title: Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection.
abstract: Three soybean [Glycine max (L) Merr.] small RNA libraries were generated and sequenced using the Illumina platform to examine the role of miRNAs during soybean nodulation. The small RNA libraries were derived from root hairs inoculated with Bradyrhizobium japonicum (In_RH) or mock-inoculated with water (Un_RH), as well as from the comparable inoculated stripped root samples (i.e. inoculated roots with the root hairs removed). Sequencing of these libraries identified a total of 114 miRNAs, including 22 novel miRNAs. A comparison of miRNA abundance among the 114 miRNAs identified 66 miRNAs that were differentially expressed between root hairs and stripped roots, and 48 miRNAs that were differentially regulated in infected root hairs in response to B. japonicum when compared to uninfected root hairs (P ≤ 0.05). A parallel analysis of RNA ends (PARE) library was constructed and sequenced to reveal a total of 405 soybean miRNA targets, with most predicted to encode transcription factors or proteins involved in protein modification, protein degradation and hormone pathways. The roles of gma-miR4416 and gma-miR2606b during nodulation were further analysed. Ectopic expression of these two miRNAs in soybean roots resulted in significant changes in nodule numbers. miRNA target information suggested that gma-miR2606b regulates a Mannosyl-oligosaccharide 1, 2-alpha-mannosidase gene, while gma-miR4416 regulates the expression of a rhizobium-induced peroxidase 1 (RIP1)-like peroxidase gene, GmRIP1, during nodulation.
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Yan
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
authors.forename: Md Shakhawat
authors.initials: MS
authors.lastname: Hossain
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
authors.forename: Oswaldo
authors.initials: O
authors.lastname: Valdés-López
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
authors.forename: Nhung T
authors.initials: NT
authors.lastname: Hoang
authors.affiliation: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
authors.forename: Jixian
authors.initials: J
authors.lastname: Zhai
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.|National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Libault
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
authors.forename: Laurent
authors.initials: L
authors.lastname: Brechenmacher
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
authors.forename: Seth
authors.initials: S
authors.lastname: Findley
authors.affiliation: Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA.
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Qiu
authors.affiliation: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
authors.forename: D Janine
authors.initials: DJ
authors.lastname: Sherrier
authors.affiliation: Department of Statistics, University of Missouri, Columbia, MO, USA.
authors.forename: Tieming
authors.initials: T
authors.lastname: Ji
authors.affiliation: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.affiliation: Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Stacey
mesh_terms: D020369:Bradyrhizobium / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D055170:Plant Root Nodulation / Q000235:genetics; D018517:Plant Roots / Q000235:genetics* / Q000382:microbiology*; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013025:Glycine max / Q000235:genetics* / Q000382:microbiology*
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D012335:RNA, Ribosomal; D012343:RNA, Transfer
keywords: gma-miR2606b; gma-miR4416; miRNA; nodulation; root hair; soybean