Abstract
KEY MESSAGE: Using the full weight matrix and deregressed pedigree-based best linear unbiased predictions in second-stage models lead to selections and genomic predictions closer to those obtained using a single-stage model. In multi-environment genomic selection, although single-stage (SS) models are generally more efficient (no loss of information), there are contexts where they are difficult to fit, making two-stage models the most practical alternative. An example is the evaluation of early-stage observational trials (OTs) of sweetpotato breeding, where several clones are tested in unreplicated trials. In this study, 1,138 clones derived from partial diallels within two gene pools had their storage root yield evaluated across six OTs. Using this scenario, we compared the selection and prediction performances of models under different two-stage strategies against the SS benchmark. We also tested whether pool-specific genomic prediction models offered advantages over models trained with the complete dataset. Given the lack of replication in OTs, we hypothesized that deregressed best linear unbiased predictions (dBLUPs) or pedigree-based dBLUPs (dABLUPs) would work more appropriately as inputs for second-stage models than best linear unbiased estimates (BLUEs). These comparisons were conducted within weighted models using either a diagonal weight matrix or the full weight matrix. For selection, differences among second-stage models were minor, with a slight advantage for those using dABLUPs as entries, combined with the full weight matrix. For prediction, however, the choice of weighting scheme had a greater impact on performance than the choice of entry. Using the complete dataset, differences between entries were marginal, but for pool-specific predictions, dABLUPs provided the best performance. Overall, if adopting a two-stage strategy for the analysis of augmented trials, we recommend using dABLUPs together with the full weight matrix.
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Claims 7
Claim · model-written summary
Using the full weight matrix and dABLUPs in second-stage models gave selections and genomic predictions closer to those of a single-stage model.
- Taxon
- sweetpotato
_Flower.jpg?width=60)
Ipomoea batatast0 - Outcome
- selections and genomic predictions closer to those obtained using a single-stage modele1
- Comparator
- single-stage modele1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
_Flower.jpg?width=500)
Verbatim
e1“Using the full weight matrix and deregressed pedigree-based best linear unbiased predictions in second-stage models lead to selections and genomic predictions closer to those obtained using a single-stage model”
t0“sweetpotato”
Claim · model-written summary
For selection, differences among second-stage models were minor.
- Taxon
- sweetpotatoIpomoea batatast0
- Outcome
- differences among second-stage modelse1
- Value
- minore1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“For selection, differences among second-stage models were minor”
t0“sweetpotato”
Claim · model-written summary
For selection, second-stage models using dABLUPs as entries combined with the full weight matrix had a slight advantage.
- Taxon
- sweetpotatoIpomoea batatast0
- Outcome
- advantage for those using dABLUPs as entriese1
- Value
- slight advantagee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“a slight advantage for those using dABLUPs as entries, combined with the full weight matrix”
t0“sweetpotato”
Claim · model-written summary
For prediction, the choice of weighting scheme had a greater impact on performance than the choice of entry.
- Taxon
- sweetpotatoIpomoea batatast0
- Outcome
- impact on performancee1
- Direction
- greatere1
- Comparator
- the choice of entrye1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“For prediction, however, the choice of weighting scheme had a greater impact on performance than the choice of entry”
t0“sweetpotato”
Claim · model-written summary
Using the complete dataset, differences between entries in prediction were marginal.
- Taxon
- sweetpotatoIpomoea batatast0
- Outcome
- differences between entriese1
- Value
- marginale1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Using the complete dataset, differences between entries were marginal”
t0“sweetpotato”
Claim · model-written summary
For pool-specific predictions, dABLUPs provided the best performance.
- Taxon
- sweetpotatoIpomoea batatast0
- Outcome
- performancee1
- Value
- best performancee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“for pool-specific predictions, dABLUPs provided the best performance”
t0“sweetpotato”
Claim · model-written summary
The authors recommend using dABLUPs together with the full weight matrix when adopting a two-stage strategy for augmented trials.
- Taxon
- sweetpotatoIpomoea batatast0
- Outcome
- dABLUPs together with the full weight matrixe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we recommend using dABLUPs together with the full weight matrix”
t0“sweetpotato”