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The influence of the semidwarfing gene  sd1  derived from the rice cultivar Jukkoku (Jukkoku _sd1 ) and IR8 (IR8 _sd1 ), which contributed to the Green Revolution,  d60  from Hokuriku 100, as well as the combination of  sd1  and  d60  (Jukkoku _sd1  plus  d60  and IR8 _sd1  plus  d60 ), was investigated using isogenic lines raised by backcrossing with the cultivar Koshihikari. The isogenic lines carrying Jukkoku _sd1 , IR8 _sd1 ,  d60 , Jukkoku _sd1  plus  d60 , and IR8 _sd1  plus  d60  had considerably shorter culm lengths than Koshihikari by 19.2%, 22.8%, 26.0%, 45.1%, and 43.4%, respectively. The  sd1  plus  d60  lines showed additively reduced culms, indicating that the function of  d60  was different from  sd1 . In contrast to the culm reduction, Jukkoku _sd1  showed productive merit with a panicle length of 2.5% greater than the origin. MiSeq next-generation sequencer was used to optimize a minimum scale to detect Jukkoku _sd1  in practical breeding. Mapping with the reference genome of Nipponbare gained the average depths of Koshihikari Jukkoku_ sd1  and Koshihikari being 9.17 and 7.29, respectively. Comparing the vcf files of the entire genomes of Koshihikari Jukkoku_ sd1  and the virtual Koshihikari revealed a G to T SNP at position 38,382,746 in the  sd1  locus on chromosome 1 of Koshihikari, causing a loss-of-function mutation of GA20-oxidase.

biomed research international

Genetic Performance of the Semidwarfing Allele<i> sd1</i> Derived from a Japonica Rice Cultivar and Minimum Requirements to Detect Its Single-Nucleotide Polymorphism by MiSeq Whole-Genome Sequencing

Genetic Performance of the Semidwarfing Allele sd1 Derived from a Japonica Rice Cultivar and Minimum Requirements to Detect Its Single-Nucleotide Polymorphism by MiSeq Whole-Genome Sequencing