title: Sequence variation and selection of small RNAs in domesticated rice.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Agronomy, Zhejiang University, Hangzhou, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.forename: Dan
authors.initials: D
authors.lastname: Shen
authors.forename: Shiping
authors.initials: S
authors.lastname: Bo
authors.forename: Huan
authors.initials: H
authors.lastname: Chen
authors.forename: Jian
authors.initials: J
authors.lastname: Zheng
authors.forename: Qian-Hao
authors.initials: QH
authors.lastname: Zhu
authors.forename: Daguang
authors.initials: D
authors.lastname: Cai
authors.forename: Chris
authors.initials: C
authors.lastname: Helliwell
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D001483:Base Sequence; D014644:Genetic Variation; D035683:MicroRNAs / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D022661:RNA, Untranslated