Avian

Genome-wide association study of bone integrity traits of femur in broiler chicken

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Abstract

Early slaughter and animal welfare concerns, both stemming from bone fractures, represent challenges and economic losses in broiler production. The objective of this study was to identify SNPs associated with femur bone integrity traits in broiler chickens. The chickens originated from the New Hampshire, White Cornish, and White Plymouth Rock breeds and has been maintained under multi-trait selection in open-sided poultry houses since 1992. A genome-wide association study (GWAS) was conducted using a linear mixed model approach assuming additive effects, implemented in GCTA software (1.94.1). The chickens were genotyped using the 600K Affymetrix® Axiom® high-density array. Quality control (QC) filtered SNPs and individuals using the following criteria: individual call rate > 95%, SNP call rate > 95%, minor allele frequency > 0.01, and Hardy-Weinberg equilibrium p-value > 1 x 10-6. After QC, the dataset included records of 1,279 chickens and 306,782 SNPs. Principal component analysis was used to evaluate population stratification. The traits studied were: femur weight (FW), length (FL), and width (FWD); calcium (CA), ash (ASH), dry matter (DM), magnesium (MG), phosphorus (P), and zinc (ZN) content; and femur breaking force (FOR) and stiffness (STI). Sex, batch, and the first three principal components of the genomic data were included as fixed effects. Multiple-test correction was conducted using the Bonferroni formula, where the numerator was the genome-wise type I error rate (0.05) and the denominator was the effective number of independent SNPs (Meff). Linkage Disequilibrium pruning was used to estimate Meff. Linkage Disequilibrium pruning was used to estimate Meff using PLINK v1.9 (window size = 50, step size = 5, r² = 0.2). This analysis resulted in a Meff of 8,320 independent SNPs, yielding a genome-wide significance threshold of 6 × 10⁻⁶. Candidate genes were searched within a 50 kb window upstream and downstream of significant SNPs. Annotation was performed using the Gallus gallus reference genome (GRCg7b, Ensembl Genes 115) and the biomaRt R package. A total of 94 genome-wide significant associations were found: one for FW on chromosome 12, two for FL on chromosome 3, four for CA on chromosome 3, four for ZN on chromosome 24, and 83 for MG on chromosome 15. The 83 significant SNPs for MG might indicate only one major QTL. No significant SNPs were found for FWD, ASH, DM, P, FOR, or STI. Following functional analysis, 70 genes were identified for the significant SNPs, of which 30 have already been described. For MG specifically, 41 genes were found, 28 of which were previously described. The large number of candidate genes for MG reflects the extent of linkage disequilibrium in the region rather than multiple independent genetic effects. These findings can help elucidate the genetic mechanisms affecting leg health in broiler chickens.

Keywords: 2026

How to Cite:

Boccaletti Ramos, S., Caetano, S., Carvalho, D., Corràªa Ledur, M., de Oliveira Peixoto, J., Lehmann Coutinho, L., Mércia Guaratini Ibelli, A. & Prado Munari, D., (2026) “Genome-wide association study of bone integrity traits of femur in broiler chicken”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287095. doi: https://doi.org/10.31274/wcgalp.24209

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