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首页> 外文期刊>Genetic Resources and Crop Evolution >A comparison of polymorphism information content and mean of transformed kinships as criteria for selecting informative subsets of barley (Hordeum vulgare L. s. l.) from the USDA Barley Core Collection
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A comparison of polymorphism information content and mean of transformed kinships as criteria for selecting informative subsets of barley (Hordeum vulgare L. s. l.) from the USDA Barley Core Collection

机译:多态性信息含量和转化亲缘关系平均值的比较,以此作为从USDA大麦核心选材中选择大麦信息性子集的标准

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摘要

Recent advances in genetic technologies have given researchers the ability to characterize genetic marker data for large germplasm collections. While some studies are able to capitalize on entire germplasm collections, others, especially those that focus on traits that are difficult to phenotype, instead focus on a subset of the collection. Typically, subsets are selected using phenotypic or geographic data. One major hurdle in identifying favorable subsets is selecting a criterion that can be used to quantify the value of a subset. This study compares two such criteria, polymorphism information content, and a new criterion based on kinship matrices, which will be called the mean of transformed kinships. These criteria were explored in terms of their ability to select subsets that are favorable for genome wide association studies, and in their ability to select subsets that contain a high number of rare phenotypes. Using phenotypic and genotypic data that has been amassed from the USDA Barley Core Collection, evidence was found to support the hypotheses that subsets based on the mean of transformed kinships were well-suited to select subsets intended for genome-wide association studies, but the same was not found for polymorphism information content. Inversely, evidence was found to support the hypothesis that subsets based on polymorphism information content were well-suited to select subsets intended for rare-phenotype discovery, but the same was not found for subsets selected using the mean of transformed kinships criterion. Tools to select subsets using these two criteria have been released in the R package "GeneticSubsetter.''
机译:基因技术的最新进展使研究人员能够表征大型种质资源的遗传标记数据。虽然一些研究能够利用整个种质资源,但其他研究,尤其是那些专注于难以表型的性状的研究,却专注于资源的子集。通常,使用表型或地理数据选择子集。识别有利子集的一个主要障碍是选择一种可用于量化子集值的标准。这项研究比较了两个这样的标准,即多态信息内容和基于亲属关系矩阵的新标准,这将被称为转化亲属关系的均值。从选择适合全基因组关联研究的子集的能力以及选择包含大量稀有表型的子集的能力方面探讨了这些标准。使用从USDA大麦核心收藏中收集的表型和基因型数据,发现证据支持以下假设:基于转化亲缘关系的平均值的子集非常适合选择打算用于全基因组关联研究的子集,但是相同找不到多态信息内容。相反,发现证据支持以下假设,即基于多态性信息内容的子集非常适合选择打算用于稀有表型发现的子集,但对于使用转化亲缘关系标准的平均值选择的子集却没有发现。使用这两个条件选择子集的工具已在R包“ GeneticSubsetter”中发布。

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