title: miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species.
abstract: BACKGROUND
  Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii.
  
  
  RESULTS
  Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems.
  
  
  CONCLUSIONS
  Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.
authors.affiliation: IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394, Montpellier, Cedex 5, France.|LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam.
authors.forename: K N
authors.initials: KN
authors.lastname: Ta
authors.affiliation: IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394, Montpellier, Cedex 5, France.
authors.forename: F
authors.initials: F
authors.lastname: Sabot
authors.affiliation: IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394, Montpellier, Cedex 5, France.
authors.forename: H
authors.initials: H
authors.lastname: Adam
authors.affiliation: IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394, Montpellier, Cedex 5, France.
authors.forename: Y
authors.initials: Y
authors.lastname: Vigouroux
authors.affiliation: IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394, Montpellier, Cedex 5, France.|Present address: INRA, Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, F-54280, Champenoux, France.
authors.forename: S
authors.initials: S
authors.lastname: De Mita
authors.affiliation: IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394, Montpellier, Cedex 5, France.
authors.forename: A
authors.initials: A
authors.lastname: Ghesquière
authors.affiliation: LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam.
authors.forename: N V
authors.initials: NV
authors.lastname: Do
authors.affiliation: LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam.|Université de Montpellier, UMR DIADE, Place Eugène Bataillon, F-34095, Montpellier, Cedex 5, France.
authors.forename: P
authors.initials: P
authors.lastname: Gantet
authors.affiliation: IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394, Montpellier, Cedex 5, France. stephane.jouannic@ird.fr.|LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam. stephane.jouannic@ird.fr.
authors.forename: S
authors.initials: S
authors.lastname: Jouannic
keywords: Domestication; Meristem; Oryza barthii; Oryza glaberrima; Panicle; Small RNAs; miR2118; phasiRNAs