Single nucleotide polymorphisms (SNPs) are the most abundant markers in the genome. Their relatively uniform distribution and high density make them ideal for genome-wide association studies (GWAS), comparative or evolutionary genomics, and marker-assisted molecular breeding studies. Whole genome sequencing (WGS) is the most direct method for genome-wide identification of SNPs and other types of variation. Until now, genotyping hundreds to thousands of individuals by whole-genome sequencing has been unaffordable for many researchers, even after taking into account the significant cost reductions associated with technological innovations and updates. Therefore, in order to fill the gaps between existing methods, considerable efforts have been made to develop Reduced-Representation Library (RRL) methods, which have the great advantage of reducing genome complexity by several orders of magnitude. The field of molecular ecology has also recently made increasing use of RRL sequencing methods in population studies.

Fig. 1. Main workflow of library construction and data analysis of RRLs. (Du et al., 2012)

Our RRL service

CD Genomics is committed to advancing agricultural genomics research by offering a suite of restriction enzyme-based RRL services tailored to the specific needs of our clients. Our solution is a relatively viable and flexible strategy for SNP identification in different species. In addition, we offer RRL to identify novel chloroplast DNA (cpDNA) polymorphisms in plants, which will allow the detection of spatial genetic structure on a regional scale. Our state-of-the-art facilities and cutting-edge technology ensure that our RRL service consistently delivers high-quality results. Whether you are embarking on population genomics studies, phylogenetic analyses, or SNP discovery, our RRL service is designed to provide you with the genomic insights you need.

We have successfully used restriction enzyme-based RRL to identify a large number of candidate SNPs in soybean, bovine, porcine, and other species. This approach can reduce genomic complexity by several orders of magnitude and facilitate the discovery of SNPs that are widely distributed across the genome, even without prior knowledge of genome sequence.

Technical characteristics

• Selective genome fragmentation: RRL involves selective fragmentation of the genome, targeting specific regions or motifs of interest. Multiple variants exist, most of which use restriction endonucleases or probes to target homologous regions of individual and population genomes.
• Improved cost efficiency: RRL provides a cost-effective alternative to whole genome sequencing. By reducing genomic complexity, it allows researchers to obtain rich genomic information while minimizing the cost of sequencing.
• Increased Depth of Coverage: RRL typically provides a higher depth of coverage for targeted regions, allowing for more accurate variant calling and genotyping.
• Reduced computational burden: The reduced complexity of RRL data reduces the computational burden associated with data analysis.

Our services can be applied to the following research areas

• SNP discovery.
• Novel chloroplast DNA identification.
• Population genomics.
• Marker-assisted breeding.
• Functional genomics.

Service workflow

Fig. 2. CD Genomics' RRL service process.

Our advantages and features

• Cutting-edge technology. We utilize the latest sequencing platforms and bioinformatics tools to ensure the highest data quality and accuracy for RRL services.
• Customized solutions. Our team of genomics experts works closely with clients to customize RRL services to their specific research goals, ensuring they get the data they need.
• Superior data analysis. We go beyond data generation to provide comprehensive data analysis services that extract meaningful insights from RRL data, including variant calling, population genetics analysis, and more.

CD Genomics has extensive experience in RRL services. Our RRL approach combined with high-throughput sequencing is an effective method for SNP discovery in individuals or populations. We provide a one-stop solution from sequencing work to tunable bioinformatics. If you are interested, please feel free to contact us.

Reference

1. Du, Ye, et al. Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method. BMC genomics. 13.1 (2012): 1-9.