SU, Börner A. Sorrells ME, Tanksley SD, Ganal MW (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246: 327–333
Senior ML, Heum M (1993) Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. Genome 36:884–889
Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471
Wang ZY, Tanksley SD (1989) Restriction fragment length polymorphism in Oryza sativa L. Genome 32:1113–1118
Wang ZY, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6
Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396
Wu K-S, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235
Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RM (1994) Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245:187–194
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Akagi, H., Yokozeki, Y., Inagaki, A. et al. Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theoret. Appl. Genetics 94, 61–67 (1997). https://doi.org/10.1007/s001220050382
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DOI: https://doi.org/10.1007/s001220050382