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Genetic control of seed shattering during African rice domestication

Abstract

Domestication represents a unique opportunity to study the evolutionary process. The elimination of seed dispersal traits was a key step in the evolution of cereal crops under domestication. Here, we show that ObSH3, a YABBY transcription factor, is required for the development of the seed abscission layer. Moreover, selecting a genomic segment deletion containing SH3 resulted in the loss of seed dispersal in populations of African cultivated rice (Oryza glaberrima Steud.). Functional characterization of SH3 and SH4 (another gene controlling seed shattering on chromosome 4) revealed that multiple genes can lead to a spectrum of non-shattering phenotypes, affecting other traits such as ease of threshing that may be important to tune across different agroecologies and postharvest practices. The molecular evolution analyses of SH3 and SH4 in a panel of 93 landraces provided unprecedented geographical detail of the domestication history of African rice, tracing multiple dispersals from a core heartland and introgression from local wild rice. The cloning of ObSH3 not only provides new insights into a critical crop domestication process but also adds to the body of knowledge on the molecular mechanism of seed dispersal.

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Fig. 1: Comparison of seed shattering and floral abscission zone morphologies between W1411 (O. barthii) and IRGC104165 (O. glaberrima).
Fig. 2: Map-based clone of ObSH3.
Fig. 3: Expression and subcellular localization of ObSH3.
Fig. 4: Additive effect of SH3 and SH4.
Fig. 5: Evolution of the non-shattering trait in African rice.

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Acknowledgements

We thank the International Rice Research Institute for providing the wild rice and cultivated rice samples. This research was supported by the Ministry of Agriculture of China (2016ZX08009-003) and the National Key R&D Program for Crop Breeding (2016YFD0100901). The funders had no role in the study design, data collection and analyses, decision to publish, or preparation of the manuscript.

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Authors

Contributions

Z.Z. designed and supervised this study. S.L. conducted the map-based cloning, genetic transformation and gene expression analyses. S.L., W.W. and H.Z. conducted the histological analyses of the seed abscission layers. M.W. performed the evolutionary analysis and R.S.M assisted in analysing the results. M.-N.N., L.T., H.C., Y.F., J.Z. and C.S. conducted the collection of rice germplasm and phenotypic data. Z.Z., R.S.M. M.W. and R.A.W. wrote the manuscript.

Corresponding author

Correspondence to Zuofeng Zhu.

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Supplementary information

Supplementary Information

Supplementary Figures 1–12

Reporting Summary

Supplementary Table 1

Geographical distribution of position in O. glaberrima and O. barthii

Supplementary Table 2

Primers used in this study

Supplementary Table 3

The ancestry of each population

Supplementary Table 4

PCA analysis of O. glaberrima and O. barthii individuals

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Lv, S., Wu, W., Wang, M. et al. Genetic control of seed shattering during African rice domestication. Nature Plants 4, 331–337 (2018). https://doi.org/10.1038/s41477-018-0164-3

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