Polymorphic proteins in rice seed embryo revealed by two-dimensional gel electrophoresis and their application for subspecies identification

Two-dimensional polyacrylamide gel electrophoresis revealed 10 polymorphic proteins in seed embryos of 29 cultivated rices (Oryza sativa L.) including 16 japonica cultivars, three so-called ‘Javanica’ ones and 10 indica ones. We attempted to use these polymorphic proteins to identify rice subspecies by scoring the polymorphisms. Since all japonica cultivars examined showed the same pattern of protein spots, we considered it to be a standard one with a score of zero, and the protein polymorphisms of other cultivars were given scores of 0.0, 0.5 or 1.0 according to spot density. This scoring method gave characteristic scores for indica and ‘Javanica’ cultivars, i.e. typical japonica cultivars selected as standards presumed the score of 0.0 whereas ‘Javanica’ cultivars and indica ones had the scores of 2.5–4.0 and of 5.0–8.0, respectively. By using this scoring method and the subspecies-specific proteins previously reported, 19 cultivars of unknown subspecies were classified as three indica cultivars and 16 japonica ones including four so-called ‘Javanica’ ones. This scoring method also detected a difference between the perennial wild rice Oryza rufipogon and the annual one O. nivara at the protein level.