title: Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress.
abstract: BACKGROUND
  MicroRNAs (miRNAs) play a vital role in growth, development, and stress response at the post-transcriptional level. Broccoli (Brassica oleracea L. var italic) is an important vegetable crop, and the yield and quality of broccoli are decreased by heat stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of miRNAomes during the broccoli head formation under heat stress is limited.
  
  
  METHODS
  In this study, molecular characterization of two nearly isogenic lines with contrasting head-forming capacity was investigated. Head-forming capacity was better for heat-tolerant (HT) than heat-sensitive (HS) broccoli under heat stress.
  
  
  RESULTS
  By deep sequencing and computational analysis, 20 known miRNAs showed significant differential expression between HT and HS genotypes. According to the criteria for annotation of new miRNAs, 24 novel miRNA sequences with differential expression between the two genotypes were identified. To gain insight into functional significance, 213 unique potential targets of these 44 differentially expressed miRNAs were predicted. These targets were implicated in shoot apical development, phase change, response to temperature stimulus, hormone and energy metabolism. The head-forming capacity of the unique HT line was related to autonomous regulation of Bo-FT genes and less expression level of heat shock protein genes as compared to HS. For the genotypic comparison, a set of miRNAs and their targets had consistent expression patterns in various HT genotypes.
  
  
  CONCLUSIONS
  This large-scale characterization of broccoli miRNAs and their potential targets is to unravel the regulatory roles of miRNAs underlying heat-tolerant head-forming capacity.
authors.affiliation: Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan. chichien0619@gmail.com.
authors.forename: Chi-Chien
authors.initials: CC
authors.lastname: Chen
authors.affiliation: Department of Biology, National Chunghua University of Education, No.1, Jin-De Road, Changhua, 500, Taiwan. sff24@mail.ncku.edu.tw.
authors.forename: Shih-Feng
authors.initials: SF
authors.lastname: Fu
authors.affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan. nomonma@nig.ac.jp.
authors.forename: Monma
authors.initials: M
authors.lastname: Norikazu
authors.affiliation: Kale Biotech. Co, No.68-1, Chongde 16th St., East Dist, Tainan, 701, Taiwan. yauwenyang@gmail.com.
authors.forename: Yau-Wen
authors.initials: YW
authors.lastname: Yang
authors.affiliation: Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan. bewithbutterfly@gmail.com.
authors.forename: Yu-Ju
authors.initials: YJ
authors.lastname: Liu
authors.affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan. kikeo@genes.nig.ac.jp.
authors.forename: Kazuho
authors.initials: K
authors.lastname: Ikeo
authors.affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan. tgojobor@genes.nig.ac.jp.
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.affiliation: Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan. haojen@mail.ncku.edu.tw.
authors.forename: Hao-Jen
authors.initials: HJ
authors.lastname: Huang
mesh_terms: D001483:Base Sequence; D001937:Brassica / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D056726:Genetic Association Studies; D005838:Genotype; D006358:Hot Temperature; D007178:Inbreeding; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D034622:RNA Interference; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics*; D013696:Temperature; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant