title: miRNA regulation in the early development of barley seed.
abstract: BACKGROUND
  During the early stages of seed development many genes are under dynamic regulation to ensure the proper differentiation and establishment of the tissue that will constitute the mature grain. To investigate how miRNA regulation contributes to this process in barley, a combination of small RNA and mRNA degradome analyses were used to identify miRNAs and their targets.
  
  
  RESULTS
  Our analysis identified 84 known miRNAs and 7 new miRNAs together with 96 putative miRNA target genes regulated through a slicing mechanism in grain tissues during the first 15 days post anthesis. We also identified many potential miRNAs including several belonging to known miRNA families. Our data gave us evidence for an increase in miRNA-mediated regulation during the transition between pre-storage and storage phases. Potential miRNA targets were found in various signalling pathways including components of four phytohormone pathways (ABA, GA, auxin, ethylene) and the defence response to powdery mildew infection. Among the putative miRNA targets we identified were two essential genes controlling the GA response, a GA3oxidase1 and a homolog of the receptor GID1, and a homolog of the ACC oxidase which catalyses the last step of ethylene biosynthesis. We found that two MLA genes are potentially miRNA regulated, establishing a direct link between miRNAs and the R gene response.
  
  
  CONCLUSIONS
  Our dataset provides a useful source of information on miRNA regulation during the early development of cereal grains and our analysis suggests that miRNAs contribute to the control of development of the cereal grain, notably through the regulation of phytohormone response pathways.
authors: CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia.
authors: Julien
authors: J
authors: Curaba
authors: Andrew
authors: A
authors: Spriggs
authors: Jen
authors: J
authors: Taylor
authors: Zhongyi
authors: Z
authors: Li
authors: Chris
authors: C
authors: Helliwell
mesh_terms: D060467:Disease Resistance / Q000235:genetics; D004722:Endoribonucleases / Q000235:genetics; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D015723:Gene Library; D001467:Hordeum / Q000235:genetics* / Q000254:growth & development; D035683:MicroRNAs / Q000235:genetics* / Q000302:isolation & purification; D009097:Multienzyme Complexes / Q000235:genetics; D009928:Organ Specificity; D010937:Plant Growth Regulators / Q000378:metabolism; D011117:Polyribonucleotide Nucleotidyltransferase / Q000235:genetics; D020365:RNA Helicases / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D012639:Seeds / Q000235:genetics / Q000254:growth & development*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D009097:Multienzyme Complexes; D010937:Plant Growth Regulators; D018749:RNA, Plant; C111244:degradosome; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; D020365:RNA Helicases