Abstract
Breeders have long appreciated the need to balance selection for short-term genetic gain with maintaining genetic variance for long-term gain. For outbred populations, the method called optimum contribution selection (OCS) chooses parental contributions to maximize the average breeding value at a prescribed inbreeding rate. With optimum mate allocation (OMA), the contribution of each mating is optimized, which allows for specific combining ability due to dominance. To enable OCS and OMA in polyploid species, new theoretical results were derived to (1) predict midparent heterosis due to dominance and (2) control inbreeding in a population of arbitrary ploidy. A new convex optimization framework for OMA, named COMA, was developed and released as public software. Under stochastic simulation of a genomic selection program, COMA maintained a target inbreeding rate of 0.5% using either pedigree or genomic IBD (identity-by-descent) kinship. Significantly more genetic gain was realized with pedigree kinship, which is consistent with previous studies showing the selective advantage of an individual under OCS is dominated by its Mendelian sampling term. Despite the higher accuracy (+0.2-0.3) when predicting mate performance with OMA compared with OCS, there was little long-term gain advantage. The sparsity of the COMA mating design and flexibility to incorporate mating constraints offer practical incentives over OCS. In a potato breeding case study with 170 candidates, the optimal solution at 0.5% inbreeding involved 43 parents but only 43 of the 903 possible matings.
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Claims 7
Claim · model-written summary
COMA maintained a target inbreeding rate of 0.5% under simulation using pedigree or genomic IBD kinship.
- Taxon
- potato
Solanum tuberosume2 - Outcome
- target inbreeding ratee1
- Value
- 0.5%e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Under stochastic simulation of a genomic selection program, COMA maintained a target inbreeding rate of 0.5% using either pedigree or genomic IBD (identity-by-descent) kinship”
e2“In a potato breeding case study with 170 candidates, the optimal solution at 0.5% inbreeding involved 43 parents but only 43 of the 903 possible matings”
Claim · model-written summary
Significantly more genetic gain was realized with pedigree kinship than with genomic IBD kinship.
- Taxon
- potatoSolanum tuberosume2
- Treatment
- pedigree kinshipe3
- Outcome
- genetic gaine3
- Direction
- moree3
- Comparator
- genomic IBD (identity-by-descent) kinshipe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Under stochastic simulation of a genomic selection program, COMA maintained a target inbreeding rate of 0.5% using either pedigree or genomic IBD (identity-by-descent) kinship”
e2“In a potato breeding case study with 170 candidates, the optimal solution at 0.5% inbreeding involved 43 parents but only 43 of the 903 possible matings”
e3“Significantly more genetic gain was realized with pedigree kinship”
Claim · model-written summary
OMA gave higher accuracy (+0.2-0.3) than OCS when predicting mate performance.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“In a potato breeding case study with 170 candidates, the optimal solution at 0.5% inbreeding involved 43 parents but only 43 of the 903 possible matings”
e4“Despite the higher accuracy (+0.2-0.3) when predicting mate performance with OMA compared with OCS, there was little long-term gain advantage”
Claim · model-written summary
OMA gave little long-term gain advantage over OCS.
- Taxon
- potatoSolanum tuberosume2
- Outcome
- long-term gain advantagee4
- Qualifier
- littlee4
- Comparator
- OCSe4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“In a potato breeding case study with 170 candidates, the optimal solution at 0.5% inbreeding involved 43 parents but only 43 of the 903 possible matings”
e4“Despite the higher accuracy (+0.2-0.3) when predicting mate performance with OMA compared with OCS, there was little long-term gain advantage”
Claim · model-written summary
The sparse COMA mating design and flexible mating constraints offer practical incentives over OCS.
- Taxon
- potatoSolanum tuberosume2
- Outcome
- practical incentivese5
- Comparator
- OCSe5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“In a potato breeding case study with 170 candidates, the optimal solution at 0.5% inbreeding involved 43 parents but only 43 of the 903 possible matings”
e5“The sparsity of the COMA mating design and flexibility to incorporate mating constraints offer practical incentives over OCS”
Claim · model-written summary
The optimal solution at 0.5% inbreeding involved 43 parents in the potato case study.
- Taxon
- potatoSolanum tuberosume2
- Outcome
- optimal solutione2
- Value
- 43 parentse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“In a potato breeding case study with 170 candidates, the optimal solution at 0.5% inbreeding involved 43 parents but only 43 of the 903 possible matings”
Claim · model-written summary
The optimal solution at 0.5% inbreeding involved only 43 of the 903 possible matings in the potato case study.
- Taxon
- potatoSolanum tuberosume2
- Outcome
- matingse2
- Value
- 43 of the 903 possible matingse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“In a potato breeding case study with 170 candidates, the optimal solution at 0.5% inbreeding involved 43 parents but only 43 of the 903 possible matings”