Heading Time Genes Responsible for the Regional Adaptability of 'Tongil-type Short-culmed Rice Cultivars' Developed in Korea

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In the Republic of Korea (South Korea), many high-yielding rice cultivars, called 'Tongil-type short-culmed (TG) cultivars', were developed by indica-japonica hybridizations in the 1970s-1990s. The TG cultivars all show a long basic vegetative growth (BVG) period and low photoperiod sensitivity (PS). Such a combination of BVG period and PS, similar to those of modern indica cultivars for the low latitudes, was absent either among Korean or among Japanese japonica cultivars. Subsequent genetic analysis revealed that the long BVG period of the TG cultivars was due to the allelic constitution between the early heading time gene lh(t) and a non-functional allele at the Se1 locus. The low PS of the TG cultivars was conferred by this allele. Sequence analysis showed that the non-functional allele harbored a 4-bp deletion in exon 2, compared with the functional allele Se1-n of the rice cultivar 'Nipponbare', and differed in sequence from the known non-functional allele Se1-e. We designated this novel allele as Se1-k. Also lh(t) was found to be a novel gene located on chromosome 8. We designated this gene as lh4 at the Lh4 locus (Late heading-4). Since both Se1-k and lh4 were not detected in japonica cultivars, it was considered that these two alleles were derived from an indica cultivar(s) used as cross parent(s).