Sequence variation and selection of small RNAs in domesticated rice

BMC Evolutionary Biology

Research Article

Qian-Hao Zhu¹  Chris Helliwell¹  Shiping Bo²  Dan Shen²  Longjiang Fan²  Yu Wang²  Jian Zheng²  Huan Chen²  Daguang Cai³ 

[1] CSIRO Plant Industry, 2601, Canberra, ACT, Australia;Department of Agronomy, Zhejiang University, 310029, Hangzhou, China;Department of Molekulare Phytopathologie, Christian-Albrechts-Universität zu Kiel, D-24118, Kiel, Germany;

关键词: Single Nucleotide Polymorphism;    Wild Rice;    miRNA Family;    miRNA Binding Site;    Rice Accession;   

DOI  :  10.1186/1471-2148-10-119

 received in 2009-07-08, accepted in 2010-04-30,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundEndogenous 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.ResultsA 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.ConclusionsSequence 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.

【 授权许可】

Unknown   
© Wang et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.