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Updated: Apr 16, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

QTL mapping using high-throughput sequencing.

Tiffany M Jamann¹, Peter J Balint-Kurti, James B Holland

¹Department of Crop Science, North Carolina State University, Raleigh, NC, 27695-7620, USA.

Methods in Molecular Biology (Clifton, N.J.)

|March 12, 2015

Summary

This summary is machine-generated.

High-throughput sequencing revolutionizes quantitative trait locus (QTL) mapping by enabling precise identification of genetic markers. This facilitates higher resolution QTL fine-mapping and genome-wide association studies for discovering causal sequence variations.

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Area of Science:

Plant genetics
Genomics
Bioinformatics

Background:

Quantitative trait locus (QTL) mapping has historically been limited by the cost and time of marker discovery and genotyping.
Earlier methods relied on sparse genetic maps and high linkage disequilibrium (LD) in biparental populations, resulting in poor QTL resolution.

Purpose of the Study:

To review advanced methods for precise QTL identification, overcoming limitations of traditional approaches.
To discuss how high-throughput sequencing facilitates higher resolution QTL mapping and fine-mapping procedures.

Main Methods:

Utilizing high-throughput sequencing for rapid discovery and genotyping of single nucleotide polymorphisms (SNPs) and other markers.
Employing techniques like restriction site-associated DNA sequencing (RAD-Seq) and genotyping-by-sequencing (GBS).
Leveraging increased marker density to enable QTL mapping in lower linkage disequilibrium (LD) scenarios.

Main Results:

High-throughput sequencing significantly enhances the efficiency and accuracy of marker genotyping in large populations.
Advanced methods, including modified biparental populations and genome-wide association studies (GWAS), provide higher resolution QTL mapping.
The ability to map QTL with greater precision aids in resolving them to causal sequence variations.

Conclusions:

High-throughput sequencing is pivotal for modern, high-resolution QTL mapping and fine-mapping studies.
Practical decisions in study design and data analysis are crucial for successful QTL resolution.
The ultimate goal of resolving QTL to causal variants is more attainable with current sequencing technologies.