title: Combined small RNA and degradome sequencing reveals microRNA regulation during immature maize embryo dedifferentiation.
abstract: Genetic transformation of maize is highly dependent on the development of embryonic calli from the dedifferentiated immature embryo. To better understand the regulatory mechanism of immature embryo dedifferentiation, we generated four small RNA and degradome libraries from samples representing the major stages of dedifferentiation. More than 186 million raw reads of small RNA and degradome sequence data were generated. We detected 102 known miRNAs belonging to 23 miRNA families. In total, we identified 51, 70 and 63 differentially expressed miRNAs (DEMs) in the stage I, II, III samples, respectively, compared to the control. However, only 6 miRNAs were continually up-regulated by more than fivefold throughout the process of dedifferentiation. A total of 87 genes were identified as the targets of 21 DEM families. This group of targets was enriched in members of four significant pathways including plant hormone signal transduction, antigen processing and presentation, ECM-receptor interaction, and alpha-linolenic acid metabolism. The hormone signal transduction pathway appeared to be particularly significant, involving 21 of the targets. While the targets of the most significant DEMs have been proved to play essential roles in cell dedifferentiation. Our results provide important information regarding the regulatory networks that control immature embryo dedifferentiation in maize.
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China. Electronic address: shenyaou@gmail.com.
authors.forename: Yaou
authors.initials: Y
authors.lastname: Shen
authors.forename: Zhou
authors.initials: Z
authors.lastname: Jiang
authors.forename: Sifen
authors.initials: S
authors.lastname: Lu
authors.forename: Haijian
authors.initials: H
authors.lastname: Lin
authors.forename: Shibin
authors.initials: S
authors.lastname: Gao
authors.forename: Huanwei
authors.initials: H
authors.lastname: Peng
authors.forename: Guangsheng
authors.initials: G
authors.lastname: Yuan
authors.forename: Li
authors.initials: L
authors.lastname: Liu
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Zhang
authors.forename: Maojun
authors.initials: M
authors.lastname: Zhao
authors.forename: Tingzhao
authors.initials: T
authors.lastname: Rong
authors.forename: Guangtang
authors.initials: G
authors.lastname: Pan
mesh_terms: D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D054337:Cell Dedifferentiation / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018257:Helix-Loop-Helix Motifs; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012639:Seeds / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D003313:Zea mays / Q000196:embryology* / Q000235:genetics / Q000378:metabolism
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D035683:MicroRNAs; D018749:RNA, Plant
keywords: ARF; CK; DEM; Dedifferentiation; Degradome sequencing; Dicer; GA; HLH; Immature embryo; MFE; Maize; NAM; QTL; RPM; Small RNA sequencing; auxin response factor; differentially expressed miRNA; double-stranded-specific RNase; gibberellin; helix-loop-helix; miRNA; miRNA regulation; microRNA; minimum free energy; no apical meristem; quantitative trait locus; reads per million clean reads; the control