Linkage Disequilibrium and Evaluation of Genome-Wide Association Mapping Models in Tetraploid Potato.
Linkage Disequilibrium and Evaluation of Genome-Wide Association Mapping Models in Tetraploid Potato.
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DOI：
10.1534/g3.118.200377
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发表时间：
2018-10-03
期刊：
影响因子：
--
通讯作者：
Bryan GJ
中科院分区：
文献类型：
--
作者：
Sharma SK;MacKenzie K;McLean K;Dale F;Daniels S;Bryan GJ
全基因组关联研究（GWAS）已成为分析作物复杂性状的有力工具。本研究评估了各种GWAS模型和方法用于阐明马铃薯群体结构的有效性。显著的群体结构的存在可以导致检测到虚假的标记-性状关联，以及掩盖真实的。虽然需要适当的统计模型来检测真正的标记-性状关联，但在大多数已发表的马铃薯GWAS中，采用了“一个模型适合所有性状”的方法。我们已经研究了各种GWAS模型上的一个大的关联面板，包括不同的四倍体马铃薯品种和育种系，基因型与单核苷酸多态性（SNP）标记。表型数据产生的20个数量性状在不同的环境中进行评估。获得了这些性状的最佳线性无偏估计值（BLUE），用于评估GWAS模型。使用分位数-分位数（Q-Q）图和基因组控制膨胀因子（λGC）评估GWAS模型的拟合优度，该模型使用所有性状的亲缘关系和群体结构的不同组合获得。亲属关系被发现发挥了重要作用，纠正人口混杂效应和结果主张一个“特徴特异性”适合不同的GWAS模型。全基因组连锁不平衡（LD），影响GWAS的关键因素之一，也提出了一项调查，我们的研究结果相比，其他最近的研究在马铃薯。这里使用的遗传物质，以及这项研究的结果代表了马铃薯遗传分析的新资源。
Genome-wide association studies (GWAS) have become a powerful tool for analyzing complex traits in crop plants. The current study evaluates the efficacy of various GWAS models and methods for elucidating population structure in potato. The presence of significant population structure can lead to detection of spurious marker-trait associations, as well as mask true ones. While appropriate statistical models are needed to detect true marker-trait associations, in most published potato GWAS, a ‘one model fits all traits’ approach has been adopted. We have examined various GWAS models on a large association panel comprising diverse tetraploid potato cultivars and breeding lines, genotyped with single nucleotide polymorphism (SNP) markers. Phenotypic data were generated for 20 quantitative traits assessed in different environments. Best Linear Unbiased Estimates (BLUEs) for these traits were obtained for use in assessing GWAS models. Goodness of fit of GWAS models, derived using different combinations of kinship and population structure for all traits, was evaluated using Quantile-Quantile (Q-Q) plots and genomic control inflation factors (λGC). Kinship was found to play a major role in correcting population confounding effects and results advocate a ‘trait-specific’ fit of different GWAS models. A survey of genome-wide linkage disequilibrium (LD), one of the critical factors affecting GWAS, is also presented and our findings are compared to other recent studies in potato. The genetic material used here, and the outputs of this study represent a novel resource for genetic analysis in potato.
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影响因子：
5.4
作者：
Hackett, Christine A.;Bradshaw, John E.;Bryan, Glenn J.
通讯作者：
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影响因子：
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通讯作者：
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5.4
作者：
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通讯作者：
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