A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice

Abstract

The rice waxy (wx) locus has two functional alleles, Wxa and Wxb, which are defined by a large difference in the amount of the gene product, called Wx protein, that accumulates in mature seeds. To elucidate the molecular mechanism underlying this difference and to identify the base change causing the alteration of the regulation of the Wx gene during rice evolution, we determined the nucleotide sequences of the regulatory region of Wx alleles and analyzed their function in a transient assay system using rice protoplasts. All Wxa alleles from Oryza sativa Indica, O. rufipogon, and O. glaberrima have a normal sequence of GT at the 5' splice junction of the first intron, representing a high expression level of the Wx transcripts in the endosperm and a high beta-glucuronidase (GUS) activity in protoplasts. On the other hand, Wxb alleles from two strains of O. sativa Japonica have TT at the 5' splice junction, representing a low expression level of the mature transcripts and a low GUS activity. Northern blot analysis also indicated that a larger transcript, consisting of the unspliced first intron, is closely correlated with the function of the Wxb allele. These results suggest that a single base change at the 5' splice junction causes inefficient splicing and, as a result, reduces the level of mature transcript and the GUS activity in the Wxb allele. The Wxb allele in O. saativa Japonica may have been differentiated from the Wxa allele of O. rufipogon, its wild progenitor, by this mutation, and, therefore, a single base change that has altered the regulation of the Wx gene at the posttranscriptional level probably occurred during the domestication of rice.

Molecular Diversity, Structure and Domestication of Grasses

“…Divergence between O. sati a ssp. japonica and indica at the waxy locus promoter is 0n83 % (Hirano et al, 1998). Isozyme data suggests that domesticated rice has roughly 71 % of the diversity of its wild relatives (Oka, 1988).…”

Molecular Characterization of Wx-mq, a Novel Mutant Gene for Low-amylose Content in Endosperm of Rice (Oryza sativa L.).

“…Judging from the amylose content of the isogenic lines, Kikuchi (1988) suggested that Koshihikari, the most popular japonica rice variety in Japan, also harbours the Wx-b gene. Recently, sequence analysis of the wx locus has revealed that the low level of expression of the Wx-b gene results from a single nucleotide substitution at the 5′ splice site of the first intron (Cai et al 1998, Hirano et al 1998, Isshiki et al 1998, Wang et al 1995.…”

Phylogenetic Origin of Waxy Rice Cultivars in Laos Based on Recent Observations for "Glutinous Rice Zone" and dCAPS Marker of Waxy Gene

“…We saw panicle-cutting using hand-knife, and also saw a farmer to harvest directly only the seeds. According to Fukuta et al (1996) (Hirano et al, 1998; Issiki er at., 1998, G-T polymorphism). To apply the G-T polymorphism for waxy rice cultivars, we can estimate whether each waxy shain was derived from indica or japonica (Yamanaka et a1.,2002).…”