PDF(Pubmed)
Abstract：
OBJECTIVE: The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens.
METHODS: The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures.
RESULTS: A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients (FROH) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable (r = 0.18-1). Five ROH islands harbouring important quantitative trait loci were identified.
CONCLUSIONS: This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions.
METHODS: The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures.
RESULTS: A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients (FROH) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable (r = 0.18-1). Five ROH islands harbouring important quantitative trait loci were identified.
CONCLUSIONS: This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions.
摘要：
■纯合性（ROH）的分析已用于评估近交水平并鉴定各种牲畜物种的选择特征。这项研究的目的是表征ROH模式，估计近亲繁殖率，并确定红棕色韩国土鸡的选择特征。
■在分析中使用了651只鸡的Illumina60KSNP芯片数据。使用PLINKv1.9软件分析纯合性的运行。使用GCTA软件估计近交系数，并检查其相关性。探索具有高水平ROH的基因组区域以鉴定选择标记。
■在这项研究中总共检测到32,176个ROH片段。大多数ROH段短于4Mb。平均ROH近交系数（FROH）随ROH片段的长度而变化。从不同方法计算的近交系数的平均值也是可变的。不同近交系数之间的相关性呈正相关且高度可变（r=0.18-1）。鉴定出五个具有重要数量性状基因座的ROH岛。
■这项研究评估了红棕色本地韩国鸡的近亲繁殖水平和纯合性模式。这项研究的结果表明，最近的近亲繁殖水平很低，这表明红棕色韩国土鸡的保护取得了实质性进展。此外,在纯合区域中检测到与重要生产性状相关的候选基因组区域。
■在分析中使用了651只鸡的Illumina60KSNP芯片数据。使用PLINKv1.9软件分析纯合性的运行。使用GCTA软件估计近交系数，并检查其相关性。探索具有高水平ROH的基因组区域以鉴定选择标记。
■在这项研究中总共检测到32,176个ROH片段。大多数ROH段短于4Mb。平均ROH近交系数（FROH）随ROH片段的长度而变化。从不同方法计算的近交系数的平均值也是可变的。不同近交系数之间的相关性呈正相关且高度可变（r=0.18-1）。鉴定出五个具有重要数量性状基因座的ROH岛。
■这项研究评估了红棕色本地韩国鸡的近亲繁殖水平和纯合性模式。这项研究的结果表明，最近的近亲繁殖水平很低，这表明红棕色韩国土鸡的保护取得了实质性进展。此外,在纯合区域中检测到与重要生产性状相关的候选基因组区域。
