Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication
Article first published online: 20 SEP 2012
© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust
Volume 196, Issue 3, pages 914–925, November 2012
How to Cite
Wang, Y., Bai, X., Yan, C., Gui, Y., Wei, X., Zhu, Q.-H., Guo, L. and Fan, L. (2012), Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication. New Phytologist, 196: 914–925. doi: 10.1111/j.1469-8137.2012.04304.x
- Issue published online: 9 OCT 2012
- Article first published online: 20 SEP 2012
- Manuscript Accepted: 28 JUL 2012
- Manuscript Received: 31 MAY 2012
- the National Natural Science Foundation of China. Grant Number: 31071393
- Foundation of Ministry of Education of China. Grant Number: 20100101110096
- MIRNA ;
- Oryza rufipogon ;
- rice domestication
- 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.