Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China.
PLoS One. 2014 Apr 16;9(4):e94911. doi: 10.1371/journal.pone.0094911. eCollection 2014.
Identifying footprints of selection can provide a straightforward insight into the mechanism of artificial selection and further dig out the causal genes related to important traits. In this study, three between-population and two within-population approaches, the Cross Population Extend Haplotype Homozygosity Test (XPEHH), the Cross Population Composite Likelihood Ratio (XPCLR), the F-statistics (Fst), the Integrated Haplotype Score (iHS) and the Tajima's D, were implemented to detect the selection footprints on the X chromosome in three pig breeds using Illumina Porcine60K SNP chip. In the detection of selection footprints using between-population methods, 11, 11 and 7 potential selection regions with length of 15.62 Mb, 12.32 Mb and 9.38 Mb were identified in Landrace, Chinese Songliao and Yorkshire by XPEHH, respectively, and 16, 13 and 17 potential selection regions with length of 15.20 Mb, 13.00 Mb and 19.21 Mb by XPCLR, 4, 2 and 4 potential selection regions with length of 3.20 Mb, 1.60 Mb and 3.20 Mb by Fst. For within-population methods, 7, 10 and 9 potential selection regions with length of 8.12 Mb, 8.40 Mb and 9.99 Mb were identified in Landrace, Chinese Songliao and Yorkshire by iHS, and 4, 3 and 2 potential selection regions with length of 3.20 Mb, 2.40 Mb and 1.60 Mb by Tajima's D. Moreover, the selection regions from different methods were partly overlapped, especially the regions around 22∼25 Mb were detected under selection in Landrace and Yorkshire while no selection in Chinese Songliao by all three between-population methods. Only quite few overlap of selection regions identified by between-population and within-population methods were found. Bioinformatics analysis showed that the genes relevant with meat quality, reproduction and immune were found in potential selection regions. In addition, three out of five significant SNPs associated with hematological traits reported in our genome-wide association study were harbored in potential selection regions.
鉴定选择的足迹可以直接了解人工选择的机制，并进一步挖掘与重要性状相关的因果基因。本研究利用 Illumina Porcine60K SNP 芯片，采用跨群体扩展单体型纯合性检验（XPEHH）、跨群体复合似然比（XPCLR）、F 统计量（Fst）、整合单体型得分（iHS）和 Tajima's D 等两种群体内和三种群体间方法，在三个猪品种的 X 染色体上检测选择足迹。在使用群体间方法检测选择足迹时，XPEHH 在长白猪、中国民猪和大约克夏猪中分别鉴定到 11、11 和 7 个潜在选择区域，长度分别为 15.62Mb、12.32Mb 和 9.38Mb；XPCLR 鉴定到 16、13 和 17 个潜在选择区域，长度分别为 15.20Mb、13.00Mb 和 19.21Mb；Fst 鉴定到 4、2 和 4 个潜在选择区域，长度分别为 3.20Mb、1.60Mb 和 3.20Mb。在使用群体内方法时，iHS 在长白猪、中国民猪和大约克夏猪中分别鉴定到 7、10 和 9 个潜在选择区域，长度分别为 8.12Mb、8.40Mb 和 9.99Mb；Tajima's D 鉴定到 4、3 和 2 个潜在选择区域，长度分别为 3.20Mb、2.40Mb 和 1.60Mb。此外，不同方法鉴定的选择区域部分重叠，尤其是在长白猪和大约克夏猪中，22∼25Mb 左右的区域在三种群体间方法下均检测到选择，而中国民猪中则没有选择。在群体间和群体内方法鉴定的选择区域之间只有很少的重叠。生物信息学分析表明，在潜在选择区域中发现了与肉质、繁殖和免疫相关的基因。此外，在全基因组关联研究中报告的与血液学性状相关的 5 个显著 SNP 中有 3 个位于潜在选择区域内。
