A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds.
A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds.
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DOI：
10.1186/s12711-016-0229-6
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发表时间：
2016-07-25
期刊：
影响因子：
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通讯作者：
Amills M
中科院分区：
文献类型：
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作者：
Manunza A;Noce A;Serradilla JM;Goyache F;Martínez A;Capote J;Delgado JV;Jordana J;Muñoz E;Molina A;Landi V;Pons A;Balteanu V;Traoré A;Vidilla M;Sánchez-Rodríguez M;Sànchez A;Cardoso TF;Amills M
当前工作的主要目标是根据 Illumina 山羊 SNP50 BeadChip 生成的全基因组多样性数据（群体规模，N = 176）推断七个西班牙山羊品种（Malagueña、Murciano-Granadina、Florida、Palmera、Mallorquina、Bermeya 和 Blanca de Rasquera）的人口历史。出于比较目的，来自欧洲（萨嫩和喀尔巴阡）和非洲（突尼斯、贾隆凯和萨赫勒）的另外 5 个种群也包含在本次分析中（N = 80）。我们的研究结果表明，西班牙山羊的遗传背景主要可以追溯到欧洲品种，尽管在两个安达卢西亚品种（马拉盖尼亚和穆尔恰诺-格拉纳迪纳）中检测到北非混血的迹象。一般来说，在分析的七个西班牙山羊品种中，观察到的和预期的杂合性非常相似，无论其种群规模和保护状况如何。对于在过去几十年中种群数量急剧下降的 Mallorquina 和 Blanca de Rasquera 品种，我们观察到大型（ROH）的频率增加，这一发现与最近的近亲繁殖一致。相比之下，帕尔梅拉山羊品种的基因组的很大一部分包含短 ROH，这表明存在强大而古老的创始人效应。与非洲山羊的杂交、遗传漂变和近亲繁殖对当前工作中分析的七个西班牙山羊品种产生了不同的影响。这产生了全基因组多样性的独特模式，为这些人群的人口统计历史提供了新的线索。本文的在线版本 (doi:10.1186/s12711-016-0229-6) 包含补充材料，可供授权用户使用。
The main goal of the current work was to infer the demographic history of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes. Our results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and Murciano-Granadina). In general, observed and expected heterozygosities were quite similar across the seven Spanish goat breeds under analysis irrespective of their population size and conservation status. For the Mallorquina and Blanca de Rasquera breeds, which have suffered strong population declines during the past decades, we observed increased frequencies of large-sized (ROH), a finding that is consistent with recent inbreeding. In contrast, a substantial part of the genome of the Palmera goat breed comprised short ROH, which suggests a strong and ancient founder effect. Admixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work. This has generated distinct patterns of genome-wide diversity that provide new clues about the demographic history of these populations. The online version of this article (doi:10.1186/s12711-016-0229-6) contains supplementary material, which is available to authorized users.