Open Access Research article

Sequence variation and selection of small RNAs in domesticated rice

Yu Wang1, Dan Shen1, Shiping Bo1, Huan Chen1, Jian Zheng1, Qian-Hao Zhu2, Daguang Cai3, Chris Helliwell2 and Longjiang Fan1*

Author Affiliations

1 Department of Agronomy, Zhejiang University, Hangzhou 310029, China

2 CSIRO Plant Industry, Canberra, ACT 2601, Australia

3 Department of Molekulare Phytopathologie, Christian-Albrechts-Universit├Ąt zu Kiel, D-24118 Kiel, Germany

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BMC Evolutionary Biology 2010, 10:119  doi:10.1186/1471-2148-10-119

Published: 30 April 2010



Endogenous non-coding small RNAs (21-24 nt) play an important role in post-transcriptional gene regulation in plants. Domestication selection is the most important evolutionary force in shaping crop genomes. The extent of polymorphism at small RNA loci in domesticated rice and whether small RNA loci are targets of domestication selection have not yet been determined.


A polymorphism survey of 94 small RNA loci (88 MIRNAs, four TAS3 loci and two miRNA-like long hairpins) was conducted in domesticated rice, generating 2 Mb of sequence data. Many mutations (substitution or insertion/deletion) were observed at small RNA loci in domesticated rice, e.g. 12 mutation sites were observed in the mature miRNA sequences of 11 MIRNAs (12.5% of the investigated MIRNAs). Several small RNA loci showed significant signals for positive selection and/or potential domestication selection.


Sequence variation at miRNAs and other small RNAs is higher than expected in domesticated rice. Like protein-coding genes, non-coding small RNA loci could be targets of domestication selection and play an important role in rice domestication and improvement.