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

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Abstract

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.

Abstract

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.

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Acknowledgements

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.

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Authors and Affiliations

  1. Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada

    Jun-Jun Liu, Holly Williams, Xiao Rui Li, Arezoo Zamany, Gary Roke & Hao Chen

  2. USDA Forest Service, Rocky Mountain Research Station, 240 West Prospect Road, Fort Collins, CO, 80526, USA

    Anna W. Schoettle

  3. USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA

    Richard A. Sniezko

  4. Ministry of Forests, Lands and Natural Resource Operations, 333 Victoria St., Nelson, BC, V1L 4K3, Canada

    Michael Murray

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  1. Jun-Jun Liu
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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.

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Correspondence to Jun-Jun Liu.

Additional information

The raw Illumina RNA-seq 100-bp PE sequences of WBP needle samples were deposited in the NCBI under BioProject ID: PRJNA352055. This Transcriptome Shotgun Assembly project has been registered at DDBJ/EMBL/GenBank under the accession GFLL00000000.

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11103_2017_655_MOESM1_ESM.xlsx

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

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)

Supplementary material 3 (BMP 4641 KB)

Supplementary material 4 (BMP 2722 KB)

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Liu, JJ., Williams, H., Li, X.R. et al. Profiling methyl jasmonate-responsive transcriptome for understanding induced systemic resistance in whitebark pine (Pinus albicaulis). Plant Mol Biol 95, 359–374 (2017). https://doi.org/10.1007/s11103-017-0655-z

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