DNA analysis for tracing the origin and evolution of cultivated rice in Thailand: (1) Distribution and molecular characterization of a retrotransposon at the waxy locus in populations of cultivated and wild rice
2002
Prathepha, P.(Mahasarakham University, Maha Sarakham (Thailand). Faculuty of Technology. Department of Biotechnology)
Rice waxy gene encodes a granule-bound starch synthase (GBSS) for synthesis of amylase in endosperm tissue. Amylose content is a key determinant of the cooking and processing quality of rice (Oryza sativa). Nucleotide length of the waxy gene is about 5.6 kilobase (kb), consisting of 14 exons and 14 introns. The level of GBSS gene expression is directly correlated with the amylase content of endosperm tissues. In 1991, Umeda et al. (1991) first reported that a short interspersed element (SINE), named p-SINE-r2, was present in intron 10 of the waxy gene of O. sativa, Theoretically, insertion into 5 flanking sequences can place element promoters, which are usually terminally located, near the TATA box of adjacent genes. However, there is no evidence to date that any of these elements are still capable of being cut and pasted into the rice genome. Currently, rice scientists have suggested that p-SINE1 members in the rice genome are inactive p-SINE1, which is not transcribed by RNA polymerase III. Thus, some of the p-SINE1 members would be useful for classifying rice strains and/or studying evolution of rice species with the AA genome. (SINEs) are retrotransposons. They have been considered as effective tools for investigating the evolution of eukaryotes. The p-SINE1-r2 at the waxy locus is a valuable DNA marker for evolutionary studies due to its polymorphic nature. It is therefore a key character for elucidating phyletic relationships within the genus Oryza. In Asia, Thailand has been recognized as a center of rice diversity. Geographical distribution and variation of this element in both cultivated and wild rice samples should be investigated. Such data would provide supporting evidence for the evolution of cultivated rice in Thailand.
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