Unlocking growth potential in Wenchang chickens: A 21 K genotyping array for trait-associated structural variations

In recent years, the poultry industry has embraced genome-wide assisted breeding techniques for broiler production, focusing primarily on single nucleotide polymorphisms (SNPs). However, the potential of genomic structural variations (SVs) in broiler traits remains largely unexplored due to cost and technology limitations. We developed a new chicken 21 K SV genotyping array and assessed its performance on 303 Wenchang chickens. Our evaluation showed a 99.20 % call rate with 57.13 % polymorphism across all microarray loci that identified SVs within the Wenchang chicken population. Genome-wide association studies (GWAS) of these SVs identified five significant variants associated with economically important traits, along with growth and development-related candidate genes including PLXAN4, ACBD3, and RNASET2. These findings demonstrate the value of SV-based approaches for improving genetic selection methods and enhancing productivity in poultry breeding programs. Our results show that high-quality 21 K SV genotyping arrays have significant potential for poultry breeding applications.