title: Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.).
abstract: BACKGROUND
  MicroRNAs (miRNAs) are small, non-coding RNAs playing essential roles in plant growth, development, and stress responses. Sequencing of small RNAs is a starting point for understanding their number, diversity, expression and possible roles in plants.
  
  
  RESULTS
  In this study, we conducted a genome-wide survey of wheat miRNAs from 11 tissues, characterizing a total of 323 novel miRNAs belonging to 276 families in wheat. A miRNA conservation analysis identified 191 wheat-specific miRNAs, 2 monocot-specific miRNAs, and 30 wheat-specific variants from 9 highly conserved miRNA families. To understand possible roles of wheat miRNAs, we determined 524 potential targets for 124 miRNA families through degradome sequencing, and cleavage of a subset of them was validated via 5' RACE. Based on the genome-wide identification and characterization of miRNAs and their associated target genes, we further identified 64 miRNAs preferentially expressing in developing or germinating grains, which could play important roles in grain development.
  
  
  CONCLUSIONS
  We discovered 323 wheat novel miRNAs and 524 target genes for 124 miRNA families in a genome-wide level, and our data will serve as a foundation for future research into the functional roles of miRNAs in wheat.
authors.forename: Fenglong
authors.initials: F
authors.lastname: Sun
authors.forename: Guanghui
authors.initials: G
authors.lastname: Guo
authors.forename: Jinkun
authors.initials: J
authors.lastname: Du
authors.forename: Weiwei
authors.initials: W
authors.lastname: Guo
authors.forename: Huiru
authors.initials: H
authors.lastname: Peng
authors.forename: Zhongfu
authors.initials: Z
authors.lastname: Ni
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China. qxsun@cau.edu.cn.
authors.forename: Qixin
authors.initials: Q
authors.lastname: Sun
authors.forename: Yingyin
authors.initials: Y
authors.lastname: Yao
mesh_terms: D015152:Blotting, Northern; D017124:Conserved Sequence / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D009711:Nucleotides / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D015203:Reproducibility of Results; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics; D014908:Triticum / Q000235:genetics* / Q000254:growth & development
chemical_list: D018076:DNA, Complementary; D035683:MicroRNAs; D009711:Nucleotides