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A simulation study on the effect of nested vs factorial mating on response to pedigree and genomic selection
Objective was to investigate the effect of nested vs factorial mating on genetic gain and inbreeding (F) in 10 generations (G) of selection. Phenotypes and marker genotypes were simulated following 850 generations of random mating in a population of size 500 (G0-800) and 100 (G801-850) to generate linkage disequilibrium between loci. The trait was controlled by 500 QTL randomly distributed across 20 chromosomes (30 Morgans), and genomic selection was based 50,000 randomly-distributed SNPs. QTL effects were from a Normal distribution and scaled to simulate a heritability of 0.1, 0.3 or 0.5. The QTL and marker loci were chosen to have minor allele frequency ≥ 0.01. Selection based on pedigree (BLUP) or genomic EBV started in G851. Genomic EBVs were predicted using GenSel-BayesB with training data from all previous generation(s). Three mating designs were compared; the first was nested mating each with 90 sires mated to 6 dams (90 mating groups); the second and third were partial factorial designs with random mating of 5 sires with 30 dams in each of 18 groups or 10 sires and 60 dams in each of 9 groups. In the designs, full- and half-sib matings were avoided and in the factorial designs a dam was allowed to mate with more than 1 sire. Each generation, 1,350 male progeny without records and 2,700 female progeny with records were simulated. Based on EBV, the top 90 males and 540 females were selected to be parents of the next generation. The average EBV, true BV, accuracy and pedigree-based F were computed from 100 replicates for each design (Table). Results were consistent for three levels of heritability. After 10 generations of pedigree or genomic selection, F was significantly higher (P < 0.05) for the nested than for the factorial designs. The mating systems had no significant effect on response to either pedigree or genomic selection, but genomic selection had greater response and less inbreeding than pedigree selection.
| Table. Estimates of F, EBV, true BV (± SE) and accuracy in G861 for heritability 0.3 |
|
Pedigree Selection |
Genomic Selection |
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|
90 Groups |
18 Groups |
9 Groups |
90 Groups |
18 Groups |
9 Groups |
F % |
8.2 ± 0.1 |
6.3 ± 0.1 |
6.2 ± 0.1 |
2.6 ± 0.0 |
2.3 ± 0.0 |
2.2 ± 0.0 |
EBV |
4.53 ± 0.03 |
4.48 ± 0.03 |
4.48 ± 0.03 |
6.47 ± 0.10 |
6.39 ± 0.10 |
6.49 ± 0.10 |
True BV |
4.55 ± 0.06 |
4.50 ± 0.06 |
4.50 ± 0.06 |
6.42 ± 0.10 |
6.39 ± 0.10 |
6.39 ± 0.10 |
Accuracy |
0.540 |
0.525 |
0.530 |
0.852 |
0.850 |
0.849 |
Keywords: factorial mating, genomic selection, nested mating