Abstract: In plant unclear genome, the intergenic spacer region (IGS) is located on the region of 18S–28S and is often used in phylogenetic analysis among species, detecting intra-specific polymorphisms. Rice (Oryza sativa L.) is differentiated into not only some subspecies but also many ecotypes of these subspecies. Can the IGS region be a useful tool to study the phylogenetic relationships among these cultivars of Oryza sativa? In the study, a comparative analysis of the rDNA intergenic spacer entire sequences of thirteen cultivars in Oryza sativa L. was carried out with O. rufipogon as outgroup. In the cultivars used, there were six for typical O. sativa ssp. japonica, five for typical O. sativa ssp. indica, two for O. sativa ssp. javanica. The result indicated that the length range of IGS sequences was from 2 130 to 2 145 bp, the content of G+C varied from 74.59% to 75.29%, there were 229 variational loci which were 10.70% of entire bases and 76 informative loci which were 3.51% of entire bases in Oryza sativa. Thirty-eight indica and japonica specific loci were found in the IGS sequences of Oryza sativa, most of them were covered a about 400 bp segment located in the upstream of IGS sequence. The indica and japonica subspecies of Oryza sativa, as well as some closely related cultivars, can be discriminated clearly based on the phylogenetic tree constructed by IGS sequences. The study supported the opinion that the O.sativa ssp.javanica is a subspecies of Oryza sativa.

Key words: Rice (Oryza sativa L.), Ribosomal DNA (rDNA), Intergenic spacer (IGS), Phylogenetic tree