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Modelling of population structure through contemporary groups in genetic evaluation
Jaroslav Klápště1, Mari Suontama2,3, Heidi S Dungey2
1Scion (New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3010, New Zealand. Jaroslav.Klapste@scionresearch.com.
BMC Genetics
|October 26, 2019
Summary
Accurately estimating genetic parameters in forest trees requires considering mating dynamics. A novel approach using phantom contemporary groups improved model fit and breeding value accuracy for wind-pollinated species.
Area of Science:
- Forestry
- Quantitative Genetics
- Plant Breeding
Background:
- Forest trees exhibit high genetic variability due to wide geographic distribution and environmental heterogeneity.
- Wind pollination in conifers facilitates extensive gene flow, potentially leading to maladaptation to local environments.
- Quantitative analyses, such as provenance/progeny tests, are crucial for obtaining unbiased genetic parameters by accounting for population differences.
Purpose of the Study:
- To investigate the impact of modeling mating dynamics on the accuracy of genetic parameter estimation in forest trees.
- To evaluate the effectiveness of different approaches for incorporating the provenance effect within mixed models.
- To improve the accuracy of breeding values by refining the modeling of contemporary genetic groups.
Main Methods:
- Utilized quantitative analyses of provenance/progeny tests.
- Implemented mixed model frameworks to analyze genetic data.
- Developed and tested a 'phantom contemporary group' for the paternal side of the pedigree to account for differential pollen genetic quality.
Main Results:
- Using a provenance effect as a fixed term or identical contemporary groups on both sides of the pedigree yielded similar precision of genetic parameters.
- A phantom contemporary group, accounting for varying pollen genetic quality, significantly improved model fit and breeding value accuracy.
- The refined model demonstrated increased accuracy in estimating genetic parameters relevant to local adaptation.
Conclusions:
- Modeling mating dynamics and gene flow vectors is essential for accurate contemporary genetic group estimation in mixed models.
- This approach is particularly vital for obtaining unbiased genetic parameters in traits related to local adaptation in forest trees.
- The use of phantom contemporary groups offers a promising method for enhancing the precision of genetic evaluations in wind-pollinated species.
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