A principal component regression based genome wide analysis approach reveals the presence of a novel QTL on BTA7 for MAP resistance in holstein cattle
A principal component regression based genome wide analysis approach reveals the presence of a novel QTL on BTA7 for MAP resistance in holstein cattle
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DOI：
10.1016/j.ygeno.2010.01.001
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发表时间：
2010-03-01
期刊：
影响因子：
4.4
通讯作者：
Karrow, Niel A.
中科院分区：
文献类型：
--
作者：
Pant, Sameer D.;Schenkel, Flavio S.;Karrow, Niel A.
牛约翰氏病（JD），由鸟分枝杆菌属（Mycobacterium avium spp.）副结核病（MAP）对奶牛和肉牛业造成重大损失。目前还没有针对这种疾病的有效疫苗接种或治疗策略，受感染的动物要么被扑杀，要么因临床疾病而死亡。管理该疾病的另一种策略是选择性地繁殖对MAP感染具有增强抗性的动物。因此，本研究的目的是使用全基因组关联方法在由荷斯坦牛组成的资源群体中鉴定与MAP感染相关的遗传位点puppulmonary。牛SNP50微珠芯片，含有54，001个单核苷酸多态性（SNP），用于对232只已知MAP感染状态的动物进行基因分型。因为，传统的病例对照分析技术是基于单标记分析，并没有考虑标记之间的连锁不平衡（艾德）的存在，我们使用了一种新的主成分回归方法，其中每个SNP被拟合在逻辑回归模型中，沿着在同一染色体上的其他SNP的主成分显示与性状的关联，作为协变量。这种方法使我们能够解释在同一染色体上显示关联的多个标记之间存在的LD。我们的分析揭示了BTA1、5、6、7、10、11和14上至少12个基因组区域的存在，这些区域与我们的资源群体的MAP感染状态相关。这些基因组区域的简要描述，并在这项研究中使用的分析的讨论，已提交。(C)2010年爱思唯尔公司All rights reserved.
Bovine Johne's disease (JD), caused by Mycobacterium avium spp. paratuberculosis (MAP), causes significant losses to the dairy and beef cattle industries. Effective vaccination or therapeutic strategies against this disease are currently unavailable and infected animals either get culled or die due to clinical disease. An alternative strategy to manage the disease is to selectively breed animals with enhanced resistance to MAP infection. Therefore, the objective of this study was to identify genetic loci putatively associated with MAP infection in a resource population consisting of Holstein cattle using a genome-wide association approach. The BovineSNP50 BeadChip, containing 54,001 single nucleotide polymorphisms (SNPs), was used to genotype 232 animals with known MAP infection status. Since, traditional case-control analytical techniques are based on single-marker analysis and do not account for the existence of linkage disequilibrium (ED) between markers, we used a novel principal component regression approach, where each SNP was fit in a logistic regression model, along with principal components of other SNPs on the same chromosome showing association with the trait, as covariates. Such an approach allowed us to account for the LD that exists between multiple markers showing an association on the same chromosome. Our analysis revealed the presence of at least 12 genomic regions on BTA1, 5, 6, 7, 10, 11 and 14 that were associated with the MAP infection status of our resource population. A brief description of these genomic regions, and a discussion of the analysis used in this study, have been presented. (C) 2010 Elsevier Inc. All rights reserved.