Optimizing Genomic Parental Selection for Categorical and Continuous–Categorical Multi-Trait Mixtures
Abstract
:1. Introduction
2. Materials and Methods
2.1. General Structure of Phenotypic and Genomic Data
2.2. General Model Formulation
2.3. Categorical Multi-Trait (CM)
2.4. Continuous–Categorical Multi-Trait Mixtures (CCMM)
2.4.1. Posterior Predictive Distribution and Posterior Expected Loss
2.4.2. Simulation Study
2.4.3. Experimental Data
3. Results
3.1. Simulated Data
3.2. Experimental Data
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
References
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CM: Categorical Multi-Trait | ||||||||
---|---|---|---|---|---|---|---|---|
Trait | Type | Category | Notation | Goal | Achieved | Average % Change | Achieved | Average % Change |
1 | Categorical | 1 | T1C1 | Decrease | Yes | −5.36 | Yes | −2.95 |
1 | Categorical | 2 | T1C2 | Increase/decrease | Yes | 6.65 | No | 4.39 |
1 | Categorical | 3 | T1C3 | Increase | Yes | 2.47 | Yes | −4.72 |
2 | Categorical | 1 | T2C1 | Decrease | Yes | −21.93 | Yes | −42.62 |
2 | Categorical | 2 | T2C2 | Increase/decrease | Yes | 8.72 | Yes | 9.09 |
2 | Categorical | 3 | T2C3 | Increase | Yes | 31.06 | Yes | 84.84 |
3 | Categorical | 1 | T3C1 | Decrease | Yes | −71.97 | Yes | −95.29 |
3 | Categorical | 2 | T3C2 | Increase/decrease | Yes | −38.96 | Yes | −71.58 |
3 | Categorical | 3 | T3C3 | Increase | Yes | 47.47 | Yes | 74.45 |
CCMM: Continuous–Categorical Multi-trait Mixture | ||||||||
Trait | Type | Category | Notation | Goal | Achieved | Average % change | Achieved | Average % change |
1 | Continuous | - | T1 | Increase | Yes | 23.96 | Yes | 50.77 |
2 | Continuous | - | T2 | Increase | Yes | 185.26 | Yes | 572.10 |
3 | Categorical | 1 | T3C1 | Decrease | Yes | −56.32 | Yes | −85.88 |
3 | Categorical | 2 | T3C2 | Increase/Decrease | Yes | −5.19 | Yes | −39.03 |
3 | Categorical | 3 | T3C3 | Increase | Yes | 100.61 | Yes | 246.36 |
Trait 2 Category 3, = 0.3 | |||||||||
---|---|---|---|---|---|---|---|---|---|
p-Value = 2.14 × 10−6 from the Kruskal–Wallis Test | |||||||||
p-Values from the Mann–Whitney U Test Using the Bonferroni Correction | |||||||||
Cycle 1 | Cycle 2 | Cycle 3 | Cycle 4 | Cycle 5 | Cycle 6 | Cycle 7 | Cycle 8 | Cycle 9 | |
Cycle 2 | NS | ||||||||
Cycle 3 | NS | NS | |||||||
Cycle 4 | NS | NS | NS | ||||||
Cycle 5 | NS | NS | NS | NS | |||||
Cycle 6 | NS | NS | NS | NS | NS | ||||
Cycle 7 | NS | NS | NS | NS | NS | NS | |||
Cycle 8 | NS | NS | NS | NS | NS | NS | NS | ||
Cycle 9 | S | S | NS | NS | NS | NS | NS | NS | |
Cycle 10 | S | S | NS | S | NS | NS | NS | NS | NS |
Trait 3 Category 3, = 0.3 | |||||||||
p-value = 7.5510−29 from the Kruskal–Wallis test | |||||||||
p-values from the Mann–Whitney U test using the Bonferroni correction | |||||||||
Cycle 1 | Cycle 2 | Cycle 3 | Cycle 4 | Cycle 5 | Cycle 6 | Cycle 7 | Cycle 8 | Cycle 9 | |
Cycle 2 | S | ||||||||
Cycle 3 | S | S | |||||||
Cycle 4 | S | S | NS | ||||||
Cycle 5 | S | S | NS | NS | |||||
Cycle 6 | S | S | S | NS | NS | ||||
Cycle 7 | S | S | S | S | NS | NS | |||
Cycle 8 | S | S | S | S | S | NS | NS | ||
Cycle 9 | S | S | S | S | S | S | NS | NS | |
Cycle 10 | S | S | S | S | S | S | S | NS | NS |
Trait 2 Category 3, = 0.6 | |||||||||
p-Value = 3.90 × 10−23 from the Kruskal–Wallis Test | |||||||||
p-Values from the Mann–Whitney U Test Using the Bonferroni Correction | |||||||||
Cycle 1 | Cycle 2 | Cycle 3 | Cycle 4 | Cycle 5 | Cycle 6 | Cycle 7 | Cycle 8 | Cycle 9 | |
Cycle 2 | NS | ||||||||
Cycle 3 | S | NS | |||||||
Cycle 4 | S | S | NS | ||||||
Cycle 5 | S | S | S | NS | |||||
Cycle 6 | S | S | S | NS | NS | ||||
Cycle 7 | S | S | S | NS | NS | NS | |||
Cycle 8 | S | S | S | S | NS | NS | NS | ||
Cycle 9 | S | S | S | S | S | S | NS | NS | |
Cycle 10 | S | S | S | S | S | NS | NS | NS | NS |
Trait 3 Category 3, = 0.6 | |||||||||
p-value = 2.74 × 10−32 from the Kruskal–Wallis test | |||||||||
p-values from the Mann–Whitney U test using the Bonferroni correction | |||||||||
Cycle 1 | Cycle 2 | Cycle 3 | Cycle 4 | Cycle 5 | Cycle 6 | Cycle 7 | Cycle 8 | Cycle 9 | |
Cycle 2 | S | ||||||||
Cycle 3 | S | S | |||||||
Cycle 4 | S | S | NS | ||||||
Cycle 5 | S | S | S | NS | |||||
Cycle 6 | S | S | S | S | NS | ||||
Cycle 7 | S | S | S | S | S | NS | |||
Cycle 8 | S | S | S | S | S | S | NS | ||
Cycle 9 | S | S | S | S | S | S | S | NS | |
Cycle 10 | S | S | S | S | S | S | S | NS | NS |
Trait 2 Continuous, = 0.3 | |||||||||
---|---|---|---|---|---|---|---|---|---|
p-Value = 8.46 × 10−22 from the Kruskal–Wallis Test | |||||||||
p-Values from the Mann–Whitney U Test Using the Bonferroni Correction | |||||||||
Cycle 1 | Cycle 2 | Cycle 3 | Cycle 4 | Cycle 5 | Cycle 6 | Cycle 7 | Cycle 8 | Cycle 9 | |
Cycle 2 | NS | ||||||||
Cycle 3 | NS | NS | |||||||
Cycle 4 | S | NS | NS | ||||||
Cycle 5 | S | NS | NS | NS | |||||
Cycle 6 | S | S | NS | NS | NS | ||||
Cycle 7 | S | S | S | NS | NS | NS | |||
Cycle 8 | S | S | S | S | S | NS | NS | ||
Cycle 9 | S | S | S | S | S | S | NS | NS | |
Cycle 10 | S | S | S | S | S | S | NS | NS | NS |
Cycle 10 | NS | NS | S | NS | S | S | S | NS | NS |
Trait 3 Category 3, = 0.3 | |||||||||
p-value = 1.79 × 10−34 from the Kruskal–Wallis test | |||||||||
p-values from the Mann–Whitney U test using the Bonferroni correction | |||||||||
Cycle 1 | Cycle 2 | Cycle 3 | Cycle 4 | Cycle 5 | Cycle 6 | Cycle 7 | Cycle 8 | Cycle 9 | |
Cycle 2 | NS | ||||||||
Cycle 3 | S | NS | |||||||
Cycle 4 | S | S | NS | ||||||
Cycle 5 | S | S | S | NS | |||||
Cycle 6 | S | S | S | S | NS | ||||
Cycle 7 | S | S | S | S | S | NS | |||
Cycle 8 | S | S | S | S | S | S | NS | ||
Cycle 9 | S | S | S | S | S | S | S | NS | |
Cycle 10 | S | S | S | S | S | S | S | S | NS |
Trait 2 Continuous, = 0.6 | |||||||||
---|---|---|---|---|---|---|---|---|---|
p-Value = 8.46 × 10−22 from the Kruskal–Wallis Test | |||||||||
p-Values from the Mann–Whitney U Test Using the Bonferroni Correction | |||||||||
Cycle 1 | Cycle 2 | Cycle 3 | Cycle 4 | Cycle 5 | Cycle 6 | Cycle 7 | Cycle 8 | Cycle 9 | |
Cycle 2 | NS | ||||||||
Cycle 3 | S | NS | |||||||
Cycle 4 | S | NS | NS | ||||||
Cycle 5 | S | S | NS | NS | |||||
Cycle 6 | S | S | S | NS | NS | ||||
Cycle 7 | S | S | S | NS | NS | NS | |||
Cycle 8 | S | S | S | S | NS | NS | NS | ||
Cycle 9 | S | S | S | S | S | NS | NS | NS | |
Cycle 10 | S | S | S | S | S | S | NS | NS | NS |
p-value = 1.79 × 10−34 from the Kruskal–Wallis test | |||||||||
p-values from the Mann–Whitney U test using the Bonferroni correction | |||||||||
Cycle 1 | Cycle 2 | Cycle 3 | Cycle 4 | Cycle 5 | Cycle 6 | Cycle 7 | Cycle 8 | Cycle 9 | |
Cycle 2 | S | ||||||||
Cycle 3 | S | S | |||||||
Cycle 4 | S | S | S | ||||||
Cycle 5 | S | S | S | S | |||||
Cycle 6 | S | S | S | S | NS | ||||
Cycle 7 | S | S | S | S | S | NS | |||
Cycle 8 | S | S | S | S | S | S | NS | ||
Cycle 9 | S | S | S | S | S | S | S | NS | |
Cycle 10 | S | S | S | S | S | S | S | S | NS |
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Villar-Hernández, B.d.J.; Pérez-Rodríguez, P.; Vitale, P.; Gerard, G.; Montesinos-Lopez, O.A.; Saint Pierre, C.; Crossa, J.; Dreisigacker, S. Optimizing Genomic Parental Selection for Categorical and Continuous–Categorical Multi-Trait Mixtures. Genes 2024, 15, 995. https://doi.org/10.3390/genes15080995
Villar-Hernández BdJ, Pérez-Rodríguez P, Vitale P, Gerard G, Montesinos-Lopez OA, Saint Pierre C, Crossa J, Dreisigacker S. Optimizing Genomic Parental Selection for Categorical and Continuous–Categorical Multi-Trait Mixtures. Genes. 2024; 15(8):995. https://doi.org/10.3390/genes15080995
Chicago/Turabian StyleVillar-Hernández, Bartolo de Jesús, Paulino Pérez-Rodríguez, Paolo Vitale, Guillermo Gerard, Osval A. Montesinos-Lopez, Carolina Saint Pierre, José Crossa, and Susanne Dreisigacker. 2024. "Optimizing Genomic Parental Selection for Categorical and Continuous–Categorical Multi-Trait Mixtures" Genes 15, no. 8: 995. https://doi.org/10.3390/genes15080995
APA StyleVillar-Hernández, B. d. J., Pérez-Rodríguez, P., Vitale, P., Gerard, G., Montesinos-Lopez, O. A., Saint Pierre, C., Crossa, J., & Dreisigacker, S. (2024). Optimizing Genomic Parental Selection for Categorical and Continuous–Categorical Multi-Trait Mixtures. Genes, 15(8), 995. https://doi.org/10.3390/genes15080995