Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.
Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.
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DOI：
10.1186/1471-2164-15-562
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发表时间：
2014-07-04
期刊：
影响因子：
4.4
通讯作者：
Distl O
中科院分区：
文献类型：
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作者：
Metzger J;Tonda R;Beltran S;Agueda L;Gut M;Distl O
驯化塑造了马，并导致了许多不同类型的群体。有些是在强烈的人类选择下，而另一些则是在与自然的密切关系中发展起来的。我们研究的目的是对品种和非品种马进行下一代测序，以深入了解遗传对选择力的影响。四个不同群体的五匹马的全基因组测序揭示了10，193，421个单核苷酸多态性（SNP）和1，361，948个插入/缺失多态性（indels）。与马的变异数据库和以前的报告相比，我们能够识别3，394，883个新的SNP和868，525个新的indel。我们分析了个体变异的分布，发现非种马中参与初级代谢过程、解剖结构、形态发生和细胞组分的基因编码区的私人突变显著富集，与此相反，影响细胞通讯、脂质代谢过程、神经系统过程、肌肉收缩、离子转运、马的神经系统和外胚层的发育过程。我们的下一代测序数据构成了非品种马与品种马相比表征的重要第一步，并为未来的分析提供了大量的新变体。功能注释表明，特定的变异，可以发挥作用的品种或非品种马的表征。本文的在线版本（doi：10.1186/1471-2164-15-562）包含补充材料，可供授权用户使用。
Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses. Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses. The online version of this article (doi:10.1186/1471-2164-15-562) contains supplementary material, which is available to authorized users.
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影响因子：
4.4
作者：
Doan R;Cohen ND;Sawyer J;Ghaffari N;Johnson CD;Dindot SV
通讯作者：
Dindot SV
影响因子：
64.8
作者：
Andersson, Lisa S.;Larhammar, Martin;Memic, Fatima;Wootz, Hanna;Schwochow, Doreen;Rubin, Carl-Johan;Patra, Kalicharan;Arnason, Thorvaldur;Wellbring, Lisbeth;Hjalm, Goran;Imsland, Freyja;Petersen, Jessica L.;McCue, Molly E.;Mickelson, James R.;Cothran, Gus;Ahituv, Nadav;Roepstorff, Lars;Mikko, Sofia;Vallstedt, Anna;Lindgren, Gabriella;Andersson, Leif;Kullander, Klas
通讯作者：
Kullander, Klas
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
4.4
作者：
Brault, Leah S.;Cooper, Caitlin A.;Penedo, M. Cecilia T.
通讯作者：
Penedo, M. Cecilia T.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
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