A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds.
A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds.
复制标题
对中国本土和商品猪品种的选择特征进行全基因组扫描
DOI：
10.1186/1471-2156-15-7
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发表时间：
2014-01-15
期刊：
影响因子：
2.9
通讯作者：
Tang Z
中科院分区：
文献类型：
--
作者：
Yang S;Li X;Li K;Fan B;Tang Z
研究背景现代育种和人工选择在猪的驯化中起着重要作用，并形成了不同品种的遗传变异。中国有许多地方猪种，它们在形态和生产性能上具有不同于国外商品猪种的各种特征。然而，中国地方猪和商品猪之间的经济性状的基因上的选择的签名一直知之甚少。ResultsWe确定了积极的选择在全基因组水平上的足迹，包括44,652 SNPs基因型在6个中国地方猪品种，一个发达的品种和两个商业品种。基于这九个品种中每个SNP的Fst估计，构建了Fst的经验全基因组分布（F统计）。我们使用High-Fst离群值方法检测了基因组水平的选择，发现81个候选基因显示出高的正选择证据。网络分析的结果表明，表现出正选择证据的基因主要与组织器官的发育和免疫反应有关。此外，我们还计算了中国地方品种和商业品种（中国VS欧洲）之间以及中国北方和南方地方品种（北方VS南方）之间的成对Fst。IGF 1 R和ESR 1基因表现出积极的选择在中国VS欧洲和北方VS南方groups.ConclusionsIn这项研究中，我们首先确定的基因组区域，表现出中国本土和商业猪品种之间的选择使用高Fst离群值方法的证据。发现这些区域参与组织和器官的发育、免疫反应、生长和产仔数。本研究结果为理解猪的遗传变异和驯化提供了新的见解。
BackgroundModern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood.ResultsWe identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively.ConclusionsIn this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
3.8
作者：
Li, J.;Yang, H.;Zhang, Y-P
通讯作者：
Zhang, Y-P
影响因子：
11.4
作者：
Offermanns, S;Zhao, LP;Wilkie, TM
通讯作者：
Wilkie, TM
影响因子：
9.8
作者：
Kijas JW;Lenstra JA;Hayes B;Boitard S;Porto Neto LR;San Cristobal M;Servin B;McCulloch R;Whan V;Gietzen K;Paiva S;Barendse W;Ciani E;Raadsma H;McEwan J;Dalrymple B;International Sheep Genomics Consortium Members
通讯作者：
International Sheep Genomics Consortium Members
影响因子：
64.5
作者：
LIU, JP;BAKER, J;EFSTRATIADIS, A
通讯作者：
EFSTRATIADIS, A