Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs.
Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs.
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DOI：
10.1371/journal.pone.0205576
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Thaller G
中科院分区：
文献类型：
--
作者：
Blaj I;Tetens J;Preuß S;Bennewitz J;Thaller G
全基因组关联研究（GWAS）已广泛应用于复杂性状的遗传分析。随着在不同的商业或资源猪群体中产生更多的基因组数据，出现的挑战是如何共同研究数据，以增加样本量和隐含的统计功效。本研究在三个猪F2群体中进行了个体群体GWAS、联合群体GWAS和荟萃分析。D1来源于欧洲型品种（皮特兰、大白色和长白猪），D2来源于亚洲品种（梅山）和皮特兰，D3来源于欧洲野猪和皮特兰，后者是共同的创始人品种。调查的性状为平均日增重、背膘厚、肉脂比和胴体长。除了通过个体群体GWAS发现的基因组簇外，联合分析和荟萃分析没有发现其他基因组簇。然而，其益处是提高了定位分辨率，其精确定位了包含致病变体的较窄簇。与荟萃分析相比，联合分析确定了更多的聚类;然而，荟萃分析中的显著性水平和显著变异的数量通常较高。这两种类型的分析有类似的产出，这表明这两种战略可以相互补充，元分析方法可以是一个有价值的工具，只要访问原始数据集是有限的。总的来说，总共20个主要在不同程度上重叠的基因组簇在染色体2、7和17上被鉴定，许多证实了先前鉴定的数量性状基因座。几个新的候选基因正在被提出，其中，一个强有力的候选基因，以考虑后续分析是BMP 2（骨形态发生蛋白2）。
Genome-wide association studies (GWAS) have been widely used in the genetic dissection of complex traits. As more genomic data is being generated within different commercial or resource pig populations, the challenge which arises is how to collectively investigate the data with the purpose to increase sample size and implicitly the statistical power. This study performs an individual population GWAS, a joint population GWAS and a meta-analysis in three pig F2 populations. D1 is derived from European type breeds (Piétrain, Large White and Landrace), D2 is obtained from an Asian breed (Meishan) and Piétrain, and D3 stems from a European Wild Boar and Piétrain, which is the common founder breed. The traits investigated are average daily gain, backfat thickness, meat to fat ratio and carcass length. The joint and the meta-analysis did not identify additional genomic clusters besides the ones discovered via the individual population GWAS. However, the benefit was an increased mapping resolution which pinpointed to narrower clusters harboring causative variants. The joint analysis identified a higher number of clusters as compared to the meta-analysis; nevertheless, the significance levels and the number of significant variants in the meta-analysis were generally higher. Both types of analysis had similar outputs suggesting that the two strategies can complement each other and that the meta-analysis approach can be a valuable tool whenever access to raw datasets is limited. Overall, a total of 20 genomic clusters that predominantly overlapped at various extents, were identified on chromosomes 2, 7 and 17, many confirming previously identified quantitative trait loci. Several new candidate genes are being proposed and, among them, a strong candidate gene to be taken into account for subsequent analysis is BMP2 (bone morphogenetic protein 2).
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影响因子：
3
作者：
Bardou P;Mariette J;Escudié F;Djemiel C;Klopp C
通讯作者：
Klopp C
影响因子：
3.3
作者：
Bernal Rubio, Y. L.;Gualdron Duarte, J. L.;Steibel, J. P.
通讯作者：
Steibel, J. P.
影响因子：
5.4
作者：
HILL W G;ROBERTSON A
通讯作者：
ROBERTSON A
DOI：
10.1098/rspb.2015.2019
发表时间：
2015-12-22
影响因子：
4.7
作者：
Bosse, Mirte;Lopes, Marcos S.;Groenen, Martien A. M.
通讯作者：
Groenen, Martien A. M.
DOI：
10.1111/j.1439-0388.1996.tb00629.x
发表时间：
1996-08-01
期刊：
JOURNAL OF ANIMAL BREEDING AND GENETICS-ZEITSCHRIFT FUR TIERZUCHTUNG UND ZUCHTUNGSBIOLOGIE
影响因子：
--
作者：
Geldermann, H;Muller, E;Moser, G
通讯作者：
Moser, G