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Differential gene expression in Eucalyptus clones in response to nutrient deficiency

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Abstract

We evaluated differential expression of genes in leaf and xylem tissues for three Eucalyptus clones in the field using Illumina sequencing, under four contrasting fertilization regimes: a control combining nitrogen (N), phosphorus (P), and potassium (K) and three regimes with N, K, and P deficiency. The field results showed significantly better performance with a control fertilizing regime for height and circumference at 14 months, but no differences between clones. The number of up and down regulated DEG (differentially expressed genes) in pairwise clone comparisons was around 5900 for leaf and 6900 for xylem at FDR < 0.01. With fertilization treatment comparisons, DEG were only observed for N deficiency versus control with 45 up and down-regulated DEG for leaf and 1022 for xylem. The number of DEGs between fertilizer deficiency treatment and control varied greatly within each clone showing important clone by fertilization interaction. Gene ontology analysis showed that a great number of genes were related to stress, transport, and transcription factors. The co-expression analysis showed some significant correlations between complex network gene expression and tree growth induced by fertilization regime. For example, the co-expression of a 54 DEG network showed a significant correlation with tree height (0.84, P value: 1e−04) and DBH (0.89, P value: 7e−06) in the case of N deficiency versus control. Our results suggest that gene expression levels between different fertilization treatments and clones can provide a basis for future research on gene function in Eucalyptus under nutrient stress with the perspective of new development in Eucalyptus breeding.

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Data availability

The data was deposited in NCBI database under BioProject accession number PRJNA627686 and BioSamples (SAMN14669553-SAMN14669610) at NCBI Short Read Archive (SRA). All raw data and analysis data are present in the supplemental material S2.

Change history

  • 22 July 2022

    Handling editor name correction.

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Acknowledgements

The authors are thankful to CIRAD (the French Agricultural Research Centre for International Development) during analysis and visits to their facility and IBTEC (Biotechnology Institute of Unesp) and FCA (Faculty of Agronomy Sciences, UNESP) for all its support in field.

Funding

This work has been carried out through funding by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES), in the scope of Programa Capes-PrInt,—Funding code: 001 “Process: 88887.194785/2018–00.” Also, this work was supported by funding from the different partners associated in the collaborative project: Cirad, Instituto de Biotecnologia (IBTEC), UNESP—Faculdade de Ciências Agronômicas, Departamento de Solos e Recursos Ambientais and Departamento de Ciência Florestal, UNESP.

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Author notes

  1. Bruno Cesar Rossini and Jean-Marc Bouvet contributed equally to this work.

Authors and Affiliations

  1. Departamento de Ciências Químicas E Biológicas, Instituto de Biociências, UNESP - Univ Estadual Paulista, Botucatu, SP, Brazil

    Bruno Cesar Rossini & Celso Luis Marino

  2. Instituto de Biotecnologia (IBTEC), UNESP - Univ Estadual Paulista, Alameda das Tecomarias, s/n. Chácara Capão Bonito, Botucatu, SP, 18607-440, Brazil

    Bruno Cesar Rossini & Celso Luis Marino

  3. AGAP, Univ Montpellier, CIRAD, INRA, and Montpellier SupAgro, Montpellier, France

    Jean-Marc Bouvet & Julien Frouin

  4. UMR AGAP, DGD-RS, CIRAD, Avenue Val de Montferrand, 34198, Montpellier, France

    Jean-Marc Bouvet & Julien Frouin

  5. FCA (Faculdade de Ciências Agronômicas Departamento de Ciência Florestal, Solos e Ambiente, UNESP Univ Estadual Paulista “Júlio de Mesquita Filho”, São Paulo, Brazil

    Iraê Amaral Guerrini, Talitha Casella Moreira de Freitas & Magali Ribeiro da Silva

  6. Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France

    Jean-Pierre Bouillet & Jean-Paul Laclau

  7. UMR Ecoa&Sols, CIRAD, 2 Place Viala, 34060, Montpellier, France

    Jean-Pierre Bouillet & Jean-Paul Laclau

Authors
  1. Bruno Cesar Rossini
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  2. Jean-Marc Bouvet
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  3. Julien Frouin
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  4. Iraê Amaral Guerrini
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  6. Magali Ribeiro da Silva
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  7. Jean-Pierre Bouillet
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  9. Celso Luis Marino
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Contributions

BCR, JF, TCMF, and MRS carried out the field experiments. BCR, JF, and TCMF performed the laboratory work of the research. BCR, JF, and JMB developed the cDNA genomic library. BCR, JF, and JMB performed analyses. BCR and JMB wrote the manuscript. JMB, JPL, JPB, IAG, and CLM designed the experiments, supervised the research, and reviewed the manuscript. JMB, BR, and JPL revised the manuscript.

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Correspondence to Bruno Cesar Rossini.

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Communicated by A.M. Dandekar

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Rossini, B.C., Bouvet, JM., Frouin, J. et al. Differential gene expression in Eucalyptus clones in response to nutrient deficiency. Tree Genetics & Genomes 18, 14 (2022). https://doi.org/10.1007/s11295-022-01546-x

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  • DOI: https://doi.org/10.1007/s11295-022-01546-x

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