Isolation and functional analysis of the gene controlling the stub‐spreading trait in rice (Oryza sativa L.)

The stub-spreading trait, also designated as ‘tiller angle’, is one of the components that determine the plant type. In rice, the trait is quite important because of its close relationship to the yield performance. The Spk(t) gene is a major determinant of the trait in the cross of ‘Kasalath’ (indica) and ‘Nipponbare’ (japonica). In this study, the Spk(t) gene was isolated by a map-based cloning strategy. Sequence analysis of the cDNA clones from the locus revealed that the Spk(t) transcripts and the spk(t) transcripts encode identical 259-aa proteins of unknown function; however, the structure of the 3′-untranslated region of each allele is quite different. Additional transgenic experiments in rice demonstrated that the difference is caused by a single-nucleotide polymorphism at the 3′-splicing site specific to the Spk(t) allele which thereby plays a critical role in the phenotypic expression. In addition to revealing the molecular mechanism underlying the allele differentiation at the Spk(t) locus, the information presented here should be useful for breeding of this trait in rice.