Genome wide association study was conducted using a mixed linear model (MLM) approach that accounted for family structure to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with body weight (BW) and feed efficiency (FE) traits in a broiler chicken population. The results of the MLM approach were compared with the results of a general linear model approach that does not take family structure in to account. In total, 11 quantitative trait loci (QTL) and 21 SNPs, were identified to be significantly associated with BW traits and 5 QTL and 5 SNPs were found associated with FE traits using MLM approach. Besides some overlaps between the results of the two GWAS approaches, there are considerable differences in the detected QTL. Even though the genomic inflation factor (λ) values indicate that there is no strong family structure in this population, using models that account for the existing family structure may reduce bias and increase accuracy of the estimated SNP effects in the association analysis. The SNPs and candidate genes identified in this study provide information on the genetic background of BW and FE traits in broiler chickens and might be used as prior information for genomic selection.

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Background The objectives of this study were to (1) simultaneously estimate genetic parameters for BW, feed intake (FI), and body weight gain (Gain) during a FI test in broiler chickens using multi-trait Bayesian analysis; (2) derive phenotypic and genetic residual feed intake (RFI) and estimate genetic parameters of the resulting traits; and (3) compute a Bayesian measure of direct and correlated superiority of a group selected on phenotypic or genetic residual feed intake. A total of 56,649 male and female broiler chickens were measured at one of two ages ($${\text{t}}$$ t or $${\text{t}} - 6$$ t - 6 days). BW, FI, and Gain of males and females at the two ages were considered as separate traits, resulting in a 12-trait model. Phenotypic RFI ($${\text{RFI}}_{\text{P}}$$ RFI P ) and genetic RFI ($${\text{RFI}}_{\text{G}}$$ RFI G ) were estimated from a conditional distribution of FI given BW and Gain using partial phenotypic and partial genetic regression coefficients, respectively. Results Posterior means of heritability for BW, FI and Gain were moderately high and estimates were significantly different between males and females at the same age for all traits. In addition, the genetic correlations between male and female traits at the same age were significantly different from 1, which suggests a sex-by-genotype interaction. Genetic correlations between $${\text{RFI}}_{\text{P}}$$ RFI P and $${\text{RFI}}_{\text{G }}$$ RFI G were significantly different from 1 at an older age but not at a younger age. Conclusions The results of the multivariate Bayesian analyses in this study showed that genetic evaluation for production and feed efficiency traits should take sex and age differences into account to increase accuracy of selection and genetic gain. Moreover, for communicating with stakeholders, it is easier to explain results from selection on $${\text{RFI}}_{\text{G}}$$ RFI G than selection on $${\text{RFI}}_{\text{P}}$$ RFI P , since $${\text{RFI}}_{\text{G}}$$ RFI G is genetically independent of production traits and it explains the efficiency of birds in nutrient utilization independently of energy requirements for production and maintenance.