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A comparison of genomic selection methods for breeding value prediction

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  • Life & Medical Sciences
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Science Bulletin

Abstract

Recent advances in molecular genetics techniques have made dense marker maps available, and the prediction of breeding value at the genome level has been employed in genetics research. However, an increasingly large number of markers raise both statistical and computational issues in genomic selection (GS), and many methods have been developed for genomic prediction to address these problems, including ridge regression-best linear unbiased prediction (RR-BLUP), genomic best linear unbiased prediction, BayesA, BayesB, BayesCπ, and Bayesian LASSO. In this paper, these methods were compared regarding inference under different conditions, using real data from a wheat data set and simulated scenarios with a small number of quantitative trait loci (QTL) (20), a moderate number of QTL (60, 180) and an extreme number of QTL (540). This study showed that the genetic architecture of a trait should be fully considered when a GS method is chosen. If a small amount of loci had a large effect on a trait, great differences were found between the predictive ability of various methods and BayesCπ was recommended. Although there was almost no significant difference between the predictive ability of BayesCπ and BayesB, BayesCπ is more feasible than BayesB for real data analysis. If a trait was controlled by a moderate number of genes, the absolute differences between the various methods were small, but BayesA was also found to be the most accurate method. Furthermore, BayesA was widely adaptable and could perform well with different numbers of QTL. If a trait was controlled by an extreme number of minor genes, almost no significant differences were detected between the predictive ability of various methods, but RR-BLUP slightly outperformed the others in both simulated scenarios and real data analysis, thus demonstrating its robustness and indicating that it was quite effective in this case.

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Acknowledgments

This work was supported by the National Basic Research Program of China (2011CB100100), the Priority Academic Program Development of Jiangsu Higher Education Institutions, the National Natural Science Foundations (31391632, 31200943, and 31171187), the National High-tech R&D Program (863 Program) (2014AA10A601-5), the Natural Science Foundations of Jiangsu Province (BK2012261), the Natural Science Foundation of the Jiangsu Higher Education Institutions (14KJA210005) and the Innovative Research Team of Universities in Jiangsu Province.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China

    Xin Wang, Zefeng Yang & Chenwu Xu

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  1. Xin Wang
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  2. Zefeng Yang
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  3. Chenwu Xu
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Corresponding author

Correspondence to Chenwu Xu.

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Wang, X., Yang, Z. & Xu, C. A comparison of genomic selection methods for breeding value prediction. Sci. Bull. 60, 925–935 (2015). https://doi.org/10.1007/s11434-015-0791-2

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  • DOI: https://doi.org/10.1007/s11434-015-0791-2

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