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Feeding represents one of the main costs of livestock production. Feed efficiency (FE) is a trait which relates the weight to feed intake, two important variables for livestock production. The aim of this study was to identify genes associate with FE in Santa Ines sheep population. Individual dry matter intake and growth were measured from 165 animals from herds at Bahia state, Brazil. Muscle samples were used for DNA extraction and genotyping was performed using the Illumina Ovine SNP50 BeadChip (Illumina Inc., San Diego, CA). Samples with call rate lower than 90%, and SNP with minor allele frequency (MAF) lower than 0.05, proportion of missing genotypes higher than 20% and frequency of heterozygote higher than 0.001 of the expected in Hardy-Weinberg Equilibrium were excluded. The genomic-wide association analyses (GWAS) were performed by using GS3 software, under Bayes C approach. This method considers the probability that a SNP has zero effect as unknown, and it assumes a common variance for all SNP additive effects. The three SNPs with greater effect on FE were: s44621.1, located on chromosome 7 (8351647 bp), near to the PDE8B gene; s45145.1, located on chromosome 22 (40276684 bp), near to the GFRA1 gene; and s60402.1, located on chromosome 18 (24579847 bp). The PDE8B gene was previously related to the thyroid gland, which affects the metabolism, being possibly correlated with FE. Some studies indicated that GFRA1 gene has effect in receptor tyrosine kinase (TK). The TK has effect on cell proliferation, growth factors, development and differentiation. The SNP s60402.1 was firstly described in this study, requiring more studies about this mechanism. The SNPs found in the present study were reported in human and mouse studies, but there are no reports about them in ovine studies. Thus, for a better understanding of the genetic control under FE, it is necessary a more detailed study about genes and SNP related with ovine populations.