Enhancing genomic selection for reproductive traits in turkeys through SNP prioritization using the fixation index

Area of Science:

• Animal Breeding and Genetics
• Quantitative Genetics
• Poultry Science

Background:

• Genomic selection (GS) improves breeding value accuracy but shows modest gains for lowly heritable traits like turkey reproduction.
• Reproductive traits in turkeys often exhibit non-normal phenotypic distributions, complicating accurate genetic evaluation.

Purpose of the Study:

• To enhance the accuracy of genomic selection for turkey reproductive traits.
• To improve the genomic relationship matrix quality and normalize phenotypic distributions.

Main Methods:

• Utilized the fixation index (F_ST) to select informative single nucleotide polymorphisms (SNPs) differentiating extreme phenotypic groups.
• Applied Box-Cox transformation to normalize phenotypic distributions of reproductive traits.
• Analyzed egg production percent (PEP), fertility (FERT), and hatchability (HOF) using BLUP, GBLUP, and ssGBLUP models.

Main Results:

• F_ST-prioritized SNPs significantly improved heritability estimates, especially for fertility (FERT).
• Prioritizing top 10% F_ST markers increased FERT heritability by 93% in GBLUP (0.15 to 0.29).
• Box-Cox transformation consistently increased heritability across all methods, with combined F_ST90 and transformation yielding highest estimates.

Conclusions:

• F_ST-based SNP prioritization and Box-Cox transformation effectively enhance genomic selection accuracy for turkey reproductive traits.
• These methods improve the identification of superior turkeys, crucial for genetic improvement programs.
• The study demonstrates a powerful strategy for optimizing GS in poultry for challenging traits.