Molecular constitution of weedy rice (Oryza sativa L.) found in Okayama prefecture, Japan

Weedy rice (Oryza saliva L.) plants found in Okayama, Japan, exhibit various morphophysiological characteristics, and are roughly classified into japonica-type and indica-type. We characterized the weedy strains collected from nine sites with molecular markers in flanking regions of two diagnostic isozyme loci, Acp1 and Sdh1. Haplotype analysis for closely-linked SSR markers flanking Acp1 revealed that 1) japonica-type weedy strains shared the same haplotypes with local varieties, and 2) indica-type weedy strains carrying an indica-specific isozyme allele possessed two haplotypes. One of the two haplotypes was common to a forage variety, 'Moretsu'. PCR analysis revealed that the dwarf weedy strains carried the deletion inside OsGA20ox2 as the semi-dwarf allele (sd1). The deletion was also found in 'Moretsu'. The other haplotype was shared with indica forage variety, 'Tetep', which showed the same sequence haplotype for Sdh1 with the indica-type weedy strains. The results obtained from this study suggested that the weedy strains in Okayama have multiple origins and semi-dwarfness possibly derived from 'Moretsu' or indica modern varieties.