Genetic gain & Inbreeding

How to manage potential negative effects of genomic selection?

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Abstract

The purpose of this study is to present mechanisms of possible negative effects of genomic selection in secondary traits and presents steps to stop or reverse the decline. Selection on production traits causes corresponding declines in antagonistic fitness traits. Under traditional selection, declines were initially compensated or slowed down by continuously improving management. When the deterioration was too strong to ignore, the fitness traits were added to a selection index. Under genomic selection the genetic progress for production traits accelerates causing accelerated declines in fitness traits, and management modifications are not fast enough to compensate. Including the fitness traits in the selection index is only partially effective because of lower accuracy of evaluation due to lower heritability, fewer phenotypes, and if categorical, less information. The decline of fitness traits under genomic selection has been investigated in all major species although it is more profound in species under stronger selection such as pigs and chickens. One of the most visible declines is the deterioration of hatchability in broiler chickens. While hatchability before genomic selection increased from 81% in 1998 to 85% in 2012, it dropped to 79% by 2024 under genomic selection. Mitigating the negative effects of genomic selection will require several steps, although, due to the low heritability of fitness traits, a noticeable improvement can take several cycles of selection. First, the selection pressure on major traits that are antagonistic to the deteriorating traits needs to be reduced, allowing for management modifications to catch up. Second, selection for recorded fitness traits needs to intensify, with weight on each trait calculated from recent genetic parameters. As genetic parameters can change rapidly under genomic selection, a challenge is to estimate these parameters for the last generation using complete data, as required for unbiased estimates. While traditional methods for parameter estimation are unfeasible with large data, new methods are emerging that are unrestricted by data size, such as genetic estimation by predictivity (GPP) or REML with traces calculated by Monte Carlo methods. Third, methods for evaluating fitness traits can be improved. While many fitness traits are categorical, current methods allow for the evaluation of a single categorical trait and multiple linear traits, and corresponding computations are expensive. New methods under development will potentially analyze any number of categorical and linear traits simultaneously by a threshold-linear model at a reasonable computing cost. Similar advancements would also be helpful for censored traits such as survival. In conclusion, sustaining the long-term progress of genomic selection while managing and preventing potential negative effects requires rebalancing selection intensity, improving the accuracy of fitness traits, and adopting cutting-edge models and computational methods. Some of these steps were successfully implemented by selected companies in broilers.

Keywords: 2026

How to Cite:

Misztal, I., Bermann, M. & Lourenco, D., (2026) “How to manage potential negative effects of genomic selection?”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2284194. doi: https://doi.org/10.31274/wcgalp.23553

Rights: 1