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A stepwise route to domesticate rice by controlling seed shattering and panicle shape

Ishikawa, Ryo; Castillo, Cristina Cobo; Htun, Than Myint; Numaguchi, Koji; Inoue, Kazuya; Oka, Yumi; Ogasawara, Miki; ... Ishii, Takashige; + view all (2022) A stepwise route to domesticate rice by controlling seed shattering and panicle shape. Proceedings of the National Academy of Sciences , 119 (26) , Article e2121692119. 10.1073/pnas.2121692119. Green open access

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Abstract

Asian rice (Oryza sativa L.) is consumed by more than half of the world's population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (Oryza rufipogon Griff.) acquired non-seed-shattering behavior, allowing humans to increase grain yield. Previous studies argued that a reduction in seed shattering triggered by the sh4 mutation led to increased yield during rice domestication, but our experiments using wild introgression lines show that the domesticated sh4 allele alone is insufficient for shattering loss in O. rufipogon. The interruption of abscission layer formation requires both sh4 and qSH3 mutations, demonstrating that the selection of shattering loss in wild rice was not as simple as previously suggested. Here we identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we further demonstrated that seed shattering alone did not significantly impact yield; rather, yield increases were observed with closed panicle formation controlled by SPR3 and further augmented by nonshattering, conferred by integration of sh4 and qSH3 alleles. Complementary manipulation of panicle shape and seed shattering results in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which together led to the loss of shattering.

Type: Article
Title: A stepwise route to domesticate rice by controlling seed shattering and panicle shape
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1073/pnas.2121692119
Publisher version: https://doi.org/10.1073/pnas.2121692119
Language: English
Additional information: Copyright © 2022 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
Keywords: Oryza rufipogon, Oryza sativa, closed panicle, domestication, seed shattering, Alleles, Domestication, Humans, Oryza, Phenotype, Polymorphism, Single Nucleotide, Seeds
UCL classification: UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Institute of Archaeology > Institute of Archaeology Gordon Square
UCL > Provost and Vice Provost Offices > UCL SLASH
UCL
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Institute of Archaeology
URI: https://discovery.ucl.ac.uk/id/eprint/10151002
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