An Improved Bayesian Shrinkage Regression Algorithm for Genomic Selection
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genetic Model
2.2. The Improved EM Algorithm for BayesA (emBayesAI) Algorithm
2.2.1. The Polygenic and Residual Noise Whitening Stage
2.2.2. EM Algorithm for BayesA Stage
- 1.
- E-step: is estimated as shown in (7).
- 2.
- M-step: updated and are given according to (9), (10) and (11).
2.3. Comparison Methods
2.4. Experimental Materials
2.4.1. The Simulation Data
2.4.2. The Arabidopsis Data
2.4.3. Evaluation Indicators
3. Results
3.1. Simulation Studies
3.2. The Arabidopsis Data Analysis
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
References
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Trait | Chr. | Position | Gene | Method |
---|---|---|---|---|
LD | 1 | 3760729 | AT1G11190, BFN1, ENDO1 | emBA |
1 | 3765344 | AT1G11190, BFN1, ENDO1 | emBAI, emML | |
2 | 13869948 | AT2G32700, LUH, MUM1 | emRR | |
2 | 16020457 | AT2G38185, APD1 | emBAI | |
AT2G38195, APD4 | emBAI | |||
AT2G38220, APD3 | emBAI | |||
4 | 14001595 | AT4G28190, ULT, ULT1 | emBC, emRR | |
5 | 18614010 | AT5G45890, ATSAG12, SAG12 | emBC | |
FT22 | 1 | 9072307 | AT1G26260, CIB5 | emML |
2 | 16020457 | AT2G38185, APD1 | emBAI, emBC | |
AT2G38195, APD4 | emBAI, emBC | |||
AT2G38220, APD3 | emBAI, emBC | |||
2 | 13869948 | AT2G32700, LUH, MUM1 | emRR | |
4 | 17263477 | AT4G36620, GATA19, HANL2 | emBC, emRR | |
5 | 22328009 | AT5G55020, ATMYB120, MYB120 | emBAI | |
5 | 6844104 | AT5G20240, PI, PISTILLATA | emBAI | |
5 | AT5G20280, ATSPS1F, SPS1F, SPSA1 | emBAI | ||
5 | 13923880 13923160 13931089 13930569 13927017 | AT5G35750, AHK2, HK2 | emBA | |
5 | 17219669 | AT5G42900, COR27 | emBA | |
5 | 9808482 | AT5G27650, PDP1 | emBA | |
5 | 17463517 17478636 | AT5G43510, ATLURE1.2, CRP810_1.2, LURE 1.2 | emBA |
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Zhang, J.; Li, L.; Lv, M.; Wang, Y.; Qiu, W.; An, Y.; Zhang, Y.; Wan, Y.; Xu, Y.; Chen, J. An Improved Bayesian Shrinkage Regression Algorithm for Genomic Selection. Genes 2022, 13, 2193. https://doi.org/10.3390/genes13122193
Zhang J, Li L, Lv M, Wang Y, Qiu W, An Y, Zhang Y, Wan Y, Xu Y, Chen J. An Improved Bayesian Shrinkage Regression Algorithm for Genomic Selection. Genes. 2022; 13(12):2193. https://doi.org/10.3390/genes13122193
Chicago/Turabian StyleZhang, Jin, Ling Li, Mingming Lv, Yidi Wang, Wenzhe Qiu, Yuan An, Ye Zhang, Yuxuan Wan, Yu Xu, and Juncong Chen. 2022. "An Improved Bayesian Shrinkage Regression Algorithm for Genomic Selection" Genes 13, no. 12: 2193. https://doi.org/10.3390/genes13122193
APA StyleZhang, J., Li, L., Lv, M., Wang, Y., Qiu, W., An, Y., Zhang, Y., Wan, Y., Xu, Y., & Chen, J. (2022). An Improved Bayesian Shrinkage Regression Algorithm for Genomic Selection. Genes, 13(12), 2193. https://doi.org/10.3390/genes13122193