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Restricting coancestry and inbreeding at a specific position on the genome by using optimized selection
T Roughsedge1, R Pong-Wong, J A Woolliams
1Sustainable Livestock Systems, SAC, West Mains Road, Edinburgh EH9 3JG, UK. tim.roughsedge@sac.ac.uk
Genetics Research
|April 23, 2008
Summary
Genetic selection methods aim to increase genetic gain while controlling inbreeding. Using genetic markers helps manage inbreeding around quantitative trait loci (QTLs), but requires random selection to restore expected relationships.
Area of Science:
- Quantitative genetics
- Animal breeding
- Population genetics
Background:
- Maximizing genetic gain while constraining inbreeding is a key goal in animal breeding.
- Pedigree-based coancestry is commonly used to control the rate of inbreeding.
- Mixed inheritance models involve segregating quantitative trait loci (QTLs) alongside polygenes.
Purpose of the Study:
- To investigate the effectiveness of selection methodologies in managing inbreeding rates around QTLs.
- To evaluate the impact of using genetic markers in relationship matrices for inbreeding control.
- To understand the relationship between group coancestry and realized inbreeding rates in mixed models.
Main Methods:
- Utilized the numerator relationship matrix computed from pedigree to constrain group coancestry.
- Incorporated genetic markers into the relationship matrix calculation for inbreeding control near QTLs.
- Applied mixed inheritance models with segregating QTLs and polygenes.
Main Results:
- Inbreeding rates around QTLs exceeded desired levels when using pedigree-based coancestry alone.
- Using marker-based relationship matrices reduced inbreeding at constraint positions below expected levels.
- Marker-based selection enabled choosing individuals with low/zero relationships due to homozygous alternative alleles, increasing offspring heterozygosity.
Conclusions:
- Standard pedigree-based methods are insufficient for controlling inbreeding around QTLs in mixed models.
- Genetic markers improve inbreeding control but alter the expected relationship between coancestry and inbreeding.
- A generation of random selection is necessary to realign realized inbreeding with coancestry expectations.
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