Population structure and history of the Welsh sheep breeds determined by whole genome genotyping.
Population structure and history of the Welsh sheep breeds determined by whole genome genotyping.
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DOI：
10.1186/s12863-015-0216-x
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发表时间：
2015-06-20
期刊：
影响因子：
2.9
通讯作者：
Larkin DM
中科院分区：
文献类型：
--
作者：
Beynon SE;Slavov GT;Farré M;Sunduimijid B;Waddams K;Davies B;Haresign W;Kijas J;MacLeod IM;Newbold CJ;Davies L;Larkin DM
威尔士农业部门中最重要的经济领域之一是养羊业，每年为英国经济贡献约2.3亿英镑。几个世纪以来，表型选择产生了一些本土绵羊品种，据推测这些品种适应了威尔士多样化和具有挑战性的景观。很少有人知道的历史，遗传多样性和这些品种与其他欧洲品种的关系。我们使用Illumina OvineSNP 50阵列对来自18个本地威尔士绵羊品种的353个个体进行基因分型，并表征了这些品种的遗传结构。然后将我们的基因分型数据与国际绵羊基因组联盟HapMap项目期间收集的74个全球品种的基因分型数据相结合并进行比较。基于模型的聚类威尔士和欧洲的品种表明共同的祖先。这一发现得到了多维尺度分析（MDS）的支持，该分析揭示了欧洲、非洲和亚洲品种的分离。正如预期的那样，商业特克塞尔和美利奴品种似乎有广泛的共同祖先与大多数欧洲品种。一致的高水平的单倍型共享之间观察到本地威尔士和其他欧洲品种。威尔士品种没有，但是，形成一个遗传同质的群体，品种之间的成对FST平均为0.107，范围在0.020和0.201之间。在18个本地品种中确定了四个亚群，在大多数山地品种中观察到高度的同质性。最近的有效人口规模估计连锁不平衡从88至825。威尔士品种是高度多样化的低至中等有效人口规模，并形成至少四个不同的遗传群体。我们的数据表明，共同的祖先之间的本土威尔士和欧洲的品种。这些发现为未来的全基因组关联研究提供了基础，也是在英国发展基因组学辅助育种策略的第一步。本文的在线版本（doi：10.1186/s12863-015-0216-x）包含补充材料，可供授权用户使用。
One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project. Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise FST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825. Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK. The online version of this article (doi:10.1186/s12863-015-0216-x) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Heaton MP;Leymaster KA;Kalbfleisch TS;Kijas JW;Clarke SM;McEwan J;Maddox JF;Basnayake V;Petrik DT;Simpson B;Smith TP;Chitko-McKown CG;International Sheep Genomics Consortium
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International Sheep Genomics Consortium
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作者：
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通讯作者：
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作者：
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通讯作者：
International Sheep Genomics Consortium Members