title: Identification of microRNAs and their mRNA targets during soybean nodule development: functional analysis of the role of miR393j-3p in soybean nodulation.
abstract: Plant microRNAs (miRNAs) play important regulatory roles in a number of developmental processes. The present work investigated the roles of miRNAs during nodule development in the crop legume soybean (Glycine max). Fifteen soybean small RNA libraries were sequenced from different stages of nodule development, including young nodules, mature nodules and senescent nodules. In order to identify the regulatory targets of the miRNAs, five parallel analysis of RNA ends (PARE) libraries were also sequenced from the same stages of nodule development. Sequencing identified 284 miRNAs, including 178 novel soybean miRNAs. Analysis of miRNA abundance identified 139 miRNAs whose expression was significantly regulated during nodule development, including 12 miRNAs whose expression changed > 10-fold. Analysis of the PARE libraries identified 533 miRNA targets, including three nodulation-related genes and eight nodule-specific genes. miR393j-3p was selected for detailed analysis as its expression was significantly regulated during nodule formation, and it targeted a nodulin gene, Early Nodulin 93 (ENOD93). Strong, ectopic expression of miR393j-3p, as well as RNAi silencing of ENOD93 expression, significantly reduced nodule formation. The data indicate that miR393j-3p regulation of ENOD93 mRNA abundance is a key control point for soybean nodule formation.
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, 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, 65211, USA.
authors.forename: Md Shakhawat
authors.initials: MS
authors.lastname: Hossain
authors.affiliation: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.
authors.forename: Siwaret
authors.initials: S
authors.lastname: Arikit
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Oswaldo
authors.initials: O
authors.lastname: Valdés-López
authors.affiliation: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, 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, 65211, USA.|National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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, 65211, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Libault
authors.affiliation: Department of Statistics, University of Missouri, 209D Middlebush Hall, Columbia, MO, 65211, USA.
authors.forename: Tieming
authors.initials: T
authors.lastname: Ji
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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, 19711, USA.
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.affiliation: Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Stacey
mesh_terms: D016000:Cluster Analysis; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D055170:Plant Root Nodulation / Q000235:genetics*; D030821:Plants, Genetically Modified; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D053204:Root Nodules, Plant / Q000235:genetics* / Q000254:growth & development*; D017423:Sequence Analysis, RNA; D013025:Glycine max / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: ENOD93; miR393j-3p; microRNA (miRNA); root hair; soybean (Glycine max); symbiosis