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Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)

文献类型： 外文期刊

作者： Martini, Johannes W. R. 1 ; Gao, Ning 1 ; Cardoso, Diercles F. 1 ; Wimmer, Valentin 1 ; Erbe, Malena 1 ; Cantet, Ro 1 ;

作者机构： 1.Georg August Univ, Dept Anim Sci, Albrecht Thaer Weg 3, Gottingen, Germany

2.South China Agr Univ, Natl Engn Res Ctr Breeding Swine Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Coll Anim Sci, Guangzhou, Guangdong, Peoples R China

3.Sao Paulo State Univ, Dept Zootecnia, Sao Paulo, Brazil

4.KWS SAAT SE, Einbeck, Germany

5.Bavarian State Res Ctr Agr, Inst Anim Breeding, Grub, Germany

6.Univ Buenos Aires, INPA CONICET, Dept Anim Prod, Buenos Aires, DF, Argentina

关键词： Genomic prediction;Epistasis model;Interaction

期刊名称：BMC BIOINFORMATICS （ 影响因子：3.169； 五年影响因子：3.629 ）

ISSN： 1471-2105

年卷期： 2017 年 18 卷

页码：

收录情况： SCI

摘要： Background: Epistasis marker effect models incorporating products of marker values as predictor variables in a linear regression approach (extended GBLUP, EGBLUP) have been assessed as potentially beneficial for genomic prediction, but their performance depends on marker coding. Although this fact has been recognized in literature, the nature of the problem has not been thoroughly investigated so far. Results: We illustrate how the choice of marker coding implicitly specifies the model of how effects of certain allele combinations at different loci contribute to the phenotype, and investigate coding-dependent properties of EGBLUP. Moreover, we discuss an alternative categorical epistasis model (CE) eliminating undesired properties of EGBLUP and show that the CE model can improve predictive ability. Finally, we demonstrate that the coding-dependent performance of EGBLUP offers the possibility to incorporate prior experimental information into the prediction method by adapting the coding to already available phenotypic records on other traits. Conclusion: Based on our results, for EGBLUP, a symmetric coding {-1, 1} or {-1, 0, 1} should be preferred, whereas a standardization using allele frequencies should be avoided. Moreover, CE can be a valuable alternative since it does not possess the undesired theoretical properties of EGBLUP. However, which model performs best will depend on characteristics of the data and available prior information. Data from previous experiments can for instance be incorporated into the marker coding of EGBLUP.

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