Feed accounts for about 70% of the total cost of poultry meat production. Residual feed intake (RFI) has become the preferred measure of feed efficiency because it is phenotypically independent of growth rate and body weight. In this study, our aim was to estimate genetic parameters and identify quantitative trait loci (QTL) for feed efficiency in 3314 purebred broilers using a genome-wide association study. Broilers were genotyped using a custom 55 K single nucleotide polymorphism (SNP) array. Estimates of genomic heritability for seven growth and feed efficiency traits, including body weight at 28 days of age (BW28), BW42, average daily feed intake (ADFI), RFI, and RFI adjusted for weight of abdominal fat (RFIa), ranged from 0.12 to 0.26. Eleven genome-wide significant SNPs and 15 suggestively significant SNPs were detected, of which 19 clustered around two genomic regions. A region on chromosome 16 (2.34–2.66 Mb) was associated with both BW28 and BW42, and the most significant SNP in this region, AX_101003762, accounted for 7.6% of the genetic variance of BW28. The other region, on chromosome 1 (91.27–92.43 Mb) was associated with RFI and ADFI, and contains the NSUN3 and EPHA6 as candidate genes. The most significant SNP in this region, AX_172588157, accounted for 4.4% of the genetic variance of RFI. In addition, a genomic region containing the gene AGK on chromosome 1 was found to be associated with RFIa. The NSUN3 and AGK genes were found to be differentially expressed in breast muscle, thigh muscle, and abdominal fat between male broilers with high and low RFI. We identified QTL regions for BW28 and BW42 (spanning 0.32 Mb) and RFI (spanning 1.16 Mb). The NSUN3, EPHA6, and AGK were identified as the most likely candidate genes for these QTL. These genes are involved in mitochondrial function and behavioral regulation. These results contribute to the identification of candidate genes and variants for growth and feed efficiency in poultry.

中文翻译：

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鉴定QTL区域和候选基因以提高肉鸡的生长和饲料效率

饲料约占家禽肉生产总成本的70％。残余饲料摄入量（RFI）已成为饲料效率的首选指标，因为它在表型上与生长速率和体重无关。在这项研究中，我们的目标是使用全基因组关联研究来估计遗传参数并确定3314只纯种肉鸡饲料效率的定量性状基因座（QTL）。使用定制的55 K单核苷酸多态性（SNP）阵列对肉鸡进行基因分型。对七个生长和饲料效率性状的基因组遗传力的估计，包括28日龄时的体重（BW28），BW42，平均每日采食量（ADFI），RFI和根据腹部脂肪重量调整的RFI（RFIa），范围从0.12至0.26。检测到11个全基因组重要SNP和15个暗示重要SNP，其中19个簇集在两个基因组区域周围。BW28和BW42都与16号染色体上的一个区域（2.34-2.66 Mb）相关，该区域中最重要的SNP AX_101003762占BW28遗传变异的7.6％。染色体1上的另一个区域（91.27-92.43 Mb）与RFI和ADFI相关，并包含NSUN3和EPHA6作为候选基因。该区域中最重要的SNP AX_172588157占RFI遗传变异的4.4％。另外，发现在染色体1上含有基因AGK的基因组区域与RFIa相关。发现NSUN3和AGK基因在RFI高和低的雄性肉鸡之间在胸肌，大腿肌肉和腹部脂肪中差异表达。我们确定了BW28和BW42（跨越0.32 Mb）和RFI（跨越1.16 Mb）的QTL区域。NSUN3，EPHA6和AGK被确定为这些QTL最可能的候选基因。这些基因参与线粒体功能和行为调控。这些结果有助于鉴定候选基因和变体，以提高家禽的生长和饲料效率。