title: Differentiation in wild-type allele of the sd1 locus concerning culm length between indica and japonica subspecies of Oryza sativa (rice).
abstract: A dwarfing gene (allele) sd1-d has been intensively utilized to develop short-culm indica varieties in southeast Asia up to now. Before the first sd1-d-carrying variety IR8 was released, rice researchers had recognized the general tendency that culm length is higher in indica varieties than in temperate-japonica ones. Inter-subspecific difference of the tall (wild-type) allele SD1 at the sd1 locus was examined on the common genetic background, using five isogenic lines developed by substituting sd1-d of the recurrent parent IR36 by SD1s of two indica varieties, two temperate-japonica varieties and one tropical-japonica variety. The two indica -donor isogenic lines had longer culms than the three japonica-donor isogenic lines consistently in two different environmental conditions. Moreover, nonsynonymous single-nucleotide polymorphism between the two subspecies was detected at two sites in Exon 1 and Exon 3 of the sd1 locus. It is demonstrated that the inter-subspecific differentiation of SD1 contributes height difference between indica and japonica. The indica-originating and japonica-originating alleles at the sd1 locus were designated as SD1-in(t) and SD1-ja(t), respectively.
authors.affiliation: Faculty of Agriculture, Kochi University, Nankoku, Kochi, Japan. muraim@kochi-u.ac.jp
authors.forename: Masayuki
authors.initials: M
authors.lastname: Murai
authors.forename: Hironori
authors.initials: H
authors.lastname: Nagano
authors.forename: Kazumitsu
authors.initials: K
authors.lastname: Onishi
authors.forename: Atsushi
authors.initials: A
authors.lastname: Ogino
authors.forename: Naofumi
authors.initials: N
authors.lastname: Ichikawa
authors.forename: Hari Bahadur
authors.initials: HB
authors.lastname: Kc
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Sano
mesh_terms: D000483:Alleles; D019943:Amino Acid Substitution / Q000235:genetics; D023061:Gene Order; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D005838:Genotype; D012275:Oryza / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D010088:Oxidoreductases / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity
chemical_list: D010088:Oxidoreductases