The influence of a first-order antedependence model and hyperparameters in BayesCπ for genomic prediction

  • Li, Xiujin (State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University) ;
  • Liu, Xiaohong (State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University) ;
  • Chen, Yaosheng (State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University)
  • Received : 2018.01.31
  • Accepted : 2018.06.02
  • Published : 2018.12.01


Objective: The Bayesian first-order antedependence models, which specified single nucleotide polymorphisms (SNP) effects as being spatially correlated in the conventional BayesA/B, had more accurate genomic prediction than their corresponding classical counterparts. Given advantages of $BayesC{\pi}$ over BayesA/B, we have developed hyper-$BayesC{\pi}$, ante-$BayesC{\pi}$, and ante-hyper-$BayesC{\pi}$ to evaluate influences of the antedependence model and hyperparameters for $v_g$ and $s_g^2$ on $BayesC{\pi}$.Methods: Three public data (two simulated data and one mouse data) were used to validate our proposed methods. Genomic prediction performance of proposed methods was compared to traditional $BayesC{\pi}$, ante-BayesA and ante-BayesB. Results: Through both simulation and real data analyses, we found that hyper-$BayesC{\pi}$, ante-$BayesC{\pi}$ and ante-hyper-$BayesC{\pi}$ were comparable with $BayesC{\pi}$, ante-BayesB, and ante-BayesA regarding the prediction accuracy and bias, except the situation in which ante-BayesB performed significantly worse when using a few SNPs and ${\pi}=0.95$. Conclusion: Hyper-$BayesC{\pi}$ is recommended because it avoids pre-estimated total genetic variance of a trait compared with $BayesC{\pi}$ and shortens computing time compared with ante-BayesB. Although the antedependence model in $BayesC{\pi}$ did not show the advantages in our study, larger real data with high density chip may be used to validate it again in the future.


Supported by : National Natural Science Foundation of China, China Postdoctoral Science Foundation, China Agriculture Research System


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