Abstract
Eighty-two varieties of rice from different regions in Thailand were selected to explore the Waxy (Wx)gene diversity and indica-japonica differentiation of chloroplast DNA. A comparison of the 5’ splice site in the first intron was made between glutinous and nonglutinous rice. It revealed that non-glutinous with low-amylose content and glutinous rice were characterized as the Wxb allele based on the G-to-T base substitution, whereas non-glutinous rice with intermediate and high amylose carried the Wxa allele. Four Wx microsatellite alleles, (CT) n repeat, (n = 16,17,18 and 19) were found in glutinous rice. In contrast, non-glutinous rice showed five Wx microsatellite alleles (n = 11, 16, 17, 18 and 19). The (CT)17 allele was prominent allele in Thai population, while the (CT)11 allele was found only in intermediate and high amylose rice varieties from southern Thailand. Almost all of upland rice grown by various ethnic groups in northern Thailand were characterized as japonica type based on their having the PstI-12 fragment in their cpDNA, whereas most of rainfed lowland varieties from other regions of Thailand were indica. This exploration of DNA-based genetic markers is important, as it enhances our ability to describe and manipulate sources of genetic variation for rice breeding programs.
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References
Ayres, N.M., A.M. McClung, P.D. Larkin, H.F.J. Bligh, C.A. Jones & W.D. Park, 1997. Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm. Theor Appl Genet 94: 773–781.
Bao, J.S., H. Corke & M. Sun, 2002. Microsatellites in starch-synthesizing genes in relation to starch physicochemical properties in waxy rice (Oryza sativa L.). Theor Appl Genet 105: 898–895.
Bergman, C.J., J.T. Delgado, A.M. McClung & R.G. Fjellstrom, 2001. An improved method for using a microsatellite in the rice waxy gene to determine amylose class. Cereal Chem 78: 257-260.
Bligh, H.F.J., P.D. Larkin, P.S. Roach, C.A. Jones, H. Fu & P.D. Park, 1998. Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Mol Biol 38: 407–415.
Cai, X., Z. Wang, Y. Xing, J. Zhang & M. Hong, 1998. Aberrant splicing of intron 1 leads to the heterogeneous 5’ UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J 14: 459–465.
Chen, W.B., Y.I. Sato, I. Nakamura & H. Nakai, 1994. Indica-Japonica differentiation in Chinese rice landraces. Euphytica 74: 195–201.
Cheng, C., R. Motohashi, S. Tsuchimoto, Y. Fukuta, H. Ohtsubo & E. Ohtsubo, 2003. Polyphyletic origin of cultivated rice based on the interspersion pattern of SINEs. Mol Biol Evol 20: 67–75.
Doyle, J.J. & J.L. Doyle, 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bull 19: 11–15.
Hirano, H.Y., M. Eiguchi & Y. Sano, 1998. A single base change altered the regulation of the Waxy gene at the post-transcriptional level during the domestication of rice. Mol Biol Evol 15: 978–987.
Isshiki, M., K. Morino, M. Nakajima, R.J. Okagaki, S.R. Wessler, T. Izawa & K. Shimamoto, 1998. A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5’ splice site of the first intron. Plant J 15: 133–138.
Isshiki, M., Y. Yamamoto, H. Satoh & K. Shimamoto, 2001. Nonsense-mediated decay of mutant waxy mRNA in rice. Plant Physiol 125: 1388–1395.
Juliano, B.O., 1971. A simple assay for milled rice amylose. Cereal Sci Today 16: 334–340.
Kanno, A., N. Watanabe, I. Nakamura & A. Hirai, 1993. Variations in chloroplast DNA from rice (Oryza sativa): Differences between deletions mediated by short direct-repeat sequences within a single species. Theor Appl Genet 86: 579–584.
Park, K.C., N.H. Kim, Y.S. Cho, K.H. Kang, J.K. Lee & N.S. Kim, 2003. Genetic variations of AA genome Oryza species measured by MITE-AFLP. Theor Appl Genet 107: 203–209.
Prathepha, P., 2003. Characterization of Waxy microsatellite classes that are closely liked to the rice Waxy gene and amylose content in Thai rice germplasm. Songklanakarin J Sci Technol 25: 1–8.
Sano, Y. & R. Sano, 1990. Variation of the intergenic spacer region of ribosomal DNA in cultivated and wild rice species. Genome 33: 209–218.
Sato, Y.I., S. Chitrakon & H. Morishima, 1986. The Indica-Japonica differentiation of native rice cultivars in Thailand and its neighboring countries. In: New Frontiers in Breeding Researches. Proceedings of the 5th International Congress SABRAO, Kasetsart University, Thailand, pp. 185–193.
Schliesinger, J., 2000a. Ethnic groups of Thailand: Non-Tai-Speaking Peoples. White Lotus, Bangkok, Thailand.
Schliesinger, J., 2000b. Tai groups of Thailand: Introduction and overview. White Lotus, Bangkok, Thailand.
Wanchana, S., T. Toojinda, S. Tragoonrung & A. Vanavichit, 2003. Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.). Plant Science 165: 1193–1199.
Wang, Z.Y., F.Q. Zheng, G.Z. Shen, J.P. Gao, D.P. Snustad, M.G. Li, J.L. Zhang & M.M. Hong, 1995. The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 7: 613–622.
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Prathepha, P., Baimai, V. Variation of Wx microsatellite allele, waxy allele distribution and differentiation of chloroplast DNA in a collection of Thai rice (Oryza sativa L.). Euphytica 140, 231–237 (2004). https://doi.org/10.1007/s10681-004-3783-x
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DOI: https://doi.org/10.1007/s10681-004-3783-x