The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution
The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution
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DOI：
10.1186/s12864-019-5727-9
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发表时间：
2019-05-07
期刊：
影响因子：
4.4
通讯作者：
Weigend, Steffen
中科院分区：
文献类型：
--
作者：
Malomane, Dorcus Kholofelo;Simianer, Henner;Weigend, Steffen
背景自驯化以来，鸡不仅分散到世界各地，而且在此过程中也发生了显着的基因组变化。许多品种、品系或品系已经形成，这些代表了物种的多样性。然而，除了自然进化的力量，驯化后的管理做法（包括那些威胁遗传多样性的持久性）塑造了今天的鸡品种之间的遗传构成和多样性。作为SYNBREED项目的一部分，从地球仪收集了来自各种鸡群的样本，并用高密度SNP阵列进行基因分型。该小组由野生型、商业蛋鸡和肉鸡、土著村庄/当地类型和优质鸡品种组成。SYNBREED鸡多样性小组（SCDP）可作为研究鸡多样性遗传结构的公共基础。在目前的研究中，我们分析了遗传多样性之间和内的SCDP，这是非常重要的明智的决策，有效地管理农场动物遗传resources.ResultsMany的花式品种涵盖了广泛的频谱和聚类与其他品种的类似假定的起源所示的系统发育树和主成分分析。然而，花式品种以及高度选择的商业蛋鸡品系降低了种群内的遗传多样性，在其品种类别中平均观察到的杂合性估计值低于0.205，多态位点的平均比例低于0.680。我们发现，在野生和较少选择的非洲人中，仍然保留了大量的遗传多样性，南美洲和一些地方的亚洲和欧洲品种的平均观察杂合度大于0.225和多态位点的平均比例大于0.720在其品种的class.ConclusionsIt是重要的，这种高度多样化的品种是保持的可持续性和灵活性，未来的养鸡业这种多样性面板提供了进一步的鸡分子遗传学研究开发的机会。随着进一步扩大的可能性，它构成了一个非常有用的社区资源，鸡遗传多样性的研究。
BackgroundSince domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been formed and those represent the diversity of the species. However, other than the natural evolutionary forces, management practices (including those that threaten the persistence of genetic diversity) following domestication have shaped the genetic make-up of and diversity between today's chicken breeds. As part of the SYNBREED project, samples from a wide variety of chicken populations have been collected across the globe and were genotyped with a high density SNP array. The panel consists of the wild type, commercial layers and broilers, indigenous village/local type and fancy chicken breeds. The SYNBREED chicken diversity panel (SCDP) is made available to serve as a public basis to study the genetic structure of chicken diversity. In the current study we analyzed the genetic diversity between and within the populations in the SCDP, which is important for making informed decisions for effective management of farm animal genetic resources.ResultsMany of the fancy breeds cover a wide spectrum and clustered with other breeds of similar supposed origin as shown by the phylogenetic tree and principal component analysis. However, the fancy breeds as well as the highly selected commercial layer lines have reduced genetic diversity within the population, with the average observed heterozygosity estimates lower than 0.205 across their breeds' categories and the average proportion of polymorphic loci lower than 0.680. We show that there is still a lot of genetic diversity preserved within the wild and less selected African, South American and some local Asian and European breeds with the average observed heterozygosity greater than 0.225 and the average proportion of polymorphic loci larger than 0.720 within their breeds' categories.ConclusionsIt is important that such highly diverse breeds are maintained for the sustainability and flexibility of future chicken breeding. This diversity panel provides opportunities for exploitation for further chicken molecular genetic studies. With the possibility to further expand, it constitutes a very useful community resource for chicken genetic diversity research.