Departamento de Producción Animal, Fac, de Veterinaria, Área de Genética, C,P,30100 Murcia, Spain.
BMC Genet. 2013 Oct 30;14:106. doi: 10.1186/1471-2156-14-106.
Inbreeding is among the major concerns in management of local livestock populations. The effective population size of these populations tends to be small, which enhances the risk of fitness reduction and extinction. High-density SNP data make it possible to undertake novel approaches in conservation genetics of endangered breeds and wild populations.A total of 97 representative samples of domestic and wild pig populations from the Iberian Peninsula, subjected to different levels of threat with extinction, were genotyped with a 60 K SNP panel. Data analyses based on: (i) allele frequency differences; (ii) linkage disequilibrium and (iii) runs of homozygosity were integrated to study population relationships, inbreeding and demographic history.
The domestic pigs analyzed belonged to local Spanish and Portuguese breeds: Iberian ─ including the variants Retinto Iberian, Negro Iberian and Manchado de Jabugo ─, Bisaro and Chato Murciano. The population structure and persistence of phase analysis suggested high genetic relations between Iberian variants, with recent crossbreeding of Manchado de Jabugo with other pig populations. Chato Murciano showed a high frequency of long runs of homozygosity indicating recent inbreeding and reflecting the recent bottleneck reported by historical records. The Chato Murciano and the Manchado de Jabugo breeds presented the lowest effective population sizes in accordance with their status of highly inbred breeds. The Iberian wild boar presented a high frequency of short runs of homozygosity indicating past small population size but no signs of recent inbreeding. The Iberian breed showed higher genetic similarities with Iberian wild boar than the other domestic breeds.
High-density SNP data provided a consistent overview of population structure, demographic history and inbreeding of minority breeds and wild pig populations from the Iberian Peninsula. Despite the very different background of the populations used, we found a good agreement between the different analyses. Our results are also in agreement with historical reports and provide insight in the events that shaped the current genetic variation of pig populations from the Iberian Peninsula. The results exposed will aid to design and implement strategies for the future management of endangered minority pig breeds and wild populations.
近亲繁殖是地方牲畜种群管理中的主要关注点之一。这些种群的有效种群规模往往较小，这增加了适应能力降低和灭绝的风险。高密度 SNP 数据使得在濒危品种和野生种群的保护遗传学中采用新方法成为可能。对来自伊比利亚半岛的 97 个国内和野生猪种群的代表性样本进行了基因分型，这些样本受到不同程度的灭绝威胁，并使用了 60 K SNP 面板。数据分析基于：（i）等位基因频率差异；（ii）连锁不平衡和（iii）纯合子运行，用于研究种群关系、近亲繁殖和人口历史。
分析的家猪属于当地的西班牙和葡萄牙品种：伊比利亚——包括变体 Retinto Iberian、Negro Iberian 和 Manchado de Jabugo——Bisaro 和 Chato Murciano。种群结构和相位分析的持久性表明，伊比利亚变体之间存在高度的遗传关系，近期 Manchado de Jabugo 与其他猪群杂交。Chato Murciano 显示出长纯合子运行的高频，表明近期近亲繁殖，并反映了历史记录中报道的近期瓶颈。Chato Murciano 和 Manchado de Jabugo 品种的有效种群规模最小，符合高度近亲繁殖品种的状况。伊比利亚野猪显示出短纯合子运行的高频，表明过去的小种群规模，但没有近期近亲繁殖的迹象。伊比利亚品种与伊比利亚野猪的遗传相似性高于其他家猪品种。
高密度 SNP 数据为伊比利亚半岛的少数品种和野猪种群的种群结构、人口历史和近亲繁殖提供了一致的概述。尽管使用的种群背景非常不同，但我们发现不同分析之间存在良好的一致性。我们的结果也与历史报告一致，并为塑造伊比利亚半岛猪种群当前遗传变异的事件提供了深入了解。所暴露的结果将有助于设计和实施未来濒危少数猪品种和野生种群的管理策略。
