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, FST),
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 STX5, that has been associated with tick resistance in
cattle, implicating it as a prime candidate in sheep. We also observed RAB6B and TF
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：蜱虫是专性吸血体外寄生虫，作为多种全球关注病原体的传播媒介与储存宿主，其重要性仅次于蚊子。已有研究报道本土绵羊的蜱虫侵染存在个体差异，但调控该性状的基因仍尚不明确。

结果：本研究采用ROH、LR-GWAS、XP-EHH、FST四种分析方法，对165只表现出高、低蜱虫感染率及梨形虫感染率的突尼斯绵羊的600K单核苷酸多态性（Single Nucleotide Polymorphism，SNP）基因型数据进行分析，共检出397个全基因组选择信号，覆盖991个基因。其中，经至少2种方法共同验证的45个信号被界定为高置信度选择扫荡区域，这些区域共涉及104个基因，包括免疫系统功能基因、溶质载体家族基因及趋化因子受体基因。有一个区域覆盖STX5基因，该基因已被证实与牛的蜱虫抗性相关，提示其可能是绵羊蜱虫抗性的核心候选基因。本研究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和TF基因，这表明在蜱虫侵染压力下，自然选择正促进绵羊的生长与发育稳定性。此外，本分析还揭示了精细的基因组结构特征，提示突尼斯绵羊存在隐秘分化现象。

结论：本研究结果提供了一套基因组学参考依据，可用于深化对非洲本土绵羊蜱虫抗性遗传结构及隐秘分化现象的认知。