基于显性模型的基因组选择中贝叶斯方法研究

doi:10.11843/j.issn.0366-6964.2017.01.007

Abstract

Abstract:

The aim of this study was to investigate the impact of dominant effects on the predictive accuracy of genomic breeding values. Based on the dependency between additive and dominant effects using BayesA model, we proposed two submodels:1) the additive effect and dominant effect were independent of each other in BayesAD1 model; 2) the dominant coefficient and absolute values of additive effect were independent of each other in BayesAD2 model, in which the dominant coefficient followed normal distribution. Using simulated datasets, we compared the predictive accuracy of genomic estimated breeding value (GEBV) among the additive model (BayesAD0) and dominant models (BayesAD1 and BayesAD2). We further investigated the effect of number of QTLs (quantitative trait loci), size of full-sibs family and ratio of additive variance to dominant variance on predictive accuracy of GEBV. The results showed that the dominant models slowed down the declining of the predictive accuracy of GEBV in subsequent generations. Moreover, the predictive accuracy of GEBV increased as the ratio of dominant variance increase. When the ratio of additive variance to dominant variance reached 0.25, BayesAD2 was 20.3% and 28.4% higher than the accuracy of the BayesAD1 and BayesAD0, respectively. In addition, the size of full-sibs family affected the predictive accuracy of GEBV positively. And an increase in the number of QTL was accompanied by a reduction on the predictive accuracy of GEBV. These results indicate that a better prediction of genetic values is intended, when the dominant variance are large just as low-heritability traits.

CLC Number:

S813.1

WANG Yan-hui, ZHU Bo, LI Jun-ya. Bayesian Models including Dominant Effects for Genomic Selection[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(1): 60-67.

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References

［1］MEUWISSEN T H E, HAYES B J, GODDARD M E. Prediction of total genetic value using genome-wide dense marker maps ［J］. Genetics，2001，157（4）：1819-1829.
［2］GIANOLA D, DE LOS CAMPOS G, HILL W G, et al. Additive genetic variability and the Bayesian Alphabet ［J］.Genetics，2009,183（1）：347-363.
［3］王重龙, 丁向东, 刘剑锋,等. 基因组育种值估计的贝叶斯方法［J］. 遗传，2014，36（2）：111-118.
WANG C L, DING X D, LIU J F, et al. Bayesian methods for genomic breeding value estimation［J］. Hereditas (Beijing)，2014， 36（2）：111-118.（in Chinese）
［4］BOLORMAA S, PRYCE J E, ZHANG Y, et al. Non-additive genetic variation in growth, carcass and fertility traits of beef cattle ［J］. Genet Sel Evol，2015，47：26.
［5］SU G, CHRISTENSEN O, OSTERSEN T, et al. Estimating additive and non-additive genetic variances and predicting genetic merits using genome-wide dense single nucleotide polymorphism markers ［J］. PLoS One，2012，7（9）：e45293.
［6］DE ALMEIDA FILHO J E, GUIMARAES J F R, E SILVA F F, et al. The contribution of dominance to phenotype prediction in a pine breeding and simulated population ［J］. Heredity，2016，117（1）：33-41.
［7］LEE S H, VAN DER WERF J, HAYES B J, et al. Predicting unobserved phenotypes for complex traits from whole-genome SNP data ［J］. PLoS Genet，2008，4（10）：e1000231.
［8］GUO X, CHRISTENSEN O F, OSTERSEN T, et al. Genomic prediction using models with dominance and imprinting effects for backfat thickness and average daily gain in Danish Duroc pigs ［J］. Genet Sel Evol，2016，48（1）：67.
［9］DOS SANTOS J P R, VASCONCELLOS R C D C, PIRES L P M, et al. Inclusion of dominance effects in the multivariate GBLUP model ［J］. PLoS One，2016，11（4）：e0152045.
［10］WELLMANN R, BENNEWITZ J. Bayesian models with dominance effects for genomic evaluation of quantitative traits ［J］. Genet Res（Camb），2012， 94（1）：21-37.
［11］ZENG Z B, WANG T, ZOU W. Modeling quantitative trait loci and interpretation of models ［J］. Genetics，2005，169（3）：1711-1725.
［12］HENDERSON C. Best linear unbiased prediction of nonadditive genetic merits［J］. J Anim Sci，1985，60：111-117.
［13］DENIS M, BOUVET J M. Efficiency of genomic selection with models including dominance effect in the context of Eucalyptus breeding ［J］. Tree Genet Genomes，2013，9（1）：37-51.
［14］VITEZICA Z G, VARONA L, LEGARRA A. On the additive and dominant variance and covariance of individuals within the genomic selection scope ［J］. Genetics，2013，195（4）：1223-1230.
［15］WELLMANN R, BENNEWITZ J. The contribution of dominance to the understanding of quantitative genetic variation ［J］. Genet Res（Camb），2011，93（2）：139-154.
［16］FINLEY A O, BANERJEE S, WALDMANN P, et al. Hierarchical spatial modeling of additive and dominance genetic variance for large spatial trial datasets ［J］. Biometrics，2009，65（2）:441-451.
［17］ZHANG Z, LIU J, DING X, et al. Best linear unbiased prediction of genomic breeding values using a trait-specific marker-derived relationship matrix ［J］. PLoS One，2010， 5（9）:e12648.
［18］WITTENBURG D, MELZER N, REINSCH N. Including non-additive genetic effects in Bayesian methods for the prediction of genetic values based on genome-wide markers ［J］. BMC Genet，2011，12：74.
［19］BENNEWITZ J, MEUWISSEN T H E. The distribution of QTL additive and dominance effects in porcine F2 crosses ［J］. J Anim Breed Genet，2010，127（3）：171-179.
［20］HAYES B J, GODDARD M. The distribution of the effects of genes affecting quantitative traits in livestock ［J］. Genet Sel Evol，2001，33（3）：209-229.
［21］NISHIO M, SATOH M. Including dominance effects in the genomic BLUP method for genomic evaluation ［J］.PLoS One，2014，9（1）：e85792.
［22］LEE S H, VAN DER WERF J H. Using dominance relationship coefficients based on linkage disequilibrium and linkage with a general complex pedigree to increase mapping resolution ［J］. Genetics，2006，174（2）：1009-1016.
［23］ZENG J, TOOSI A, FERNANDO R L, et al. Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action ［J］. Genet Sel Evol，2013，45：11.
［24］ERTL J, LEGARRA A, VITEZICA Z G, et al. Genomic analysis of dominance effects on milk production and conformation traits in Fleckvieh cattle ［J］. Genet Sel Evol，2014，46：40.
［25］CABALLERO A, KEIGHTLEY P D. A pleiotropic nonadditive model of variation in quantitative traits ［J］. Genetics，1994，138（3）：883-900.
［26］MEUWISSEN T H E, GODDARD M. Accurate prediction of genetic values for complex traits by whole-genome resequencing ［J］. Genetics，2010，185（2）：623-631.
［27］DUANGJINDA M, BERTRAND J, MISZTAL I, et al. Estimation of additive and nonadditive genetic variances in Hereford, Gelbvieh, and Charolais by method R ［J］. J Anim Sci，2001， 79（12）：2997-3001.

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Bayesian Models including Dominant Effects for Genomic Selection

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