Data from: Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds

We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (FROH) with pedigree-based inbreeding coefficients (FPED). The linear relationship between FROH and FPED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.本研究采用山羊50K Illumina基因分型芯片（caprine 50k Illumina BeadChip）的基因型数据，对10个瑞士本地山羊品种的品种内及品种间遗传多样性进行评估。通过三种不同的聚类方法，可将山羊样本归类至对应的品种类群，但内拉韦尔扎斯卡山羊（Nera Verzasca）与提契诺灰山羊（Tessin Grey）的样本无法相互区分。不同遗传多样性指标的分析结果显示，阿彭策尔山羊（Appenzell）、托根堡山羊（Toggenburg）、瓦莱山羊（Valais）与博特山羊（Booted）应在未来的保护工作中得到优先关注。此外，本研究分析了纯合子片段（runs of homozygosity, ROH），并将基于纯合子片段的基因组近交系数（FROH）与基于系谱的近交系数（FPED）进行了对比。通过纳入三个主要山羊品种（萨能山羊（Saanen）、查莫瓦山羊（Chamois）与托根堡山羊（Toggenburg））的样本，本研究验证了山羊群体中FROH与FPED之间的线性相关关系。FROH可作为描述缺乏系谱信息的山羊品种近交水平的适宜指标。最后，本研究挖掘了不同品种间的选择信号，共鉴定得到384个候选选择信号。其中25个最显著的基因组窗口内包含了与多种性状相关的已知基因：如毛色变异相关基因（MITF、KIT、ASIP）、生长性状相关基因（IGF2、IGF2R、HRAS、FGFR3）以及乳成分相关基因（PITX2）。本研究还重点标注了多个与种群形成相关的候选基因，这些基因可能因适应高山环境而受到选择。本研究结果为瑞士本地山羊品种的遗传多样性管理提供了当代参考依据。