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Whole-genome versus per-chromosome targeted recombination: Simulations and predicted gains in maize with an integer
John N Cameron1, Rex Bernardo2
1Bayer Crop Science, Chesterfield, Missouri, USA.
The Plant Genome
|September 5, 2023
Summary
Whole-genome targeted recombination, using an integer programming model, increases predicted genetic gains in maize (Zea mays L.) more than per-chromosome methods. This approach optimizes recombination placement for enhanced breeding outcomes.
Area of Science:
- Plant breeding and genetics
- Quantitative genetics
- Bioinformatics and computational biology
Background:
- Per-chromosome targeted recombination aims to double genetic gains in biparental populations by focusing on specific marker intervals.
- Previous studies on targeted recombination's effectiveness may have overestimated gains due to methodological assumptions.
Purpose of the Study:
- To develop and evaluate an integer programming model for optimizing whole-genome targeted recombination placement.
- To compare whole-genome versus per-chromosome targeted recombination strategies in maize (Zea mays L.) for predicted genetic gains.
Main Methods:
- Developed an integer programming model to determine optimal recombination locations across the entire genome.
- Compared whole-genome and per-chromosome targeted recombination strategies using 392 biparental maize populations and simulation experiments.
- Assessed predicted gains for yield, moisture, test weight, and a simulated trait controlled by 2000 quantitative trait loci (QTL).
Main Results:
- Whole-genome targeted recombination yielded 8%-9% greater predicted genetic gains than per-chromosome methods for 10 targeted recombinations.
- Recombination frequency in whole-genome strategy correlated with chromosome size (r = 0.76-0.91).
- Simulations indicated overestimation of gains by ~20% compared to non-targeted recombination and a 25%-33% reduction in response when using marker effects as QTL proxies.
Conclusions:
- The developed integer programming model effectively increases predicted and true genetic gains from targeted recombination.
- Predicted gains from targeted recombination may overestimate actual gains, particularly when using genomewide marker effects as proxies for unknown QTL.
- Optimizing recombination distribution across the whole genome is crucial for maximizing breeding efficiency in maize.
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