DOI: 10.1101/479725Nov 27, 2018Paper

A Statistical Procedure for Genome-wide Detection of QTL Hotspots Using Public Databases with Application to Rice

BioRxiv : the Preprint Server for Biology
Chen-Hung KaoDong-Hong Wu

Abstract

Genome-wide detection of quantitative trait loci (QTL) hotspots underlying variation in many molecular and phenotypic traits has been a key step in various biological studies since the QTL hotspots are highly informative and can be linked to the genes for the quantitative traits. Several statistical methods have been proposed to detect QTL hotspots. These hotspot detection methods rely heavily on permutation tests performed on summarized QTL data or individual-level data (with genotypes and phenotypes) from the genetical genomics experiments. In this article, we propose a statistical procedure for QTL hotspot detection by using the summarized QTL (interval) data collected in public web-accessible databases. First, a simple statistical method based on the uniform distribution is derived to convert the QTL interval data into the expected QTL frequency (EQF) matrix. And then, to account for the correlation structure among traits, the QTLs for correlated traits are grouped together into the same categories to form a reduced EQF matrix. Furthermore, a permutation algorithm on the EQF elements or on the QTL intervals is developed to compute a sliding scale of EQF thresholds, ranging from strict to liberal, for assessing the significa...Continue Reading

Related Concepts

Extracellular Matrix
Genes
Genome
Laboratory Procedures
Local
Quantitative Trait Loci
Structure
Simulation
Research Study
Comparative Analysis

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