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qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

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Published on: May 25, 2015

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping.

Omar A Ali¹, Sean M O'Rourke¹, Stephen J Amish²

¹Department of Animal Science, University of California, Davis, California 95616.

|December 31, 2015

Summary

Researchers developed Rapture, a new method combining restriction site-associated DNA (RAD) sequencing and sequence capture. This approach significantly reduces costs and increases efficiency for analyzing large numbers of individuals in genetic studies.

Keywords:

genotyping massively parallel sequencing population genetics rainbow trout restriction-site associated DNA (RAD)sequence capture

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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

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Published on: March 22, 2018

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Massively parallel sequencing is powerful but cost-prohibitive for large-scale DNA analysis in many individuals.
Genomic complexity reduction methods, like sequence capture and restriction enzyme-based techniques, improve cost-efficiency but have limitations.
Existing methods face challenges when analyzing a high number of individuals.

Purpose of the Study:

To develop an improved restriction site-associated DNA (RAD) sequencing protocol.
To introduce a novel method, Rapture (RAD capture), integrating RAD sequencing and sequence capture.
To enhance the efficiency and cost-effectiveness of large-scale genetic analyses.

Main Methods:

Developed an improved RAD sequencing protocol separating tag isolation and library preparation.
Introduced Rapture, which uses in-solution capture of selected RAD tags to target specific genomic loci.
The new RAD protocol enhances recovery of unique RAD fragments for improved analysis.

Main Results:

The improved RAD protocol increases versatility and recovers more unique fragments.
Rapture effectively targets sequencing reads to desired loci, combining RAD and sequence capture benefits.
Demonstrated Rapture as a rapid, flexible technology for analyzing numerous individuals cost-effectively.

Conclusions:

Rapture offers a significant advancement in genetic analysis efficiency and cost reduction.
The developed methods enable analysis of a large number of individuals with minimal sequencing and library preparation costs.
These advancements are applicable to agricultural, environmental, and biomedical sciences.