Genomic prediction using models with dominance and imprinting effects for backfat thickness and average daily gain in Danish Duroc pigs.

Xiangyu Guo,Guosheng Su,Yachun Wang,Mogens Sandø Lund,Ole Fredslund Christensen,Tage Ostersen

doi:10.1186/s12711-016-0245-6

Abstract

BackgroundDominance and imprinting genetic effects have been shown to contribute to genetic variance for certain traits but are usually ignored in genomic prediction of complex traits in livestock. The objectives of this study were to estimate variances of additive, dominance and imprinting genetic effects and to evaluate predictions of genetic merit based on genomic data for average daily gain (DG) and backfat thickness (BF) in Danish Duroc pigs.MethodsCorrected phenotypes of 8113 genotyped pigs from breeding and multiplier herds were used. Four Bayesian mixture models that differed in the type of genetic effects included: (A) additive genetic effects, (AD) additive and dominance genetic effects, (AI) additive and imprinting genetic effects, and (ADI) additive, dominance and imprinting genetic effects were compared using Bayes factors. The ability of the models to predict genetic merit was compared with regard to prediction reliability and bias.ResultsBased on model ADI, narrow-sense heritabilities of 0.18 and 0.31 were estimated for DG and BF, respectively. Dominance and imprinting genetic effects accounted for 4.0 to 4.6 and 1.3 to 1.4 % of phenotypic variance, respectively, which were statistically significant. Across the four models, reliabilities of the predicted total genetic values (GTV, sum of all genetic effects) ranged from 16.1 (AI) to 18.4 % (AD) for DG and from 30.1 (AI) to 31.4 % (ADI) for BF. The least biased predictions of GTV were obtained with model AD, with regression coefficients of corrected phenotypes on GTV equal to 0.824 (DG) and 0.738 (BF). Reliabilities of genomic estimated breeding values (GBV, additive genetic effects) did not differ significantly among models for DG (between 16.5 and 16.7 %); however, for BF, model AD provided a significantly higher reliability (31.3 %) than model A (30.7 %). The least biased predictions of GBV were obtained with model AD with regression coefficients of 0.872 for DG and 0.764 for BF.ConclusionsDominance and genomic imprinting effects contribute significantly to the genetic variation of BF and DG in Danish Duroc pigs. Genomic prediction models that include dominance genetic effects can improve accuracy and reduce bias of genomic predictions of genetic merit.

Highlights

Dominance and imprinting genetic effects have been shown to contribute to genetic variance for certain traits but are usually ignored in genomic prediction of complex traits in livestock
Quantitative traits such as carcass composition, growth, and reproduction traits have been found to be influenced by imprinting effects [4,5,6,7,8]. de Vries et al [9] reported that imprinting accounted for approximately 5 % of the phenotypic variance of backfat thickness and up to 4 % for average daily gain in Landrace and Yorkshire pigs
The full model ADI, which included additive, dominance and imprinting effects, resulted in the smallest additive genetic, litter and residual variances, while model A, which only considered additive genetic effects, provided the largest estimates for these variances; models AD and AI had estimates for these variances that were intermediate to those of models ADI and A. These results indicate that when dominance and imprinting effects are excluded from a model, the variance due to these effects was assigned to other variance components in the model

Summary

Introduction

Dominance and imprinting genetic effects have been shown to contribute to genetic variance for certain traits but are usually ignored in genomic prediction of complex traits in livestock. The objectives of this study were to estimate variances of additive, dominance and imprinting genetic effects and to evaluate predictions of genetic merit based on genomic data for average daily gain (DG) and backfat thickness (BF) in Danish Duroc pigs. De Vries et al [9] reported that imprinting accounted for approximately 5 % of the phenotypic variance of backfat thickness and up to 4 % for average daily gain in Landrace and Yorkshire pigs. Dominance and imprinting effects contribute to the variation in backfat and daily gain [2, 9], these sources of variation are usually not included in models for genetic evaluation

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