Investigating the impact of non-additive genetic effects in the estimation of variance components and genomic predictions for heat tolerance and performance traits in crossbred and purebred pig populations

Authors: FERNANDA DE OLIVEIRA, LETICIA - Universidade Federal De Vicosa; BRITO, LUIS - Purdue University; DINIZ MARQUES, DANIELE - Universidade Federal De Vicosa; ALVES DA SILVA, DELVAN - Universidade Federal De Vicosa; SAVIO LOPES, PAULO - Federal University Of Viçosa; GOMES DOS SANTOS, CASSIANE - Universidade Federal De Vicosa; Johnson, Jay; VERONEZE, RENATA - Universidade Federal De Vicosa

Submitted to: BMC Genomic Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2023
Publication Date: 12/13/2023
Citation: Fernanda De Oliveira, L., Brito, L.F., Diniz Marques, D.B., Alves Da Silva, D., Savio Lopes, P., Gomes Dos Santos, C., Johnson, J.S., Veroneze, R. 2023. Investigating the impact of non-additive genetic effects in the estimation of variance components and genomic predictions for heat tolerance and performance traits in crossbred and purebred pig populations. BMC Genomic Data. https://doi.org/10.1186/s12863-023-01174-x.
DOI: https://doi.org/10.1186/s12863-023-01174-x

Interpretive Summary: Heat stress negatively impacts swine welfare and productivity. To address this issue, recent work by our group has evaluated the use of genomic selection to improve heat stress resilience in pigs. However, it is unknown whether the inclusion of non-additive genetic effects will improve the prediction accuracy of the models for producing heat stress tolerant individuals. Therefore, the study objective was to estimate variance components and assess the predictive performance of genomic predictions based on alternative models in purebred and crossbred pigs. It was determined that the inclusion of non-additive genetic effects in the models did not impact the predictive accuracy for performance traits related to heat stress tolerance. However, individual rankings for heat stress tolerance were altered. Therefore, it can be concluded that there is a negligible impact of including non-additive genetic effects within heat stress tolerance genetic selection models.

Technical Abstract: Background: Non-additive genetic effects are often ignored in livestock genetic evaluations, but fitting them within the models could improve the prediction accuracy of breeding values. Furthermore, non-additive genetic effects contribute to heterosis effects and can be optimized through mating designs. In general, traits related to fitness and adaptation, such as heat tolerance, tend to be more influenced by non-additive genetic effects. In this context, this study aimed to estimate variance components and assess the predictive performance of genomic predictions based on alternative models and two datasets, including performance records from purebred pigs and heat tolerance indicators from crossbred pigs. Results: Including non-additive genetic effects when modelling performance traits in purebred pigs had no effect on the residual variance estimates for most of the traits, but lower additive genetic variances were observed, especially when additive-by-additive epistasis was included in the models. Furthermore, including non-additive genetic effects did not improve the prediction accuracy of genomic breeding values, but there was animal re-ranking across models. For the heat tolerance indicators recorded in a crossbred population, most traits had small non-additive genetic variance with large standard error estimates. Nevertheless, panting score (PS) and hair density (HD) presented notable additive-by-additive epistatic variance of 0.1513 (86.76% of total genetic variance) and from 0.4618 to 0.4912 (66.91% to 71.87% of total genetic variance) for PS and HD, respectively. Conclusions: Including non-additive genetic effects in the models did not improve the predictive ability of genomic breeding values for performance traits in purebred pigs, but there was substantial re-ranking of selection candidates. With the exception of PS and HD, negligible non-additive effects were observed for heat tolerance indicators in crossbred pigs.