Regulator of Awn Elongation 3 , an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication

Author:

Bessho-Uehara Kanako1ORCID,Masuda Kengo2,Wang Diane R.3ORCID,Angeles-Shim Rosalyn B.4ORCID,Obara Keisuke5ORCID,Nagai Keisuke1ORCID,Murase Riri2,Aoki Shin-ichiro2,Furuta Tomoyuki1,Miura Kotaro6,Wu Jianzhong7ORCID,Yamagata Yoshiyuki8ORCID,Yasui Hideshi8,Kantar Michael B.9ORCID,Yoshimura Atsushi8,Kamura Takumi5ORCID,McCouch Susan R.3ORCID,Ashikari Motoyuki1

Affiliation:

1. Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan

2. Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan

3. Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853

4. Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409

5. Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan

6. Faculty of Biotechnology, Fukui Prefectural University, Eiheiji-Town, Fukui 910-1195, Japan

7. Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8634, Japan

8. Faculty of Agriculture, Kyushu University, Nishiku, Fukuoka 819-0395, Japan

9. Department of Tropical Plant and Soil Sciences, University of Hawaiʻi, Mānoa Honolulu, HI 96822

Abstract

Two species of rice have been independently domesticated from different ancestral wild species in Asia and Africa. Comparison of mutations that underlie phenotypic and physiological alterations associated with domestication traits in these species gives insights into the domestication history of rice in both regions. Asian cultivated rice, Oryza sativa, and African cultivated rice, Oryza glaberrima , have been modified and improved for common traits beneficial for humans, including erect plant architecture, nonshattering seeds, nonpigmented pericarp, and lack of awns. Independent mutations in orthologous genes associated with these traits have been documented in the two cultivated species. Contrary to this prevailing model, selection for awnlessness targeted different genes in O. sativa and O. glaberrima . We identify Regulator of Awn Elongation 3 ( RAE3 ) a gene that encodes an E3 ubiquitin ligase and is responsible for the awnless phenotype only in O. glaberrima . A 48-bp deletion may disrupt the substrate recognition domain in RAE3 and diminish awn elongation. Sequencing analysis demonstrated low nucleotide diversity in a ~600-kb region around the derived rae3 allele on chromosome 6 in O. glaberrima compared with its wild progenitor. Identification of RAE3 sheds light on the molecular mechanism underlying awn development and provides an example of how selection on different genes can confer the same domestication phenotype in Asian and African rice.

Funder

MEXT | Japan Society for the Promotion of Science

MEXT | JST | Science and Technology Research Partnership for Sustainable Development

National Science Foundation

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

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