Origin and evolution of twin microsatellites in the genus Oryza

Abstract

An ancestral sequence of twin microsatellites of rice was found in a wild species. Twin microsatellite loci, RM20A and RM20B, were located on separate regions of chromosomes 11 and 12, which had been duplicated during rice evolution. These twin microsatellites showed different allele diversities in A genome species of the genus Oryza. This difference was caused by repetition of a simple sequence consisting of (TAA)n. Oryza longistaminata contains a short poly(A) sequence in this region instead of the poly(TAA) found in other species. A sequence comparison of RM20-related amplicons suggested that the poly(A)-containing sequence is the ancestral sequence of the RM20A and RM20B microsatellites. A simple base substitution in the poly(A) sequence may have produced the longer microsatellite motif (TAA). This mutation may have occurred on one of the chromosomes of a hypothetical ancestor of the A genome species before duplication of the chromosome segments.