Mosaic structure of Japanese rice genome composed mainly of two distinct genotypes

To learn the genome constitution and the origin of Japanese current rice (Oryza sativa) cultivars, we studied the number of distinct genotypes and the organization of genome segments with these genotypes in these cultivars. We studied the genotype divergence in 25 Japanese elite and local cultivars by analyzing their DNA sequence divergence at 23 loci and restriction fragment length polymorphisms (RFLP) at 44 loci. These analyses showed that most of the polymorphic loci among the cultivars comprised only two sequence types or alleles, suggesting that their genomes are constituted mostly by a limited number of (possibly as few as two) genotypes. Each of the distinct genome segments appeared to have originated from distinct progenitors of the Japanese current cultivars. The graphical representation of genotypes generated based on the polymorphism data revealed that the genomes of Japanese rice cultivars were mosaics constituted mainly from the two types of progenitor chromosome segments, and that the organization of these genotypes was specific to each cultivar. In contrast to the Japanese cultivars, Chinese and Korean local japonica rice cultivars exhibited greater divergence both in the number of constitutive genotypes and in the pattern of their organization. Our results indicate that Japanese rice cultivars are composed of one subgroup of japonica cultivars that have undergone "population bottlenecks" through the course of their introduction to Japan and during subsequent selection and dissemination.