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Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa

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Abstract

Main conclusion

Co-expression networks based on transcriptomes of Populus trichocarpa major tissues and specific cell types suggest redundant control of cell wall component biosynthetic genes by transcription factors in wood formation.

We analyzed the transcriptomes of five tissues (xylem, phloem, shoot, leaf, and root) and two wood forming cell types (fiber and vessel) of Populus trichocarpa to assemble gene co-expression subnetworks associated with wood formation. We identified 165 transcription factors (TFs) that showed xylem-, fiber-, and vessel-specific expression. Of these 165 TFs, 101 co-expressed (correlation coefficient, r > 0.7) with the 45 secondary cell wall cellulose, hemicellulose, and lignin biosynthetic genes. Each cell wall component gene co-expressed on average with 34 TFs, suggesting redundant control of the cell wall component gene expression. Co-expression analysis showed that the 101 TFs and the 45 cell wall component genes each has two distinct groups (groups 1 and 2), based on their co-expression patterns. The group 1 TFs (44 members) are predominantly xylem and fiber specific, and are all highly positively co-expressed with the group 1 cell wall component genes (30 members), suggesting their roles as major wood formation regulators. Group 1 TFs include a lateral organ boundary domain gene (LBD) that has the highest number of positively correlated cell wall component genes (36) and TFs (47). The group 2 TFs have 57 members, including 14 vessel-specific TFs, and are generally less correlated with the cell wall component genes. An exception is a vessel-specific basic helix-loop-helix (bHLH) gene that negatively correlates with 20 cell wall component genes, and may function as a key transcriptional suppressor. The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation.

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Acknowledgements

This work was supported by the US National Science Foundation, Plant Genome Research Program Grant DBI-0922391, and the US Department of Energy Grant DE-SC000691. We acknowledge additional supports from the NC State University Jordan Family Distinguished Professor Endowment, the NC State University Forest Biotechnology Industrial Research Consortium, and the National Natural Science Foundation of China (NSFC).

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    Authors and Affiliations

    1. Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA

      Rui Shi, Jack P. Wang, Ying-Chung Lin, Hao Chen, Ronald R. Sederoff & Vincent L. Chiang

    2. Mountain Horticultural Crops Research and Extension Center, Department of Horticulture, North Carolina State University, Mills River, NC, 28759, USA

      Rui Shi

    3. State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China

      Jack P. Wang, Ying-Chung Lin & Vincent L. Chiang

    4. Department of Life Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan

      Ying-Chung Lin

    5. State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China

      Quanzi Li

    6. Department of Forestry, National Chung Hsing University, Taichung, 40227, Taiwan

      Ying-Hsuan Sun

    7. Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695, USA

      Vincent L. Chiang

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    R. Shi and J. P. Wang contributed equally to this work.

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    Shi, R., Wang, J.P., Lin, YC. et al. Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa . Planta 245, 927–938 (2017). https://doi.org/10.1007/s00425-016-2640-1

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