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A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication
Author(s) -
Win Khin Thanda,
Yamagata Yoshiyuki,
Doi Kazuyuki,
Uyama Kazuhiro,
Nagai Yasuko,
Toda Yosuke,
Kani Takahiro,
Ashikari Motoyuki,
Yasui Hideshi,
Yoshimura Atsushi
Publication year - 2017
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.14290
Subject(s) - domestication , biology , oryza rufipogon , oryza sativa , genetics , oryza , gene , gene pool , single nucleotide polymorphism , allele , plant genetics , botany , genome , genetic diversity , genotype , population , demography , sociology
Summary 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 SH 3 / SH 4 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 SH 3/ SH 4 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 SH 3 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.