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

Wild Rice PipelineThe 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 team led by researchers at the Zhejiang University, China sequenced three small RNA populations and a degradome of O. rufipogon by the Illumina sequencing platform and investigated the expression levels of microRNAs (miRNAs) 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. They 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. Their 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.

  • Wang Y, Bai X, Yan C, Gui Y, Wei X, Zhu QH, Guo L, Fan L. (2012) Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication. New Phytol 196(3), 914-25. [abstract]