title: A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication.
abstract: Reduced seed shattering was a critical evolutionary step in crop domestication. Two cultivated rice species, Oryza sativa and Oryza glaberrima, were independently domesticated from the wild species Oryza rufipogon in Asia and Oryza barthii in Africa, respectively. A single nucleotide polymorphism (SNP) in the c gene, which encodes a trihelix transcription factor, causes nonshattering in O. sativa. However, the genetic mechanism of nonshattering in O. glaberrima is poorly understood. We conducted an association analysis for the coding sequences of SH3/SH4 in AA- genome rice species and the mutation suggested to cause nonshattering was demonstrated to do so using a positional-cloning approach in the O. sativa genetic background. We found that the loss of seed shattering in O. glaberrima was caused by an SNP resulting in a truncated SH3/SH4 protein. This mutation appears to be endemic and to have spread in the African gene pool by hybridization with some O. barthii accessions. We showed that interaction between the O. sativa and O. glaberrima domestication alleles of SH3 in heterozygotes induces a 'throwback' seed-shattering phenotype similar to that in the wild species. Identification of the causative SNP provides new insights into the molecular basis of seed shattering in crops and may facilitate investigation of the history of African rice domestication.
authors.affiliation: Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
authors.forename: Khin Thanda
authors.initials: KT
authors.lastname: Win
authors.affiliation: Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Yamagata
authors.affiliation: Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.|Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan.
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Doi
authors.affiliation: Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Uyama
authors.affiliation: Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
authors.forename: Yasuko
authors.initials: Y
authors.lastname: Nagai
authors.affiliation: Laboratory of Biological Systems, Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Toda
authors.affiliation: Biosciences and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Kani
authors.affiliation: Biosciences and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan.
authors.forename: Motoyuki
authors.initials: M
authors.lastname: Ashikari
authors.affiliation: Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
authors.forename: Hideshi
authors.initials: H
authors.lastname: Yasui
authors.affiliation: Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yoshimura
mesh_terms: D000349:Africa; D000483:Alleles; D001483:Base Sequence; D000071278:Domestication; D017343:Genes, Plant; D008040:Genetic Linkage; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D010940:Plant Proteins
keywords: 
  Oryza glaberrima
  ; artificial selection; causative mutation; convergent domestication; intragenic complementation; rice; seed shattering