Patterns of homozygosity in insular and continental goat breeds

<b>Abstract</b> <b>Background</b> Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. <b>Results</b> Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and <i>F</i>_ROH values (<i>P</i>-value &lt; 0.05). Goats from Mediterranean islands represent a more complex case because certain populations displayed a significantly increased level of homozygosity (<i>e.g.</i> Girgentana) and others did not (<i>e.g.</i> Corse and Sarda). Correlations of number and total length of ROH for insular goat populations with the distance between islands and the nearest continental locations revealed an effect of extremely long distances on the patterns of homozygosity. <b>Conclusions</b> These results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management.<b></b>

**摘要**
**研究背景** 品种的遗传隔离可能导致遗传多样性显著丧失，并对健康与生产性能造成不利影响。本研究采用山羊50K SNP分型芯片（Goat SNP50 BeadChip）对25个欧洲和非洲山羊品种的480个个体进行基因分型，通过比较海岛种群与邻近大陆种群的纯合子分布格局，探究地理隔离对山羊遗传多样性格局的影响。
**研究结果** 在所分析的山羊品种中，纯合子区域（Runs of Homozygosity, ROH）的数量与总长度存在显著品种差异；部分品种的ROH可覆盖基因组的较大比例，冰岛山羊的ROH总长度可达1.6 Gb。与对应大陆种群相比，冰岛、马达加斯加、拉帕尔马岛以及爱尔兰（比尔贝里山羊与阿伦山羊）的山羊种群的ROH覆盖度、ROH数量与基于ROH的近交系数（F_ROH）均显著升高（P值<0.05）。地中海岛屿山羊种群的情况更为复杂：部分种群的纯合度显著升高（如吉尔真塔纳山羊），而其余种群则无此现象（如科西嘉山羊与撒丁岛山羊）。对海岛山羊种群的ROH数量、总长度与岛屿距最近大陆的距离进行相关性分析，结果显示极远距离的地理隔离对纯合子分布格局存在显著影响。
**研究结论** 本研究结果表明，岛屿化对山羊纯合子分布格局的影响存在差异。马达加斯加、冰岛、爱尔兰（比尔贝里山羊与阿伦山羊）以及拉帕尔马岛的山羊种群呈现较高的纯合度，而地中海岛屿的山羊种群的纯合子分布格局则与大陆种群相似。上述结果表明，海岛山羊种群的遗传多样性受多种因素共同调控，包括地理分布、种群规模、种群历史、贸易活动以及品种管理策略。