Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.
Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.
Poult Sci. 2019 Feb 1;98(2):581-589. doi: 10.3382/ps/pey426.
Selection for rapid growth in chickens has always been accompanied by increased fat deposition and excessive fat deposition, especially abdominal fat, cannot only decrease feed efficiency but also cause many diseases. Finding the candidate genes associated with abdominal fat deposition is essential for breeding. To identify these candidate genes, we applied linkage disequilibrium and selection signature analysis using chicken 60 k single nucleotide polymorphism (SNP) chips in two broiler lines divergently selected for abdominal fat content for 11 generations. After quality control, 46,033 SNPs were left for analysis. Using these SNPs, we found that r2 was 0.06 to 0.14 in the lean line and 0.07 to 0.13 in the fat line for all 28 chromosomes (except GGA16). Pairwise SNP distances <25 kb showed a mean r2 = 0.33 in the lean line and r2 = 0.32 in the fat line. The fixation index (FST) analysis was carried out and 46 SNPs with the top 0.1% of the FST value was detected as the loci with selection signatures. Besides FST, hapFLK was also used to detect selection signatures for abdominal fat content. A total of 11 genes, including transient receptor potential cation channel subfamily C member 4, estrogen related receptor gamma, fibroblast growth factor 13, G-protein-signaling modulator 2, RAR related orphan receptor A, phospholipase A2 group X, mitochondrial ribosomal protein L28, metadherin, calcitonin receptor like receptor, serine/threonine kinase 39, and nuclear factor I A, were detected as the important candidate genes for abdominal fat deposition based on their basic functions. The results of the present study may benefit the understanding of genetic mechanism of abdominal fat deposition in chicken.
选择快速生长的鸡种通常伴随着脂肪沉积的增加，过多的脂肪沉积，尤其是腹部脂肪，不仅会降低饲料效率，还会导致许多疾病。寻找与腹部脂肪沉积相关的候选基因对于育种至关重要。为了鉴定这些候选基因，我们在两个肉鸡品系中应用连锁不平衡和选择信号分析，这两个品系经过 11 代的腹部脂肪含量选择已经呈现出明显差异。经过质量控制，留下了 46033 个 SNP 进行分析。利用这些 SNP，我们发现 r2 在瘦肉系为 0.06 到 0.14，在脂肪系为 0.07 到 0.13，覆盖了所有 28 条染色体（除了 GGA16）。在瘦肉系和脂肪系中，两条 SNP 之间的距离小于 25 kb 时 r2 的平均值分别为 0.33 和 0.32。固定指数（FST）分析显示，在脂肪系和瘦肉系中，有 46 个 SNP 的 FST 值排在前 0.1%，被认为是具有选择信号的基因座。除了 FST，hapFLK 也被用来检测与腹部脂肪含量相关的选择信号。总共检测到 11 个基因，包括瞬时受体电位阳离子通道亚家族 C 成员 4、雌激素相关受体 γ、成纤维细胞生长因子 13、G 蛋白信号调节因子 2、视黄酸相关孤儿受体 A、磷脂酶 A2 组 X、线粒体核糖体蛋白 L28、metadherin、降钙素受体样受体、丝氨酸/苏氨酸激酶 39 和核因子 I A，它们被认为是与腹部脂肪沉积相关的重要候选基因，基于它们的基本功能。本研究的结果可能有助于理解鸡腹部脂肪沉积的遗传机制。
