Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication

Authors

  • Yu Wang,

    1. Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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  • Xuefei Bai,

    1. Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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  • Chenghai Yan,

    1. Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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  • Yiejie Gui,

    1. Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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  • Xinghua Wei,

    1. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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  • Qian-Hao Zhu,

    1. CSIRO Plant Industry, Canberra, ACT, Australia
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  • Longbiao Guo,

    Corresponding author
    1. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
    • Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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  • Longjiang Fan

    Corresponding author
    • Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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Authors for correspondence:

Longjiang Fan

Tel: +86 571 88982730

Email: fanlj@zju.edu.cn

Longbiao Guo

Tel: +86 571 63370537

Email: longbiaoguo@yahoo.com.cn

Summary

  • The lack of a MIRNA set and genome sequence of wild rice (Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication.
  • In this study, a genome, three small RNA populations and a degradome of O. rufipogon were sequenced by Illumina platform and the expression levels of microRNAs (miRNAs) were investigated by miRNA chips.
  • A de novo O. rufipogon genome was assembled using c. 55× coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family.
  • Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication.

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