Planta

, Volume 236, Issue 2, pp 647–657

Genome-wide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis

  • Junhong Zhang
  • Shougong Zhang
  • Suying Han
  • Tao Wu
  • Xinmin Li
  • Wanfeng Li
  • Liwang Qi
Original Article

DOI: 10.1007/s00425-012-1643-9

Cite this article as:
Zhang, J., Zhang, S., Han, S. et al. Planta (2012) 236: 647. doi:10.1007/s00425-012-1643-9

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.

Keywords

Larix leptolepisMicroRNAMicroRNA targetqRT-PCRSomatic embryogenesis

Abbreviations

miRNA

MicroRNA

SE

Somatic embryogenesis

PEM

Proembryogenic mass

qRT-PCR

Quantitative reverse transcription PCR

5′ RACE

5′ Rapid amplification of cDNA ends

EST

Expressed sequence tag

Supplementary material

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Supplementary material 1 (XLS 42 kb)
425_2012_1643_MOESM2_ESM.doc (48 kb)
Supplementary material 2 (DOC 48 kb)
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Supplementary material 3 (DOC 142 kb)
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Supplementary material 4 (DOC 31 kb)
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Supplementary material 5 (DOC 283 kb)
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Supplementary material 6 (DOC 165 kb)
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Supplementary material 7 (DOC 205 kb)

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Junhong Zhang
    • 1
  • Shougong Zhang
    • 1
  • Suying Han
    • 2
  • Tao Wu
    • 1
  • Xinmin Li
    • 1
    • 3
  • Wanfeng Li
    • 1
  • Liwang Qi
    • 1
  1. 1.Laboratory of Cell Biology, Research Institute of ForestryChinese Academy of ForestryBeijingChina
  2. 2.Key Laboratory of Research Institute of Forest Ecology and ProtectionChinese Academy of ForestryBeijingChina
  3. 3.Department of Pathology and Laboratory MedicineUniversity of California at Los AngelesLos AngelesUSA