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Dynamic expression of small RNA populations in larch (Larix leptolepis)

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Abstract

Small RNAs (sRNAs) are emerging as essential regulators of biological processes. However, several studies have reported that gymnosperms do not express appreciable amounts of 24-nt sRNAs, and conifers in particular may have a unique sRNA-silencing signature. Here, we compared the sRNA transcriptomes of Japanese larch somatic embryos (SE) and seedlings. SE sRNAs exhibited a length bias toward 24 nt, while seedlings showed a bias toward a 21-nt length. We also confirmed that larch is capable of producing 24-nt sRNAs based on a polyacrylamide gel analysis. The sRNA expression patterns varied according to developmental stage, which might be associated with Dicer-like 3 and RNA-dependent RNA polymerase2 (RDR2) levels. Our data suggest that many MIR loci that produce canonical microRNAs (miRNAs, 20–22 nt) and long sRNAs (23–26 nt) have dual functions; the latter were preferentially produced in SE compared to seedlings. However, the ratio of miRNAs to total sRNAs in seedlings was higher than in SE, and most miRNAs were upregulated in seedlings. Trans-acting small interfering RNAs (ta-siRNAs) generated from TAS3 triggered by miR390 were identified, and levels of the three detected ta-siRNAs peaked in mature embryos, which was not consistent with the lowest RDR6 level. These findings indicate that larch, and possibly other gymnosperms, shares a common sRNA pathway with other land plants, and that the sRNA distribution pattern varies according to developmental stage, which may be attributable to the expression of sRNA pathway genes.

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Abbreviations

sRNA:

Small RNA

nt:

Nucleotide

SE:

Somatic embryo

MiRNA:

MicroRNA

siRNA:

Small interfering RNA

RDR:

RNA-dependent RNA polymerase

DCL:

Dicer like

DsRNA:

Double-stranded RNA

Pol IV:

Polymerase IV

ta-siRNA:

Trans-acting siRNA

nat-siRNA:

Natural antisense transcript-derived siRNA

exo-siRNA:

Exogenous siRNA

ca-siRNA:

Cis-acting siRNA

lsiRNA:

Long siRNA

PEM:

Proembryogenic mass

qRT-PCR:

Quantitative RT-PCR

PAGE:

Polyacrylamide gel

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (grant no. 30830086), the National Basic Research Program of China (grant no. 2009CB119106), and the National High Technology Research and Development Program of China (grant no. SQ2010AA1000687004).

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Authors and Affiliations

  1. Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, People’s Republic of China

    Junhong Zhang, Tao Wu, Xinmin Li, Shougong Zhang & Liwang Qi

  2. Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, 311300, Zhejiang, People’s Republic of China

    Junhong Zhang

  3. Key Laboratory of Research Institute of Forest Ecology and Protection, Chinese Academy of Forestry, Beijing, 100091, People’s Republic of China

    Long Li & Suying Han

  4. Department of Pathology and Laboratory Medicine, University of California at Los Angeles, 1000 Veteran Ave, Los Angeles, CA, 90095, USA

    Xinmin Li

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  1. Junhong Zhang
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  2. Tao Wu
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  3. Long Li
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  4. Suying Han
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  5. Xinmin Li
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  6. Shougong Zhang
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Correspondence to Shougong Zhang or Liwang Qi.

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J. Zhang and T. Wu contributed equally to this work.

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Zhang, J., Wu, T., Li, L. et al. Dynamic expression of small RNA populations in larch (Larix leptolepis). Planta 237, 89–101 (2013). https://doi.org/10.1007/s00425-012-1753-4

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