A Bayesian Decision Theory Approach for Genomic Selection

G3 : Genes - Genomes - Genetics
Bartolode Jesús Villar-HernándezJuan Burgueño

Abstract

Plant and animal breeders are interested in selecting the best individuals from a candidate set for the next breeding cycle. In this paper, we propose a formal method under the Bayesian decision theory framework to tackle the selection problem based on genomic selection (GS) in single- and multi-trait settings. We proposed and tested three univariate loss functions (Kullback-Leibler, KL; Continuous Ranked Probability Score, CRPS; Linear-Linear loss, LinLin) and their corresponding multivariate generalizations (Kullback-Leibler, KL; Energy Score, EnergyS; and the Multivariate Asymmetric Loss Function, MALF). We derived and expressed all the loss functions in terms of heritability and tested them on a real wheat dataset for one cycle of selection and in a simulated selection program. The performance of each univariate loss function was compared with the standard method of selection (Std) that does not use loss functions. We compared the performance in terms of the selection response and the decrease in the population's genetic variance during recurrent breeding cycles. Results suggest that it is possible to obtain better performance in a long-term breeding program using the single-trait scheme by selecting 30% of the best individ...Continue Reading

References

Apr 6, 2001·Genetics·T H MeuwissenM E Goddard
Aug 1, 1995·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·J R Brisbane, J P Gibson
Jun 13, 2015·PloS One·Mathieu BlondelNaonori Ueda
May 14, 2016·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Govindan VeluGurvinder Singh Mavi
Dec 15, 2016·Frontiers in Genetics·Deniz Akdemir, Julio I Sánchez
Oct 3, 2017·Trends in Plant Science·José CrossaRajeev K Varshney

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Citations

Feb 28, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sebastian MichelHermann Bürstmayr
Mar 12, 2021·G3 : Genes - Genomes - Genetics·Bartolo de Jesús Villar-HernándezJosé Crossa

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Software Mentioned

BGLR R
Rcpp package
EnergyS
LinLin
MALF
R

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