Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds.
Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds.
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DOI：
10.1186/1471-2164-15-601
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发表时间：
2014-07-16
期刊：
影响因子：
4.4
通讯作者：
Crooijmans RP
中科院分区：
文献类型：
--
作者：
Herrero-Medrano JM;Megens HJ;Groenen MA;Bosse M;Pérez-Enciso M;Crooijmans RP
保护遗传学的一个主要问题是保持种群的遗传多样性。牲畜品种的遗传变异受到世界各地地方品种逐渐边缘化的威胁，从而有利于高产猪。我们使用高密度SNP和重测序数据来评估来自欧洲的地方猪品种的遗传多样性。此外，我们对来自商品品种的猪进行了重新测序，以确定导致这些品种之间表型差异的潜在候选突变。我们的研究结果指出了一些遗传多样性低的地方品种，它们的基因组显示出高比例的纯合子区域（约50%），并且含有大量潜在的破坏性突变。我们还观察到高密度SNP数据与下一代测序数据之间的遗传多样性估计高度相关（在个体水平上r = 0.96）。对商品品种和任何地方品种中固定的非同义snp进行研究，但具有不同的等位基因，发现99个非同义snp影响65个基因。AZGP1和TAS2R40基因是可能导致环境适应差异的候选突变的例证。我们还观察到，高产品种可能在涉及免疫应答的基因中失去了有利的基因型，例如IL12RB2和STAB1，这可能是猪集约化生产系统中强人工干预的结果。60K SNP计算的遗传多样性与全基因组重测序数据之间的高度相关性表明，尽管存在预期的偏差，但猪60K SNP Beadchip提供了可靠的欧洲猪群体基因组多样性估计。此外，该分析还为地方品种的遗传表征策略提供了见解。重新测序的本地猪和重新测序的商品猪之间的比较使得报告候选突变有可能导致这些品种群体之间的表型差异。这项研究强调了低投入品种作为养猪生产行业有价值的遗传库的重要性。然而，高水平的ROHs、近亲繁殖和潜在的破坏性突变强调了对地方品种进行遗传表征以保持其基因组变异性的重要性。本文的在线版本（doi:10.1186/1471-2164-15-601）包含补充材料，可供授权用户使用。
A major concern in conservation genetics is to maintain the genetic diversity of populations. Genetic variation in livestock species is threatened by the progressive marginalisation of local breeds in benefit of high-output pigs worldwide. We used high-density SNP and re-sequencing data to assess genetic diversity of local pig breeds from Europe. In addition, we re-sequenced pigs from commercial breeds to identify potential candidate mutations responsible for phenotypic divergence among these groups of breeds. Our results point out some local breeds with low genetic diversity, whose genome shows a high proportion of regions of homozygosis (>50%) and that harbour a large number of potentially damaging mutations. We also observed a high correlation between genetic diversity estimates using high-density SNP data and Next Generation Sequencing data (r = 0.96 at individual level). The study of non-synonymous SNPs that were fixed in commercial breeds and also in any local breed, but with different allele, revealed 99 non-synonymous SNPs affecting 65 genes. Candidate mutations that may underlie differences in the adaptation to the environment were exemplified by the genes AZGP1 and TAS2R40. We also observed that highly productive breeds may have lost advantageous genotypes within genes involve in immune response – e.g. IL12RB2 and STAB1–, probably as a result of strong artificial in the intensive production systems in pig. The high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations despite the expected bias. Moreover, this analysis gave insights for strategies to the genetic characterization of local breeds. The comparison between re-sequenced local pigs and re-sequenced commercial pigs made it possible to report candidate mutations to be responsible for phenotypic divergence among those groups of breeds. This study highlights the importance of low input breeds as a valuable genetic reservoir for the pig production industry. However, the high levels of ROHs, inbreeding and potentially damaging mutations emphasize the importance of the genetic characterization of local breeds to preserve their genomic variability. The online version of this article (doi:10.1186/1471-2164-15-601) contains supplementary material, which is available to authorized users.
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