Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China.
PLoS One. 2012;7(7):e40736. doi: 10.1371/journal.pone.0040736. Epub 2012 Jul 11.
We conducted a selection signature analysis using the chicken 60k SNP chip in two chicken lines that had been divergently selected for abdominal fat content (AFC) for 11 generations. The selection signature analysis used multiple signals of selection, including long-range allele frequency differences between the lean and fat lines, long-range heterozygosity changes, linkage disequilibrium, haplotype frequencies, and extended haplotype homozygosity. Multiple signals of selection identified ten signatures on chromosomes 1, 2, 4, 5, 11, 15, 20, 26 and Z. The 0.73 Mb PC1/PCSK1 region of the Z chromosome at 55.43-56.16 Mb was the most heavily selected region. This region had 26 SNP markers and seven genes, Mar-03, SLC12A2, FBN2, ERAP1, CAST, PC1/PCSK1 and ELL2, where PC1/PCSK1 are the chicken/human names for the same gene. The lean and fat lines had two main haplotypes with completely opposite SNP alleles for the 26 SNP markers and were virtually line-specific, and had a recombinant haplotype with nearly equal frequency (0.193 and 0.196) in both lines. Other haplotypes in this region had negligible frequencies. Nine other regions with selection signatures were PAH-IGF1, TRPC4, GJD4-CCNY, NDST4, NOVA1, GALNT9, the ESRP2-GALR1 region with five genes, the SYCP2-CADH4 with six genes, and the TULP1-KIF21B with 14 genes. Genome-wide association analysis showed that nearly all regions with evidence of selection signature had SNP effects with genome-wide significance (P<10(-6)) on abdominal fat weight and percentage. The results of this study provide specific gene targets for the control of chicken AFC and a potential model of AFC in human obesity.
我们使用鸡 60k SNP 芯片在两个已经进行了 11 代腹部脂肪含量（AFC）分歧选择的鸡系中进行了选择信号分析。选择信号分析使用了多种选择信号，包括瘦线和胖线之间的长距离等位基因频率差异、长距离杂合性变化、连锁不平衡、单倍型频率和扩展单倍型同型性。多种选择信号在染色体 1、2、4、5、11、15、20、26 和 Z 上鉴定出了 10 个信号。Z 染色体上的 55.43-56.16 Mb 的 PC1/PCSK1 区域是选择最强烈的区域。该区域有 26 个 SNP 标记和 7 个基因，Mar-03、SLC12A2、FBN2、ERAP1、CAST、PC1/PCSK1 和 ELL2，其中 PC1/PCSK1 是鸡/人类对同一基因的命名。瘦线和胖线有两个主要的单倍型，26 个 SNP 标记的 SNP 等位基因完全相反，几乎是特定于系的，并且在两条线中具有几乎相等频率（0.193 和 0.196）的重组单倍型。该区域的其他单倍型频率可忽略不计。其他具有选择信号的 9 个区域是 PAH-IGF1、TRPC4、GJD4-CCNY、NDST4、NOVA1、GALNT9、包含五个基因的 ESRP2-GALR1 区域、包含六个基因的 SYCP2-CADH4 区域以及包含 14 个基因的 TULP1-KIF21B 区域。全基因组关联分析表明，几乎所有具有选择信号证据的区域都有 SNP 效应，对腹部脂肪重量和百分比具有全基因组显著性（P<10(-6)）。这项研究的结果为控制鸡 AFC 的特定基因靶标提供了依据，也为人类肥胖的 AFC 提供了一个潜在模型。
