PDF(Pubmed)
Abstract：
African swine fever (ASF) is a rapidly fatal viral haemorrhagic fever in Chinese domestic pigs. Although very high mortality is observed in pig farms after an ASF outbreak, clinically healthy and antibody-positive pigs are found in those farms, and viral detection is rare from these pigs. The ability of pigs to resist ASF viral infection may be modulated by host genetic variations. However, the genetic basis of the resistance of domestic pigs against ASF remains unclear. We generated a comprehensive set of structural variations (SVs) in a Chinese indigenous Xiang pig with ASF-resistant (Xiang-R) and ASF-susceptible (Xiang-S) phenotypes using whole-genome resequencing method. A total of 53,589 nonredundant SVs were identified, with an average of 25,656 SVs per individual in the Xiang pig genome, including insertion, deletion, inversion and duplication variations. The Xiang-R group harboured more SVs than the Xiang-S group. The F-statistics (FST) was carried out to reveal genetic differences between two populations using the resequencing data at each SV locus. We identified 2,414 population-stratified SVs and annotated 1,152 Ensembl genes (including 986 protein-coding genes), in which 1,326 SVs might disturb the structure and expression of the Ensembl genes. Those protein-coding genes were mainly enriched in the Wnt, Hippo, and calcium signalling pathways. Other important pathways associated with the ASF viral infection were also identified, such as the endocytosis, apoptosis, focal adhesion, Fc gamma R-mediated phagocytosis, junction, NOD-like receptor, PI3K-Akt, and c-type lectin receptor signalling pathways. Finally, we identified 135 candidate adaptive genes overlapping 166 SVs that were involved in the virus entry and virus-host cell interactions. The fact that some of population-stratified SVs regions detected as selective sweep signals gave another support for the genetic variations affecting pig resistance against ASF. The research indicates that SVs play an important role in the evolutionary processes of Xiang pig adaptation to ASF infection.
摘要：
非洲猪瘟（ASF）是中国家猪的一种快速致命的病毒性出血热。尽管在ASF爆发后，猪场的死亡率非常高，在这些农场发现了临床健康和抗体阳性的猪，这些猪很少有病毒检测。猪抵抗ASF病毒感染的能力可能受宿主遗传变异的调节。然而,家猪对ASF的抗性的遗传基础仍不清楚。我们使用全基因组重测序方法，在具有抗ASF（Xiang-R）和易感ASF（Xiang-S）表型的中国本土香猪中生成了一套全面的结构变异（SV）。总共确定了53,589个非冗余SV，香猪基因组中平均每个个体25656SV，包括插入，删除,反转和重复变化。Xiang-R组比Xiang-S组拥有更多的SV。使用每个SV基因座的重测序数据进行F统计（FST）以揭示两个种群之间的遗传差异。我们确定了2,414个群体分层的SV，并注释了1,152个Ensembl基因（包括986个蛋白质编码基因），其中1,326个SV可能会干扰Ensembl基因的结构和表达。这些蛋白质编码基因主要富集在Wnt,河马,和钙信号通路。还确定了与ASF病毒感染相关的其他重要途径，例如内吞作用，凋亡，病灶粘连,FcγR介导的吞噬作用，交界处,NOD样受体,PI3K-Akt,和c型凝集素受体信号通路。最后,我们确定了135个候选适应性基因,这些基因与166个SVs重叠,参与病毒进入和病毒-宿主细胞相互作用.作为选择性扫描信号检测到的一些群体分层SVs区域的事实为影响猪对ASF抗性的遗传变异提供了另一种支持。研究表明，SVs在香猪适应ASF感染的进化过程中起着重要作用。
