A novel quantitative trait locus, qCL1, involved in semi-dwarfism derived from Japanese rice cultivar Nipponbare

To identify quantitative trait loci (QTLs) associated with culm length in Japanese japonica rice varieties, we conducted QTL analyses using a set of reciprocal backcrossed inbred lines (BILs) from crosses between Nipponbare and Koshihikari. We detected five QTLs in the two BILs that are involved in the culm-length difference between Nipponbare and Koshihikari. A QTL located on the short arm of chromosome 1, qCL1, was commonly detected near the simple sequence repeat (SSR) marker RM8068 in both BILs in three growing seasons. The Nipponbare allele of qCL1 shortened from 1.9 to 3.0 cm of culm length. Substitution lines (SLs) of Koshihikari in which the QTL was replaced with the Nipponbare allele exhibited decreased lengths of lower internodes. qCL1 was mapped within about 2.6 Mbp in the region distal from SSR marker RM10132, suggesting qCL1 differed from the dwarf or semi-dwarf genes that have been previously reported. Japanese japonica rice landraces with Nipponbare alleles of DNA markers around qCL1 had significantly shorter culm length than other landraces. The results suggest that the novel allele for short culm length was originally distributed in Japanese rice landraces and has been used for introducing the semi-dwarf phenotype and improving plant architecture during practical breeding.

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