Genomic variation in tick infestation and cryptic divergence in Tunisian indigenous sheep

Background: Ticks are obligate haematophagous ectoparasites considered second to mosquitos as vectors and reservoirs of multiple pathogens of global concern. Individual variation in tick infestation has been reported in indigenous sheep, but the genes regulating the trait are poorly understood. Results: Here, we report 397 genome-wide signatures of selection overlapping 991 genes from the analysis, using four methods (ROH, LR-GWAS, XP-EHH, F_ST), of 600K SNP genotype data from 165 Tunisian sheep exhibiting high and low tick infestations and piroplasm infections. We considered 45 signatures that were detected by consensus results of at least two methods as high-confidence selection sweep regions. These spanned 104 genes which included immune system function genes, solute carriers and chemokine receptor. One region spanned <i>STX5</i>, that has been associated with tick resistance in cattle, implicating it as a prime candidate in sheep. We also observed <i>RAB6B</i> and<i> TF</i> in a high confidence candidate region that has been associated with growth traits suggesting natural selection is enhancing growth and developmental stability under tick challenge. The analysis also revealed fine-scale genome structure suggesting the existence of cryptic divergence in Tunisian sheep. Conclusion: Our findings provide a genomic reference that could be used to enhance the understanding of genetic architecture of tick resistance and cryptic divergence in indigenous African sheep.

背景：蜱虫是专性吸血外寄生节肢动物，作为全球范围内多种重要病原体的传播媒介与储存宿主，其危害仅次于蚊子。已有研究报道地方品种绵羊的蜱虫感染存在个体差异，但调控该性状的基因仍未得到充分解析。结果：本研究基于165只表现出高、低蜱虫感染率以及梨形虫感染的突尼斯绵羊的600K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因型数据，采用四种分析方法（ROH、LR-GWAS、XP-EHH、F_ST）开展分析，共鉴定出397个全基因组选择信号，覆盖991个基因。我们将至少两种方法共同检测到的45个选择信号定义为高置信度的选择性清除区域，这些区域共覆盖104个基因，其中包括免疫功能基因、溶质转运蛋白以及趋化因子受体。其中一个区域包含STX5，该基因已被证实与牛的蜱虫抗性相关，提示其可作为绵羊蜱虫抗性的核心候选基因。我们还在一个与生长性状相关的高置信度候选区域中发现了RAB6B与TF，这提示在蜱虫感染压力下，自然选择正强化绵羊的生长与发育稳定性。本分析还揭示了精细的基因组结构特征，提示突尼斯绵羊中存在隐秘分化现象。结论：本研究结果为解析非洲地方品种绵羊的蜱虫抗性遗传架构以及隐秘分化现象提供了基因组学参考依据。