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Quantitative trait loci related to growth and wood quality traits in Eucalyptus grandis W. Hill identified through single- and multi-trait genome-wide association studies

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Abstract

The aim of this study was to conduct single- and multi-trait genome wide association studies (GWAS) and identify quantitative trait loci (QTLs) for the expression of phenotypic traits in Eucalyptus grandis. We evaluated an open-pollinated breeding population with 1772 genotypes composed of 25 different families established using a randomized complete block design. We performed single-trait GWAS using the fixed and random model circulating probability unification (FarmCPU) and multi-trait GWAS for genetically correlated phenotypic traits using the multi-trait mixed model (MTMM). Then, gene annotation was identified through the Phytozome database. The FarmCPU model identified 43 and 38 QTLs that are significantly associated with growth and wood quality traits, respectively. Similarly, 40 pleiotropic QTLs were discovered using the MTMM model. Gene ontology for single-trait analysis identified loci responsible for regulating several important biological processes in different tissues and at different stages of maturation. On the other hand, the multi-trait model identified loci associated with gibberellin signaling, which regulates several aspects of plant growth and development, as well as loci related to the reinforcement of cell wall composition. Our study demonstrates the complex nature of E. grandis quantitative traits and provides new evidence of loci not described before which are associated with the expression of important phenotypic traits.

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Acknowledgements

We acknowledge Suzano S.A. for providing the phenotypic and genotypic data.

Funding

This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior — Brasil (CAPES) — Finance Code 001. The German Academic Exchange Service (DAAD) co-financed a short-term research grant (ref. no.: 91781916). Evandro V. Tambarussi is supported by a research productivity fellowship (grant number 304899/2019–4) and Post-Doctoral Scholarship (grant number 200727/2020–6) from “Conselho Nacional de Desenvolvimento Científico e Tecnológico” (CNPq).

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Authors and Affiliations

  1. Department of Forest Science, FCA/UNESP, São Paulo State University, Botucatu, Sao Paulo, Brazil

    Lucas Fernandes Rocha & Evandro Vagner Tambarussi

  2. SUZANO S.A, Salvador, Bahia, Brazil

    Thiago Romanos Benatti, Leandro de Siqueira, Izabel Christina Gava de Souza, Isadora Bianchin, Aguinaldo José de Souza, Aline Cristina Miranda Fernandes, Shinitiro Oda & José Luiz Stape

  3. “Luiz de Queiroz” College of Agriculture, Department of Genetics, (ESALQ/USP), University of São Paulo, Piracicaba, Brazil

    Rafael Massahiro Yassue

  4. Universidad Politécnica de Madrid, 28040, Madrid, Spain

    Humberto Fanelli Carvalho

  5. Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany

    Niels A. Müller & Matthias Fladung

  6. North Carolina State University, NCSU, Raleigh, USA

    Juan Jose Acosta

  7. H. Rouse Caffey Rice Research Station - LSUAgCenter, Baton Rouge, LA, USA

    Roberto Fritsche-Neto

  8. Department of Forest Engineering, State University of the Central-West, Irati, PR, Brazil

    Evandro Vagner Tambarussi

  9. “Luiz de Queiroz” College of Agriculture, Department of Forest Sciences, University of Sao Paulo, Sao Paulo, Piracicaba, Brazil

    Evandro Vagner Tambarussi

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  1. Lucas Fernandes Rocha
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  16. Evandro Vagner Tambarussi
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Contributions

LFR conceptualization, methodology, software, formal analysis and writing — original draft. TRB conceptualization, resources, visualization, investigation and writing — review & editing. LS conceptualization, resources, visualization and funding acquisition. ICGS conceptualization, visualization, resources and methodology. AJS methodology and visualization. ACMF methodology, software and writing — original draft. SO methodology, conceptualization and visualization. JLS conceptualization and methodology. RMY methodology and visualization. HFC methodology, software, formal analysis and writing — original draft. NAM methodology, software, formal analysis and writing — original draft. MF methodology, software, formal analysis and writing — original draft. JJA methodology, software, formal analysis and writing — original draft. RFN methodology, software, formal analysis and writing — original draft. EVT writing — review and editing, visualization, supervision and project administration.

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Correspondence to Evandro Vagner Tambarussi.

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Rocha, L.F., Benatti, T.R., de Siqueira, L. et al. Quantitative trait loci related to growth and wood quality traits in Eucalyptus grandis W. Hill identified through single- and multi-trait genome-wide association studies. Tree Genetics & Genomes 18, 38 (2022). https://doi.org/10.1007/s11295-022-01570-x

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