Enhancing genomic selection for reproductive traits in Turkeys through SNP prioritization using the Fixation Index

Authors: HARTONO, EVAN - University Of Georgia; WILLEMS, OWEN - Hybrid Turkeys; BAI, XUECHUN - Hybrid Turkeys; WOOD, BENJAMIN - University Of Queensland; Toghiani, Sajjad; REKAYA, ROMDHANE - University Of Georgia; AGGREY, SAMUEL - University Of Georgia

Submitted to: Poultry Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Improving the accuracy of genomic selection for reproductive traits in turkeys is a challenging task due to the low heritability of these traits and the non-normal distribution of their phenotypic data. Accurate selection is crucial for enhancing productivity and breeding efficiency in turkey farming. This study focused on developing and testing new strategies to improve the accuracy of genomic selection for reproductive traits in turkeys. By prioritizing informative genetic markers and applying data transformation techniques, researchers were able to enhance the quality of genetic evaluations. Specifically, they used the fixation index (FST) to select important genetic markers and applied the Box-Cox transformation to normalize data distributions, significantly improving heritability estimates and selection accuracy. The improved methods for genomic selection demonstrated in this study will benefit turkey producers by enabling more precise breeding decisions, leading to better reproductive performance and overall productivity. Enhanced accuracy in identifying superior animals means that producers can expect higher fertility rates, better egg production, and improved hatchability, which translates to increased profitability. Moreover, the advancements in genomic selection techniques contribute to the scientific community by providing robust methods that can be applied to other animal breeding programs, driving forward agricultural research and technology.

Technical Abstract: Genomic selection (GS) has revolutionized the field of animal breeding by enabling more accurate estimates of breeding values through a more precise assessment of the additive relationships between individuals. For lowly heritable traits, the increase in accuracy was in general modest at best. This is specifically the case for reproductive traits in turkeys which also suffer from a lack of normality of their phenotypic distributions. This study aimed to increase the accuracy of genomic selection for reproductive traits in turkeys by enhancing the quality of the genomic relationship matrix and by improving the normality of the phenotypic distributions. The fixation index (FST) was used to prioritize and select informative subsets of single nucleotide polymorphisms (SNPs) associated with genetic differentiation between extreme phenotypic groups. Concurrently, the Box-Cox transformation was applied to improve the normality of the reproductive trait phenotypic distributions. A total of 6,103, 5,564, and 5,548 records for egg production rate (PEP), egg fertility rate (FERT) and fertile eggs hatchability rate (HOF) traits were analyzed using univariate pedigree-based BLUP (BLUP), genomic BLUP (GBLUP), and single-step GBLUP (ssGBLUP) approaches. Incorporating FST-prioritized SNPs generally improved heritability estimates, with substantial gains observed for the lowly heritable fertility (FERT) trait when combined with the ssGBLUP approach. Furthermore, the Box-Cox transformation consistently resulted in higher heritability estimates across all methods compared to untransformed data, with ssGBLUP exhibiting the highest estimates after transformation. The high re-ranking in the top 10% after using SNP-prioritization suggests that marker filtering is likely to improve the accuracy of the selection decision through the correct identification of superior animals. These findings highlight the potential of FST-based SNP prioritization and data transformation techniques to enhance the accuracy of genomic selection for reproductive traits in turkeys.