Genomic selection models for directional dominance: an example for litter size in pigs

Abstract

BackgroundThe quantitative genetics theory argues that inbreeding depression and heterosis are founded on the existence of directional dominance. However, most procedures for genomic selection that have included dominance effects assumed prior symmetrical distributions. To address this, two alternatives can be considered: (1) assume the mean of dominance effects different from zero, and (2) use skewed distributions for the regularization of dominance effects. The aim of this study was to compare these approaches using two pig datasets and to confirm the presence of directional dominance.ResultsFour alternative models were implemented in two datasets of pig litter size that consisted of 13,449 and 11,581 records from 3631 and 2612 sows genotyped with the Illumina PorcineSNP60 BeadChip. The models evaluated included (1) a model that does not consider directional dominance (Model SN), (2) a model with a covariate b for the average individual homozygosity (Model SC), (3) a model with a parameter λ that reflects asymmetry in the context of skewed Gaussian distributions (Model AN), and (4) a model that includes both b and λ (Model Full). The results of the analysis showed that posterior probabilities of a negative b or a positive λ under Models SC and AN were higher than 0.99, which indicate positive directional dominance. This was confirmed with the predictions of inbreeding depression under Models Full, SC and AN, that were higher than in the SN Model. In spite of differences in posterior estimates of variance components between models, comparison of models based on LogCPO and DIC indicated that Model SC provided the best fit for the two datasets analyzed.ConclusionsOur results confirmed the presence of positive directional dominance for pig litter size and suggested that it should be taken into account when dominance effects are included in genomic evaluation procedures. The consequences of ignoring directional dominance may affect predictions of breeding values and can lead to biased prediction of inbreeding depression and performance of potential mates. A model that assumes Gaussian dominance effects that are centered on a non-zero mean is recommended, at least for datasets with similar features to those analyzed here.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0374-1) contains supplementary material, which is available to authorized users.

Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties1

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Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats

“…The selection of one desirable allele over the rest normally implies the simultaneous selection and frequency increase of epistatically linked alleles, which in turn may not have a favorable effect on milk production traits and their components [ 10 ]. The approaches that are regularly followed to perform association analyses [ 11 ] normally overlook this genetic epistatic effects change during lactation [ 12 ], which renders the study of genetic association inefficient.…”

Selecting for changes in average “parity curve” pattern of litter size in Large White pigs

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