Plant Molecular Biology

, Volume 95, Issue 4–5, pp 359–374 | Cite as

Profiling methyl jasmonate-responsive transcriptome for understanding induced systemic resistance in whitebark pine (Pinus albicaulis)

  • Jun-Jun Liu
  • Holly Williams
  • Xiao Rui Li
  • Anna W. Schoettle
  • Richard A. Sniezko
  • Michael Murray
  • Arezoo Zamany
  • Gary Roke
  • Hao Chen


Key message

RNA-seq analysis on whitebark pine needles demonstrated that methyl jasmonate (MeJA)-triggered transcriptome re-programming substantially overlapped with defense responses against insects and fungal pathogens in Pinus species, increasing current knowledge regarding induced systemic resistance (ISR) to pathogens and pests in whitebark pine.


Many whitebark pine populations are in steep decline due to high susceptibility to mountain pine beetle and the non-native white pine blister rust (WPBR). Resistance, including induced systemic resistance (ISR), is not well characterized in whitebark pine, narrowing the current options for increasing the success of restoration and breeding programs. Exogenous jasmonates are known to trigger ISR by activating the plant’s immune system through regulation of gene expression to produce chemical defense compounds. This study reports profiles of whitebark pine needle transcriptomes, following methyl jasmonate (MeJA) treatment using RNA-seq. A MeJA-responsive transcriptome was de novo assembled and transcriptome profiling identified a set of differentially expressed genes (DEGs), revealing 1422 up- and 999 down-regulated transcripts with at least twofold change (FDR corrected p < 0.05) in needle tissues in response to MeJA application. GO analysis revealed that these DEGs have putative functions in plant defense signalling, transcription regulation, biosyntheses of secondary metabolites, and other biological processes. Lineage-specific expression of defense-related genes was characterized through comparison with MeJA signalling in model plants. In particular, MeJA-triggered transcriptome re-programming substantially overlapped with defense responses against WPBR and insects in related Pinus species, suggesting that MeJA may be used to improve whitebark pine resistance to pathogens/pests. Our study provides new insights into molecular mechanisms and metabolic pathways involved in whitebark pine ISR. DEGs identified in this study can be used as candidates to facilitate identification of genomic variation contributing to host resistance and aid in breeding selection of elite genotypes with better adaptive fitness to environmental stressors in this endangered tree species.


Induced systemic resistance Jasmonate-signaling RNA-seq Transcriptome profiling Whitebark pine 



Authors are grateful to Gary Zhang and Aimin Guan at CFS for computer programming and bioinformatics analyses, and to Andrew Dyk at CFS for photographing. This work was financially supported in part by the CFS-GRDI fund and CFS-PFC DG’s fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author contributions

J-JL, AWS and RAS conceived the project. J-J L and HW designed the experiments. MM provided plant materials. HW, XRL, AZ, and GR performed the experiments. J-JL, HW, XRL, and HC performed the bioinformatics of the transcriptome and the statistical analyses of the experimental data. J-JL interpreted the data and wrote the manuscript. J-JL, HW, MM, AWS, RAS, and AZ edited the manuscript.

Supplementary material

11103_2017_655_MOESM1_ESM.xlsx (37 kb)
Figure S1: Pearson’s correlation analysis to evaluate variations in transcript levels detected by RNA-seq analysis among biological repeats of whitebark pine. Pearson’s correlation coefficient was calculated between biological repeats at each time point based on the RPKM data. Here present the correlations for two comparisons (sample_1 vs. sample_2, sample_1 vs. sample_3) at day 0, day 1, day 2, and day 4 post MeJA treatment. Correlations between sample_2 and sample_3 at these time points were in a similar range Supplementary material 1 (XLSX 37 KB)
11103_2017_655_MOESM2_ESM.xlsx (184 kb)
Figure S2: Regression analysis comparing fold changes of transcript expression as estimated by qRT-PCR and RNA-seq (r = 0.9533, p < 0.00001) Supplementary material 2 (XLSX 183 KB)
11103_2017_655_MOESM3_ESM.bmp (4.5 mb)
Supplementary material 3 (BMP 4641 KB)
11103_2017_655_MOESM4_ESM.bmp (2.7 mb)
Supplementary material 4 (BMP 2722 KB)


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Copyright information

© Her Majesty the Queen in Right of Canada 2017

Authors and Affiliations

  • Jun-Jun Liu
    • 1
  • Holly Williams
    • 1
  • Xiao Rui Li
    • 1
  • Anna W. Schoettle
    • 2
  • Richard A. Sniezko
    • 3
  • Michael Murray
    • 4
  • Arezoo Zamany
    • 1
  • Gary Roke
    • 1
  • Hao Chen
    • 1
  1. 1.Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
  2. 2.USDA Forest ServiceRocky Mountain Research StationFort CollinsUSA
  3. 3.USDA Forest ServiceDorena Genetic Resource CenterCottage GroveUSA
  4. 4.Ministry of ForestsLands and Natural Resource OperationsNelsonCanada

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