title: Genome-wide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis.
abstract: MicroRNAs (miRNAs) are emerging as essential regulators of biological processes. Somatic embryogenesis is one of the most important techniques for gymnosperm-breeding programs, but there is little understanding of its underlying mechanism. To investigate the roles of miRNAs during somatic embryogenesis in larch, we constructed a small RNA library from somatic embryos. High-throughput sequencing of the library identified 83 conserved miRNAs from 35 families, 16 novel miRNAs, and 14 plausible miRNA candidates, with a high proportion specific to larch or gymnosperms. qRT-PCR analysis demonstrated that both the conserved and novel or candidate miRNAs were expressed in larch. Several miRNA precursor sequences were obtained via RACE. We predicted 110 target genes using bioinformatics, and validated 9 of them by 5' RACE. 11 conserved miRNA families including 17 miRNAs with critical functions in plant development and six target mRNAs were detected by qRT-PCR in the larch SE. Stage-specific expression of miRNAs and their targets indicate their possible modulation on SE of larch: miR171a/b might exert function on PEMs, while miR171c acts in the induction process of larch SE; miR397 and miR398 mainly involved in modulation of PEM propagation and transition to single embryo; miR162 and miR168 exert their regulatory function during total SE process, especially during stages 5-8; miR156, miR159, miR160, miR166, miR167, and miR390 might play regulatory roles during cotyledonary embryo development. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving specific and common miRNAs operating post-transcriptionally during embryogenesis.
authors.affiliation: Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China. zjh6719036@163.com
authors.forename: Junhong
authors.initials: J
authors.lastname: Zhang
authors.forename: Shougong
authors.initials: S
authors.lastname: Zhang
authors.forename: Suying
authors.initials: S
authors.lastname: Han
authors.forename: Tao
authors.initials: T
authors.lastname: Wu
authors.forename: Xinmin
authors.initials: X
authors.lastname: Li
authors.forename: Wanfeng
authors.initials: W
authors.lastname: Li
authors.forename: Liwang
authors.initials: L
authors.lastname: Qi
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence; D018548:Cotyledon / Q000196:embryology / Q000235:genetics / Q000502:physiology; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D028221:Larix / Q000196:embryology / Q000235:genetics* / Q000502:physiology; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058439:Plant Somatic Embryogenesis Techniques; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant