Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Subsequently, the two types were classified by associations of a number of genetically independent traits.The characteristic associations of traits have been explained by a series of hybrid sterility or reproductive barriers, in which a duplicate recessive gene model was proposed to cause varietal differentiation. In 1990s, most of hybrid sterility genes were
proved to be caused by an interaction of allelic genes at each locus. In a well-known case of hybrid sterility, the indica, japonica,and wide-compatibility type which gives fertile hybrids in its cross to indica and japonica type, are proved to contain an allele, S5-i, S5-j and S5-n, respectively at a locus on Chromosome 6. Those gametes having S5-j allele is found to be partially aborted in the hybrid genotypes of S5-i/ S5-j while no gamete abortion occurred in S5-i/S5-n and S5-j/S5-n genotype. Since then, the S5-n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between indica and japonica types. For the last decade the action of S5-n is found to be due to a deletion in its gene sequence, while functional enzymes are produced by

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