title: Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are important regulators in plant development. They post-transcriptionally regulate gene expression during various biological and metabolic processes by binding to the 3'-untranslated region of target mRNAs to facilitate mRNA degradation or inhibit translation. Chrysanthemum (Chrysanthemum morifolium) is one of the most important ornamental flowers with increasing demand each year. However, embryo abortion is the main reason for chrysanthemum cross breeding failure. To date, there have been no experiments examining the expression of miRNAs associated with chrysanthemum embryo development. Therefore, we sequenced three small RNA libraries to identify miRNAs and their functions. Our results will provide molecular insights into chrysanthemum embryo abortion.
  
  
  RESULTS
  Three small RNA libraries were built from normal chrysanthemum ovules at 12 days after pollination (DAP), and normal and abnormal chrysanthemum ovules at 18 DAP. We validated 228 miRNAs with significant changes in expression frequency during embryonic development. Comparative profiling revealed that 69 miRNAs exhibited significant differential expression between normal and abnormal embryos at 18 DAP. In addition, a total of 1037 miRNA target genes were predicted, and their annotations were defined by transcriptome data. Target genes associated with metabolic pathways were most highly represented according to the annotation. Moreover, 52 predicted target genes were identified to be associated with embryonic development, including 31 transcription factors and 21 additional genes. Gene ontology (GO) annotation also revealed that high-ranking miRNA target genes related to cellular processes and metabolic processes were involved in transcription regulation and the embryo developmental process.
  
  
  CONCLUSIONS
  The present study generated three miRNA libraries and gained information on miRNAs and their targets in the chrysanthemum embryo. These results enrich the growing database of new miRNAs and lay the foundation for the further understanding of miRNA biological function in the regulation of chrysanthemum embryo abortion.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China; Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & Equipment, Nanjing, China.
authors.forename: Fengjiao
authors.initials: F
authors.lastname: Zhang
authors.affiliation: China Rural Technology Development Center, Beijing, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Dong
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Lulu
authors.initials: L
authors.lastname: Huang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Aiping
authors.initials: A
authors.lastname: Song
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Haibin
authors.initials: H
authors.lastname: Wang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Weimin
authors.initials: W
authors.lastname: Fang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Fadi
authors.initials: F
authors.lastname: Chen
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China; Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & Equipment, Nanjing, China.
authors.forename: Nianjun
authors.initials: N
authors.lastname: Teng
mesh_terms: D001483:Base Sequence; D031202:Chrysanthemum / Q000196:embryology* / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D006824:Hybridization, Genetic / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D018749:RNA, Plant / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant