基因渐渗有助于牛群中结构变异的分布。

Introgression contributes to distribution of structural variations in cattle.

作者信息

Upadhyay Maulik, Derks Martijn F L, Andersson Göran, Medugorac Ivica, Groenen Martien A M, Crooijmans Richard P M A

机构信息

Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, 80539 Munich, Germany.

Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.

出版信息

Genomics. 2021 Sep;113(5):3092-3102. doi: 10.1016/j.ygeno.2021.07.005. Epub 2021 Jul 7.

DOI:10.1016/j.ygeno.2021.07.005

PMID:34242710

Abstract

Structural variations (SVs) are an important source of phenotypic diversity in cattle. Here, 72 whole genome sequences representing taurine and zebu cattle were used to identify SVs. Applying multiple approaches, 16,738 SVs were identified. A comparison against the Database of Genomic Variants archives revealed that 1575 SVs were novel in our data. A novel duplication covering the entire GALNT15 gene, was observed only in N'Dama. A duplication, which was previously reported only in zebu and associated with navel length, was also observed in N'Dama. Investigation of a novel deletion located upstream of CAST13 gene and identified only in Italian cattle and zebu, revealed its introgressed origin in the former. Overall, our data highlights how the SVs distribution in cattle is also shaped by forces such as demographical differences and gene flow. The cattle SVs of this study and its meta-data can be visualized on an interactive genome browser at https://tinyurl.com/svCowArs.

摘要

结构变异（SVs）是牛表型多样性的重要来源。在此，使用了代表普通牛和瘤牛的72个全基因组序列来鉴定结构变异。应用多种方法，共鉴定出16738个结构变异。与基因组变异数据库档案进行比较后发现，我们的数据中有1575个结构变异是新发现的。仅在恩达马牛中观察到一个覆盖整个GALNT15基因的新型重复。在恩达马牛中还观察到一种重复，此前仅在瘤牛中报道过，且与肚脐长度有关。对位于CAST13基因上游且仅在意大利牛和瘤牛中发现的一个新型缺失进行研究，发现其在意大利牛中具有渐渗起源。总体而言，我们的数据突出表明，牛中结构变异的分布也受到人口统计学差异和基因流等因素影响。本研究的牛结构变异及其元数据可在交互式基因组浏览器（https://tinyurl.com/svCowArs）上查看。