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Association genetics of wood traits in European black poplar (Populus nigra L.)

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Abstract

An association genetics approach was used to examine individual genes and alleles at several loci responsible for complex traits controlling wood traits (cellulose, lignin, and 6C sugar) in European black poplar (Populus nigra). Due to fast growth, clonal propagation and availability of genomic resources have allowed us to investigate further genetic control of wood traits in the species. From thirty-nine candidate genes, 384 SNPs were successfully genotyped in a clonally replicated 288 P. nigra clone population. Only 50.5% of these markers were polymorphic that could be used in association mappings.

The association population (4 ramets per clone) was phenotyped for cellulose, lignin, and 6C sugar contents. Moderately high heritabilities were observed for cellulose and 6C sugar while it was low in lignin. Furthermore, a moderately strong and positive genetic correlation was found between cellulose and lignin which may hinder genetic improvement in cellulose content due to the correlated response on lignin. The LD, across all candidate genes, showed a rapid decay with physical distance. Single-marker-based association tests using GLM and MLM models were implemented to identify associations for cellulose, lignin, and 6C sugar contents.

Eleven unique single marker associations for cellulose, 5 for lignin, and 6C sugar contents were identified from 39 candidate genes, but only one marker for cellulose content (CesA3A-15-456) had a significant association with cellulose and with dominant gene effect after multiple test correction was applied. The percent of total variation explained by significant single marker associations ranged from 3 to 9.2% in cellulose, 2.8 to 3.8% in lignin, and 3.2–5.5% in  6C sugar contents, respectively. Given the rapid decay of within-gene linkage disequilibrium, limitation of sample size, overcorrection for false positives, and intensity of phenotypic selection, it is likely that some of these single marker associations are genuine and deserve to be further investigated with a larger and diverse study population.

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Data availability

Datasets which were not already publicly available at the time of submission will be deposited to The Species database of Tree Genes database (http://treegenesdb.org) upon the acceptance of the paper.

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Acknowledgements

We thank Vanessa Rashbrook for performing the SNP genotyping and J. Liechty and B. Figueroa for bioinformatics support. The help of F. P. Guerra on data formatting for association genetic analysis is also appreciated. The study materials and test sites were made available to us by The General Directorate of Forestry, Turkish Ministry of Agriculture and Forestry. The preliminary results on SNP diversity of candidate genes and linkage disequilibrium were presented as poster presentation at PAGXXI. The wood traits related phenotypic data collected as part of the project TOVAG-110O570 and were subject of Bircan Taşkıran’s Master of Science Thesis and available for the study. We also express our gratitude to the Fulbright Scholar Program for offering Prof. Z. Kaya a research grant at UC-Davis, CA, USA in 2022.

Code availability

The name, version, and parameters of the software used in this study are described in the “Materials and methods” section.

Funding

Funding for this project was made by the Scientific and Technological Council of Turkey (project number: TOVAG-110O570) granted to Zeki Kaya as principal investigator.

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Authors and Affiliations

  1. Department of Biological Sciences, Middle East Technical Universities, Ankara, Turkey

    Zeki Kaya, Bircan Taşkıran, Asiye Uluğ & Aysun D. Güvendiren

  2. Department of Plant Sciences, University of California, Davis, CA, USA

    Zeki Kaya, Jill L. Wegrzyn & David B. Neale

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  1. Zeki Kaya
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  5. Jill L. Wegrzyn
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Contributions

Data analysis and writing the manuscript: ZK; Wood trait data collection: BT; DNA extraction and population structure analysis: ADG, AU; SNP markers and data management: JLW; Review and editing of the manuscript and hosting ZK: DBN

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Correspondence to Zeki Kaya.

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Kaya, Z., Taşkıran, B., Uluğ, A. et al. Association genetics of wood traits in European black poplar (Populus nigra L.). Tree Genetics & Genomes 19, 38 (2023). https://doi.org/10.1007/s11295-023-01612-y

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