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Ad hoc breeding of a genetically depauperate landrace of noble fir (Abies procera Rehder) using SNP genotyping via high-throughput targeted sequencing

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Abstract

Pedigree reconstruction via DNA markers and subsequent quantitative genetic analyses in production stands of trees is an alternative to traditional forest tree breeding. The method requires variable DNA markers; preferably cost-efficient to genotype. We tested the approach in breeding for Christmas tree traits in a Danish landrace of Abies procera. Initial analysis with simple sequence repeats (SSRs) revealed a substantial reduction in genetic diversity of Danish A. procera compared with direct imports from the USA, indicating a genetic bottleneck. Due to the reduced genetic variation, the SSRs were not variable enough for pedigree reconstruction, and 145 single nucleotide polymorphisms (SNPs) were therefore identified and genotyped via high-throughput targeted sequencing. In the field, we phenotypically selected 674 superior trees, based on criteria for good Christmas trees, among 21,000 trees in three Christmas tree plantations originating from an A. procera clonal seed orchard. By SNP-genotyping and parentage analysis, pedigree was reconstructed for the selected individuals, and genetic predictions for the Christmas tree traits were estimated. A final selection of 45 trees out of the 674 genotyped, based on an index of predicted values for different traits, foresees a gain in the Christmas tree score and branch angle score of 16% and 10%, respectively. The study clearly demonstrated the benefits of pedigree reconstruction, even though mass selection seemed to give similar gain. Primarily, the possibilities to control the level of inbreeding, and to check whether the production stands, from where we select trees, actually originate from the declared and desired parent pool.

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Acknowledgments

We would like to thank Poul Elgaard, HedeDanmark Seed, who has been a big part of the work of finding production stands, identifying plus tree candidates, and making all the practical arrangements. Thanks also go to the following persons: Gerner Frederiksen for measurements of phenotypic traits in the stands; Lene Hasmark Andersen, Juliane Sørensen, and Maria Meyhoff-Madsen for the needle preparations and DNA extractions; Lars Nørgård Hansen for collecting twigs for both DNA extractions as well as for N. neomacrospora tests; the owners of the production stands for their cooperation in the selection and marking of plus tree candidates as well harvest of scions for the new seed orchard. Furthermore, we are indebted to Foreningen Plan-Danmark, who made the start of this project possible by a donation to develop SNP markers and also to Dalgas Innovation for supporting the N. neomacrospora tests financially. Finally, we thank the associate editor and two anonymous reviewers for the valuable comments that improved the manuscript.

Data archiving statement

The data behind this study is stored at the data storage facility of the University of Copenhagen and can be downloaded from there: https://doi.org/10.17894/ucph.e9dea24d-48e0-42c5-a17f-8b149ffa5309

Funding

The majority of the project has been financed by the Green Development and Demonstration Program (Grønt Udviklings- og Demonstrationsprogram (GUDP)—grant number: 34009-13-0611) of the Danish Ministry of Food, Agriculture, and Fisheries.

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Authors and Affiliations

  1. Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark

    Ole K. Hansen, Jing Xu, Argelia Cuenca, Md. Shofiqul Islam & Ulrik Braüner Nielsen

  2. Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA

    Kurt Lamour

  3. Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA

    Ross Whetten

  4. National Institute of Aquatic Resources, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark

    Argelia Cuenca

  5. Noble Research Institute, LLC 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

    Md. Shofiqul Islam

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  1. Ole K. Hansen
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  3. Ross Whetten
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  4. Jing Xu
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  6. Md. Shofiqul Islam
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  7. Ulrik Braüner Nielsen
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Correspondence to Ole K. Hansen.

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Hansen, O.K., Lamour, K., Whetten, R. et al. Ad hoc breeding of a genetically depauperate landrace of noble fir (Abies procera Rehder) using SNP genotyping via high-throughput targeted sequencing. Tree Genetics & Genomes 16, 63 (2020). https://doi.org/10.1007/s11295-020-01460-0

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