PDF(Pubmed)
Abstract：
BACKGROUND: Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding.
RESULTS: To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima\'s D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively.
CONCLUSIONS: Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.
RESULTS: To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima\'s D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively.
CONCLUSIONS: Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.
摘要：
背景：土著鸡是通过自然选择和人工选择相结合而开发的；本质上，基因组的变化通过混合事件导致了这些现代品种的形成。然而,他们令人困惑的遗传背景包括调节复杂性状的基因组足迹，不利于现代动物育种。
结果：为了更好地评估本地鸡驯化的候选区域，我们考虑了13只本地鸡的纯合性（ROHs）和选择性特征。Silkie羽毛鸡的基因组呈现出最高的杂合性，而在鲁花鸡中发现了最高的近亲繁殖状态和ROH数。短路功率(<1Mb),是所有鸡的主要类型。共检测出291个ROH岛,QTLdb作图结果表明，体重和car体性状是最重要的性状。在12个种群中检测到覆盖VSTM2A基因的2号染色体ROH。结合Tajima的D指数分析显示，18个基因(例如，VSTM2A,BBOX1和RYR2）处于选择范围内，并被ROH岛覆盖。转录分析结果显示，RYR2和BBOX1在心脏和肌肉组织中特异性表达，分别。
结论：基于ROH和选择性特征的全基因组扫描，我们评估了基因组特征,并检测到被ROH岛和选择性特征覆盖的重要候选基因.这项研究的发现促进了对遗传多样性的理解，并为鸡的育种和保护策略提供了有价值的见解。
结果：为了更好地评估本地鸡驯化的候选区域，我们考虑了13只本地鸡的纯合性（ROHs）和选择性特征。Silkie羽毛鸡的基因组呈现出最高的杂合性，而在鲁花鸡中发现了最高的近亲繁殖状态和ROH数。短路功率(<1Mb),是所有鸡的主要类型。共检测出291个ROH岛,QTLdb作图结果表明，体重和car体性状是最重要的性状。在12个种群中检测到覆盖VSTM2A基因的2号染色体ROH。结合Tajima的D指数分析显示，18个基因(例如，VSTM2A,BBOX1和RYR2）处于选择范围内，并被ROH岛覆盖。转录分析结果显示，RYR2和BBOX1在心脏和肌肉组织中特异性表达，分别。
结论：基于ROH和选择性特征的全基因组扫描，我们评估了基因组特征,并检测到被ROH岛和选择性特征覆盖的重要候选基因.这项研究的发现促进了对遗传多样性的理解，并为鸡的育种和保护策略提供了有价值的见解。
