title: Artificial selection for a green revolution gene during japonica rice domestication.
abstract: The semidwarf phenotype has been extensively selected during modern crop breeding as an agronomically important trait. Introduction of the semidwarf gene, semi-dwarf1 (sd1), which encodes a gibberellin biosynthesis enzyme, made significant contributions to the "green revolution" in rice (Oryza sativa L.). Here we report that SD1 was involved not only in modern breeding including the green revolution, but also in early steps of rice domestication. We identified two SNPs in O. sativa subspecies (ssp.) japonica SD1 as functional nucleotide polymorphisms (FNPs) responsible for shorter culm length and low gibberellin biosynthetic activity. Genetic diversity analysis among O. sativa ssp. japonica and indica, along with their wild ancestor O. rufipogon Griff, revealed that these FNPs clearly differentiate the japonica landrace and O. rufipogon. We also found a dramatic reduction in nucleotide diversity around SD1 only in the japonica landrace, not in the indica landrace or O. rufipogon. These findings indicate that SD1 has been subjected to artificial selection in rice evolution and that the FNPs participated in japonica domestication, suggesting that ancient humans already used the green revolution gene.
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Asano
authors.forename: Masanori
authors.initials: M
authors.lastname: Yamasaki
authors.forename: Shohei
authors.initials: S
authors.lastname: Takuno
authors.forename: Kotaro
authors.initials: K
authors.lastname: Miura
authors.forename: Satoshi
authors.initials: S
authors.lastname: Katagiri
authors.forename: Tomoko
authors.initials: T
authors.lastname: Ito
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Doi
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Wu
authors.forename: Kaworu
authors.initials: K
authors.lastname: Ebana
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Hideki
authors.initials: H
authors.lastname: Innan
authors.forename: Hidemi
authors.initials: H
authors.lastname: Kitano
authors.forename: Motoyuki
authors.initials: M
authors.lastname: Ashikari
authors.forename: Makoto
authors.initials: M
authors.lastname: Matsuoka
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D001947:Breeding; D018556:Crops, Agricultural / Q000145:classification / Q000235:genetics; D017343:Genes, Plant; D049810:Genetic Speciation; D014644:Genetic Variation; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D017386:Sequence Homology, Amino Acid
chemical_list: D010940:Plant Proteins