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Comparison of genetic parameters from marker-based relationship, sibship, and combined models in Scots pine multi-site open-pollinated tests

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Abstract

Nine microsatellite DNA markers (simple sequence repeats, SSRs) were used to estimate pairwise relationships among 597 Scots pine (Pinus sylvestris) trees as well as to generate a sibship structure for quantitative genetic parameters’ estimation comparison. The studied trees were part of an open-pollinated progeny test of 102 first-generation parents. Three methods were used to estimate variance components and heritabilities, namely, structured pedigree (half- and full-sib), marker-based pairwise relationships (four pairwise estimators), and a combined pedigree and marker-based relationship. In each of the three methods, the same animal model was used to compute variances except when marker-based relationship was used wherein we substituted the average numerator relationship matrix (i.e., pedigree-based matrix) with that computed based on markers’ pairwise relationships. Our results showed a high correlation in estimated breeding values between the pedigree (full-sib) and the combined marker-pedigree estimates. The marker-based relationship method produced high correlations when individual site data were analyzed. In contrast, the marker-based relationship method resulted in a significant decrease in both variance estimation and their standard errors which were in concordance with earlier published results; however, no estimates were produced when across-site analyses were attempted. We concluded that the combined pedigree method is the best approach as it represents the historical (pairwise) and contemporary (pedigree) relationships among the tested individuals, a situation that cannot be attained by any of the used methods individually. This method is dependent on the number and informativeness of the markers used.

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Acknowledgments

We would like to thank to T. Funda for his help with the selection of Scots pine primers. Funds from the NAZV (research grants no. QH81172 and QH81160) and the TAČR (grant no. TA01020512) to M. Lstibůrek and J. Kobliha and from the Natural Sciences and Engineering Research Council of Canada, Industrial Applied Forest Genetics and Biotechnology to Y. A. El-Kassaby, and partial support provided by USDA Forest Service, Southern Research Station through Cooperative Agreement SRS-05-IC-11330126-234 are hugely appreciated.

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Authors and Affiliations

  1. Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Praha, Czech Republic

    Jiří Korecký, Jaroslav Klápště, Milan Lstibůrek & Jaroslav Kobliha

  2. Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada

    Jaroslav Klápště & Yousry A. El-Kassaby

  3. Southern Institute of Forest Genetics, USDA Forest Service, Southern Research Station, 23332 Success Road, Saucier, MS, 39574-9344, USA

    C. Dana Nelson

Authors
  1. Jiří Korecký
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  2. Jaroslav Klápště
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  3. Milan Lstibůrek
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  4. Jaroslav Kobliha
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  5. C. Dana Nelson
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  6. Yousry A. El-Kassaby
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Corresponding author

Correspondence to Yousry A. El-Kassaby.

Additional information

Communicated by Y. Tsumura

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplement 1

Information pertaining to the PIC (Polymorphic Information Content) per SSR locus across the nine loci. (DOC 32 kb)

Supplement 2

Assignments of 597 individuals Scots pine into 30 maternal/maternal trees. Figure was generated by software COLONY (Jones and Wang 2010) (DOC 304 kb)

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Korecký, J., Klápště, J., Lstibůrek, M. et al. Comparison of genetic parameters from marker-based relationship, sibship, and combined models in Scots pine multi-site open-pollinated tests. Tree Genetics & Genomes 9, 1227–1235 (2013). https://doi.org/10.1007/s11295-013-0630-z

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  • DOI: https://doi.org/10.1007/s11295-013-0630-z

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