Genetic analysis of semidwarfism of the japonica rice cultivar Kinuhikari

Abstract

The origin of the semidwarfing gene(s) in the japonica rice cultivar Kinuhikari and its location on chromosome was studied. A quantitative trait locus (QTL) analysis using restriction fragment length polymorphism (RFLP) markers was conducted in the F2 from the cross Kinuhikari/Koshihikari and B1F1 from the cross Koshihikari/Kinuhikari//Koshihikari. Seven RFLP loci showed a polymorphism between Kinuhikari and Koshihikari. A strong QTL reducing culm length when the genotype was of the Kinuhikari-type (homozygous) was detected close to the RFLP loci C86 and C385 on chromosome 1. This QTL explained 74% of the total variation of culm length in the F2 population. The analysis of polymorphism for the C86 and C385 loci among Kinuhikari and all the cultivars used to breed it showed that the region containing the semidwarfing QTL on chromosome 1 in Kinuhikari was derived from the indica rice cultivar IRS, which is known to harbour a semidwarfing gene sd1 between these two RFLP loci. These results indicate that the semidwarfing gene in this chromosome region in Kinuhikari is sd1. An allelism test using QTL analysis showed that the sd1 in Kinuhikari was different from a semidwarfing gene d49 in Reimei, which had been assumed to be identical with sd1. Another QTL was found near the RFLP locus G1073 on chromosome 8. This QTL led to a longer culm when the allelic constitution corresponded to the Kinuhikari-type, and explained about 18% of the total variation of culm length. In the F2 population from the crosses Kinuhikari/Koshihikari and Kinuhikari/Reimei, the homozygous plants for the sd1 locus showed a transgressive segregation for short culm. The combined effect of the two QTLs could not completely explain the distinct transgressive segregation. It was suggested that other genes modify the effect of sd1 (a recessive allele at the QTL on chromosome 1) in Kinuhikari.