Restriction site-associated DNA sequencing (RAD-seq) is a method that uses certain restriction enzymes to fragment genomic DNA samples, and then size-selects and sequences molecules within a certain size range. RAD-seq is an alternative to whole-genome NGS sequencing that can be used to detect SNPs and indel variations in DNA without preconceptions. This approach involves targeted sequencing of regions adjacent to common restriction sites distributed throughout the genome. Using multiple restriction enzymes improves genome coverage without the need for a reference genome. RAD-seq can be used for population genetics studies of species with no or limited existing sequence data and has several advantages over previous marker discovery methods. RAD-seq differs from RNA-seq in that non-transcribed sites are also sequenced, increasing the opportunity to expand on known SNPs.

Fig. 1. The process of RAD-seq. (Davey et al., 2010)

Our RAD-seq service

CD Genomics provides high-quality RAD-seq services that sequence DNA flanking specific restriction sites, providing high-resolution population genome data (thousands of sequenced markers for many individuals) for any organism. Our RAD-seq is typically applied to multiplexed samples, where DNA fragments are ligated to sample-specific barcode sequences for pooled sequencing, and reads are subsequently assigned to samples in silico, enabling individual and population-level genotyping. RAD-seq data can be easily analyzed without the need for a reference genome, especially for non-model organisms.

Technical characteristics

• High-throughput: RAD-seq can generate a large number of RAD markers in a single sequencing run. This efficiency, along with up to ten times as many markers, accelerates the pace of genetic research compared to traditional methods.
• High precision: RAD-seq's precision is invaluable in studies involving genetic variation, making RAD-seq superior to traditional molecular markers.
• Cost-effective: The reduction in genomic complexity in RAD-seq significantly lowers the cost of sequencing, especially when analyzing populations, ensuring that more projects can be undertaken without budgetary constraints.
• Short turnaround time: The high-throughput nature of RAD-seq enables the rapid generation of tens of thousands of markers in a single sequencing run.
• Genome-independent: RAD-seq can screen SNP loci on a large scale, even in species without a reference genome, removes the barriers that previously limited genomic research.

Our services can be applied to the following research areas

• Identification of SNPs near restriction enzyme digestion sites.
• Association mapping.
• Population genetics inference.
• Genetic mapping.
• Allele frequency estimation.

Instructions for providing samples

Note that we only ran RAD-seq library preparation in batches of 96 samples.

Service workflow

Fig. 2. CD Genomics' RAD-seq service process.

Our advantages and features

• Cutting-edge technology. We use the latest sequencing technologies and bioinformatics tools to ensure accuracy and reliability.
• Comprehensive support. CD Genomics provides end-to-end support from project design to data analysis, making the process seamless.
• Genetic analysis of non-model organisms. We support genetic analysis of model and non-model organisms, making our services available to a wide range of researchers.
• High-throughput SNP marker development. Our proven platform supports high-throughput SNP marker development, ensuring that your research goals are met efficiently and effectively.

CD Genomics has extensive experience with RAD-seq services, with the ability to accurately and efficiently explore SNPs in a wide range of organisms. RAD-seq enables population genetics studies of unprecedented depth and complexity. If you are interested, please feel free to contact us.

Reference

1. Davey, John W., and Mark L. Blaxter. RAD-Seq: next-generation population genetics." Briefings in functional genomics. 9.5-6 (2010): 416-423.