Double Digest Restriction-site Associated DNA (ddRAD) Sequencing

Focused, Cost-Effective Genotyping with ddRAD

Introduction and Workflow

ddRAD sequencing (Double Digest Restriction-site Associated DNA) is based on the Restriction Fragmentation technique combined with Next-Generation Sequencing (NGS). It is a robust approach for "genotyping and SNP discovery" that doesn't require a reference genome.
The ddRAD workflow utilizes the precise cut-site specificity of restriction endonucleases to create library fragments from unique genomic regions. These fragments are then selected and sequenced, capturing data from identical genomic regions across samples.
In the bioinformatics analysis, reads are aligned to either a reference genome or de novo assembly to detect SNVs and other genetic variations. This analysis supports studies on genetic diversity, population structure, and trait associations, with advanced tools enabling the processing of large datasets to achieve high genotyping accuracy.
With the potential to develop hundreds to tens of thousands of genetic markers, ddRAD is ideal for applications in population genetics, germplasm assessment, marker-trait associations, GWAS, and QTL mapping. Its targeted, reproducible approach makes it a valuable tool for ecological and agricultural genomics.

Advantages of SNP-based Genotyping

Allows for precise identification of genetic variations at a single nucleotide level, enabling detailed mapping of genetic diversity.
Provides an efficient, cost-effective solution for analyzing thousands of SNPs across large populations, ideal for high-throughput studies.
SNP markers are stable and abundant across genomes, providing high data quality, reproducibility, and scalability, which are essential for reliable genetic studies, comparative analyses across multiple populations or species, and make SNP-based genotyping a powerful tool for both research and applied genomics.
Can reveal associations between genetic variations and complex traits, allowing researchers to identify genetic contributors to health, disease, or productivity in agriculture.

Applications of SNP-based Genotyping

Genome-wide association studies (GWAS)- SNP-based genotyping is widely utilized in Genome-Wide Association Studies (GWAS) to identify genetic variants linked to specific traits or diseases, providing insights into genetic predispositions and the mechanisms underlying complex conditions such as diabetes, heart disease, and neurological disorders.
Plant and animal breeding- In agriculture, SNP-based genotyping facilitates marker-assisted selection (MAS) to enhance desirable traits such as yield, disease resistance, and environmental adaptability in crops and livestock.
Personalized medicine- SNP genotyping can guide personalized treatment strategies by identifying genetic variations that affect drug metabolism, efficacy, and toxicity, leading to more tailored healthcare approaches.
Forensic science- SNPs are employed in forensic analysis for human identification and paternity testing, providing reliable genetic markers that can help solve criminal cases or establish family relationships.
Evolutionary biology- Researchers use SNP genotyping to study evolutionary relationships, population dynamics, and the genetic basis of adaptation in various species, contributing to our understanding of evolutionary processes.
Disease prediction and prevention- SNP-based genotyping is applied in public health to assess genetic risk factors for diseases, enabling early interventions and prevention strategies in at-risk populations.
Double Digest Restriction-site Associated DNA (ddRAD) Sequencing- ddRAD sequencing is based on the Restriction Fragmentation technique combined with Next-Generation Sequencing (NGS). It is a robust approach for genotyping and SNP discovery that doesn't require a reference genome. With the potential to develop hundreds to tens of thousands of genetic markers, ddRAD is ideal for applications in population genetics, germplasm assessment, marker-trait associations, GWAS, and QTL mapping.

Service Specifications

Sample Requirement

Genomic DNA ≥300 ng

Minimum Quantity: 100 ng

Concentration ≥10 ng/µL

DNA samples require an OD260/280 as close to 1.8~2.0 as possible

All DNA should be RNase-treated and should show no degradation or contamination

Please refer to sample submission guidelines or Contact Us!

Sequencing Platform

Illumina NovaSeq 6000/ NovaSeq X

Deliverables

The original sequencing data
Experimental results
Bioinformatics and Data analysis report
Details of SNP-based Genotyping (customizable)