A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits.
A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits.
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全面调查 18 个不同猪群的拷贝数变异并鉴定与复杂性状相关的候选拷贝数可变基因
DOI：
10.1186/1471-2164-13-733
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发表时间：
2012-12-27
期刊：
影响因子：
4.4
通讯作者：
Huang L
中科院分区：
文献类型：
--
作者：
Chen C;Qiao R;Wei R;Guo Y;Ai H;Ma J;Ren J;Huang L
拷贝数变异(Copy Number Variation，CNV)是结构变异的主要来源，在哺乳动物基因组中普遍存在。它与基因表达有关，可能是表型多样性的主要遗传成分。与许多其他哺乳动物基因组中CNV已经被很好地注释不同的是，不同品种的猪CNV的研究仍然有限。结果我们使用猪SNP60珠芯片和PennCNV算法在18个不同群体的1,693头猪中鉴定出1315个可能的CNV，分别属于565个CNV区域(CNV)。在一个白色杜洛克 × 二花脸F2群体中，6 83个CNV中有5 38个符合孟德尔传播，随机选择的7个CNV中有6个得到了实时定量聚合酶链式反应的证实。CNVR在猪基因组中呈非随机分布。在猪的6、11、13、14和17号染色体上发现了几个CNV热点。不同猪种间的CNV数量差异很大。杜洛克猪被确定为每个个体拥有最多的CNV数量。在位于CNVR内的1,765个转录本中，已有634个基因被报道为人类基因组中拷贝数可变的基因。结合QTL定位、CNVRs分析和基因敲除小鼠的表型描述，我们确定了7个拷贝数可变基因作为候选基因，这些基因与屠体长度、背脂厚度、腹脂重、肩胛长、后肢肌肌间脂肪含量、240日龄体重、后肢肌糖酵解潜能、平均红细胞血红蛋白、平均红细胞体积和肱骨直径相关。结论揭示了565个拷贝数可变基因在猪基因组中的分布，并研究了拷贝数可变基因作为表型性状的可能候选基因。这些发现为猪CNV提供了新的见解，并为识别与特征相关的CNV提供了资源。
BackgroundCopy number variation (CNV) is a major source of structural variants and has been commonly identified in mammalian genome. It is associated with gene expression and may present a major genetic component of phenotypic diversity. Unlike many other mammalian genomes where CNVs have been well annotated, studies of porcine CNV in diverse breeds are still limited.ResultHere we used Porcine SNP60 BeadChip and PennCNV algorithm to identify 1,315 putative CNVs belonging to 565 CNV regions (CNVRs) in 1,693 pigs from 18 diverse populations. Total 538 out of 683 CNVs identified in a White Duroc × Erhualian F2population fit Mendelian transmission and 6 out of 7 randomly selected CNVRs were confirmed by quantitative real time PCR. CNVRs were non-randomly distributed in the pig genome. Several CNV hotspots were found on pig chromosomes 6, 11, 13, 14 and 17. CNV numbers differ greatly among different pig populations. The Duroc pigs were identified to have the most number of CNVs per individual. Among 1,765 transcripts located within the CNVRs, 634 genes have been reported to be copy number variable genes in the human genome. By integrating analysis of QTL mapping, CNVRs and the description of phenotypes in knockout mice, we identified 7 copy number variable genes as candidate genes for phenotypes related to carcass length, backfat thickness, abdominal fat weight, length of scapular, intermuscle fat content of logissimus muscle, body weight at 240 day, glycolytic potential of logissimus muscle, mean corpuscular hemoglobin, mean corpuscular volume and humerus diameter.ConclusionWe revealed the distribution of the unprecedented number of 565 CNVRs in pig genome and investigated copy number variable genes as the possible candidate genes for phenotypic traits. These findings give novel insights into porcine CNVs and provide resources to facilitate the identification of trait-related CNVs.
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影响因子：
2.4
作者：
Johansson, A;Pielberg, G;Edfors-Lilja, I
通讯作者：
Edfors-Lilja, I
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DOI：
10.1083/jcb.200111080
发表时间：
2002-01-21
期刊：
The Journal of cell biology
影响因子：
--
作者：
Dabovic B;Chen Y;Colarossi C;Obata H;Zambuto L;Perle MA;Rifkin DB
通讯作者：
Rifkin DB
影响因子：
4.6
作者：
Chen, CH;Ware, SM;Brown, CW
通讯作者：
Brown, CW
影响因子：
64.8
作者：
通讯作者：
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影响因子：
7
作者：
Doan R;Cohen N;Harrington J;Veazey K;Juras R;Cothran G;McCue ME;Skow L;Dindot SV
通讯作者：
Dindot SV