title: Identification of miRNAs involved in pear fruit development and quality.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs.
  
  
  RESULTS
  Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor.
  
  
  CONCLUSIONS
  Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species.
authors.affiliation: College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. wujun@njau.edu.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
authors.forename: Defu
authors.initials: D
authors.lastname: Wang
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Liu
authors.forename: Long
authors.initials: L
authors.lastname: Wang
authors.forename: Xin
authors.initials: X
authors.lastname: Qiao
authors.forename: Shaoling
authors.initials: S
authors.lastname: Zhang
mesh_terms: D000143:Acids / Q000378:metabolism; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D005638:Fruit / Q000235:genetics* / Q000254:growth & development*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D017343:Genes, Plant; D008031:Lignin / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D031989:Pyrus / Q000235:genetics* / Q000254:growth & development*; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA
chemical_list: D000143:Acids; D035683:MicroRNAs; D008031:Lignin