Data from: Multiple genomic signatures of selection amongst caprovines indigenous to a hot arid environment

Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species but, natural selection has played the major role amongst indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes are involved in multiple signaling and, signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes which directly or indirectly influence traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (several MYH, TRHDE, ALDH1A3) and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) are identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosome 12 and 10 respectively, providing, most likely, evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

山羊与绵羊均为适应性广泛的家养畜禽，已被融入各类不同环境与生产体系之中。自然选择与人工选择共同塑造了这两个物种种群的遗传变异，但在地方畜禽群体中，自然选择占据主导地位。为探究自然选择的选择信号，本研究利用基于山羊和绵羊50K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）微珠芯片（BeadChip）生成的基因型数据，对产自埃及西部沙漠沿海地带炎热干旱环境中的巴尔基（Barki）山羊与绵羊地方群体展开分析。本研究共鉴定出多个受选择的候选基因组区域，覆盖119个功能基因。其中绝大多数基因参与了多种信号通路与信号转导途径，参与调控各类细胞生理与生化过程。具体而言，我们鉴定到多个覆盖功能基因的选择印记，这些基因可直接或间接调控适应炎热干旱环境的相关性状：包括耐热性（黑素生成，涉及FGF2、GNAI3、PLCB1）、体尺与发育（涉及BMP2、BMP4、GJA3、GJB2）、能量与消化代谢（涉及多个MYH家族基因、TRHDE、ALDH1A3）以及神经与自身免疫应答（涉及GRIA1、IL2、IL7、IL21、IL1R1）。此外，本研究还在两个物种中鉴定出8个受选择的共同候选基因，以及一处共享的选择印记：该印记覆盖了一段与牛12号染色体保守同线的基因组区段，分别对应山羊12号染色体与绵羊10号染色体，这一发现大概率为两个不同但亲缘关系紧密的物种在共同环境下受到选择提供了证据。本研究凸显了地方畜禽作为探究选择扫荡与全基因组关联作图的模式生物的重要价值。