Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle
Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle
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DOI：
10.1038/s41598-020-71375-2
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发表时间：
2020-09-03
影响因子：
4.6
通讯作者：
Ciani, Elena
中科院分区：
文献类型：
--
作者：
Mastrangelo, Salvatore;Tolone, Marco;Ciani, Elena
基因分型检测的可用性允许对全世界牛的遗传多样性进行详细评估。然而，这些全面的研究并没有包括一些当地的欧洲人群，包括土生土长的意大利牛。在这项研究中，我们收集了一个大规模的全基因组单核苷酸多态性数据集，该数据集来自全球205个牛种群的3，283个个体，以评估全基因组的同源性，并更好地了解这些种群之间的遗传关系。我们优先考虑欧洲牛，特别关注意大利品种。从纯合性（F-ROH）运行计算的分子近亲繁殖的估计值的中度差异，观察驯化牛种群从不同的地理区域，除了巴厘牛。我们的研究结果表明，一些意大利品种显示在本研究中评估的牛种群之间的分子近亲繁殖水平的最高估计。遗传分化的模式，共同的祖先，和系统发育分析都表明发生的基因流，特别是来自同一地理区域的人群。对于欧洲牛，我们观察到沿沿着三个主要方向的分布，反映了所分析品种的已知历史和形成。意大利品种分为两个主要群体，根据其历史起源和祖先基因组成分的保护程度。结果指出，西西里品种，很像Podolian衍生品种，在过去经历了类似的非欧洲的影响，非洲和indicine渐渗。
The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (F-ROH) were observed among domesticated bovid populations from different geographic areas, except for Bali cattle. Our findings indicated that some Italian breeds show the highest estimates of levels of molecular inbreeding among the cattle populations assessed in this study. Patterns of genetic differentiation, shared ancestry, and phylogenetic analysis all suggested the occurrence of gene flow, particularly among populations originating from the same geographical area. For European cattle, we observed a distribution along three main directions, reflecting the known history and formation of the analyzed breeds. The Italian breeds are split into two main groups, based on their historical origin and degree of conservation of ancestral genomic components. The results pinpointed that also Sicilian breeds, much alike Podolian derived-breeds, in the past experienced a similar non-European influence, with African and indicine introgression.