A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication

Khin Thanda Win, Yoshiyuki Yamagata, Kazuyuki Doi, Kazuhiro Uyama, Yasuko Nagai, Yosuke Toda, Takahiro Kani, Motoyuki Ashikari, Hideshi Yasui, Atsushi Yoshimura

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1925-1935
Number of pages11
JournalNew Phytologist
Volume213
Issue number4
DOIs
Publication statusPublished - Mar 1 2017

Fingerprint

seed shattering
Oryza glaberrima
domestication
single nucleotide polymorphism
Seeds
Genes
Oryza barthii
genes
Single Nucleotide Polymorphism
Oryza rufipogon
mutation
rice
crops
genetic background
molecular cloning
heterozygosity
Oryza sativa
hybridization
transcription factors
Gene Pool

All Science Journal Classification (ASJC) codes

  • Physiology
  • Plant Science

Cite this

Win, K. T., Yamagata, Y., Doi, K., Uyama, K., Nagai, Y., Toda, Y., ... Yoshimura, A. (2017). A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication. New Phytologist, 213(4), 1925-1935. https://doi.org/10.1111/nph.14290

A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication. / Win, Khin Thanda; Yamagata, Yoshiyuki; Doi, Kazuyuki; Uyama, Kazuhiro; Nagai, Yasuko; Toda, Yosuke; Kani, Takahiro; Ashikari, Motoyuki; Yasui, Hideshi; Yoshimura, Atsushi.

In: New Phytologist, Vol. 213, No. 4, 01.03.2017, p. 1925-1935.

Research output: Contribution to journalArticle

Win, KT, Yamagata, Y, Doi, K, Uyama, K, Nagai, Y, Toda, Y, Kani, T, Ashikari, M, Yasui, H & Yoshimura, A 2017, 'A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication', New Phytologist, vol. 213, no. 4, pp. 1925-1935. https://doi.org/10.1111/nph.14290
Win, Khin Thanda ; Yamagata, Yoshiyuki ; Doi, Kazuyuki ; Uyama, Kazuhiro ; Nagai, Yasuko ; Toda, Yosuke ; Kani, Takahiro ; Ashikari, Motoyuki ; Yasui, Hideshi ; Yoshimura, Atsushi. / A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication. In: New Phytologist. 2017 ; Vol. 213, No. 4. pp. 1925-1935.
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