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Comparative transcriptomic analysis uncovers conserved pathways involved in adventitious root formation in poplar

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Abstract

Cutting propagation is widely used in establishing poplar plantations, and this approach requires efficient adventitious root (AR) forming capacities. Although poplar species are considered to form roots easily, interspecific variations in AR formation are still observed. To better understand the gene regulatory network underlying the conserved modified pathways that are essential for AR formation in poplar species, comparative transcriptomic approaches were applied to identify the conserved common genes that were differentially expressed during the AR formation processes in two poplar species (Populus × euramericana and P. simonii) in woody plant medium (WPM). A total of 2146 genes were identified as conserved genes that shared similar gene expression profiles in at least one comparison. These conserved genes were enriched in diverse hormone signaling pathways, as well as the mitogen-associated protein kinase (MAPK) signaling pathway, suggesting an important role for signaling transduction in coordinating external stimuli and endogenous physiological status during AR regulation in poplar. Furthermore, the co-expression network analysis of conserved genes allowed identification of several co-expressed modules (CM) that are co-expressed with distinct biological functions, for instance, CM1 was enriched in defense response and hormone signaling, CM2 and CM3 were overrepresented in defense response-related pathways and for cell cycle, respectively. These results suggest that the AR formation processes in poplar were finely tuned at the transcriptomic level by integrating multiple biological processes essential for AR formation. Our results suggest conserved machinery for AR formation in poplar and generated informative gene co-expression networks that describe the basis of AR formation in these species.

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Fig. 1
Fig. 2
Fig. 3

adapted from the MAPK signaling pathway in the KEGG pathway. The gene expression levels in P. × euramericana (Pe) and P. simonii (Ps) of each time point during AR formation are shown in different columns in the colored grids, and the different rows represent the different genes. The colors indicate the levels of gene expression with red representing upregulation and blue representing downregulation. The gene expression levels of Pe and Ps during the different time points were normalized to 0 days after excision (DAE0) of the corresponding poplar species

Fig. 4

adapted from the phytohormone signaling pathways in the KEGG pathway. The gene expression levels in P. × euramericana (Pe) and P. simonii (Ps) of each time point during AR formation are shown in different columns in the colored grids, and the different rows represent the different genes. The colors indicate the levels of gene expression with red representing upregulation and blue representing downregulation. The gene expression levels of Pe and Ps during the different time points were normalized to 0 days after excision (DAE0) of the corresponding poplar species

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Acknowledgements

This Project was financially supported by the National Natural Science Foundation of China (NSFC accession No. 31901282), and the Fundamental Research Funds for the Central Universities (No. 2662019PY047).

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  1. College of Horticulture and Forestry Sciences, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China

    Jie Luo, Tashbek Nvsvrot & Nian Wang

  2. Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China

    Jie Luo & Nian Wang

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J. Luo and N. Wang designed experiments; J. Luo and T. Nvsvrot carried out experiments; J. Luo and N. Wang conducted the bioinformation analysis; J. Luo and N. Wang wrote and revised the manuscript; N. Wang supervised the entire work.

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Correspondence to Nian Wang.

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Luo, J., Nvsvrot, T. & Wang, N. Comparative transcriptomic analysis uncovers conserved pathways involved in adventitious root formation in poplar. Physiol Mol Biol Plants 27, 1903–1918 (2021). https://doi.org/10.1007/s12298-021-01054-7

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  • DOI: https://doi.org/10.1007/s12298-021-01054-7

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