--- title: "ddRAD genotyping" search_description: "IGATech’s ddRAD genotyping services offer high-resolution SNP discovery and population analysis for plant, animal, and microbial studies. Ideal for genetic diversity, evolutionary research, and breeding programs. Leverage our precise genotyping expertise." published: 2026-08-30 16:39:25.581951+00:00 locale: "it" --- # ddRAD genotyping [Request a quote](https://igatechnology.com/igatech/contacts/#contact-form) ## Technologies ![NovaSeq X Plus](/media/images/Illumina_NovaSeq_XPlus_Left_561x375.width-500.png) ### NovaSeq X Plus The NovaSeq X Plus is a powerful and scalable ultra-high-throughput sequencing system that supports the broadest range of applications and study sizes. Unrivaled data quality using Illumina's proven SBS chemistry has made the NovaSeq X Plus the instrument of choice for all major genome centers and leading institutions throughout the world. Producing up to 25 billion reads \(7.5 Tbp\) per flowcell, yielding up to 120 human genomes in about 2 days at full capacity. ![Nucleic acids extraction](/media/images/DNA_extraction.width-500.png) ### Nucleic acids extraction DNA and RNA extraction is routinely performed at IGATech, providing support to our customers directly from raw material. Relying on automated systems and consolidated protocols we can help you in accelerating the path to analyzed data. We also work with non standard substrates, such as [plants](https://igatechnology.com/genomics-research-services/?area=plant) and [food](https://igatechnology.com/agrigenomics-solutions/). Our expertise in the isolation of high molecular weigth DNA for long-molecule sequencing applications will also be a specialized complement for [*de novo*](http://igatechnology.com/genomics-research-services/?area=plant#denovo) applications*.* Pleas [enquire](https://igatechnology.com/igatech/contacts/) to obtain further details*.* ![Reduced-Representation libraries](/media/images/Reduced-Representation_libraries.width-500.png) ### Reduced-Representation libraries Reducing the complexity of genomes has enabled NGS to pursue massive genotyping experiments with very competitive costs. One system relies on the cleavage of the genomic DNA by means of two restriction enzymes \(ddRAD\). Another approach, known as RRBS-Seq, utilizes reduced-representation libraries to perform survey of the methylation states of genomes in relevant regions. See [ddRAD](https://igatechnology.com/genomics-research-services/plantanimal/ddrad-genotyping/) - [RRBS-Seq](https://igatechnology.com/genomics-research-services/bs-seq/). ## Features and benefits 1. KeyGene **licensed** 2. Ascertain **bias-free** experiment 3. Discover and **genotype diversity** in one experiments 4. Customized and reproducible selection of genomic loci 5. **Scalability** of markers yield from thousands to hundreds of thousands 6. High recall rate ## Services 1. DNA extraction service 2. **DNA normalization** 3. **Library preparation** and **QCs** 4. **150bp paired-end sequencing** 5. **Data analysis** to **genotype tables** 6. **Complementary analyses:** linkage - QTL mapping association studies \(GWAS\) molecular barcoding / varietal identification diversity and population structure​ ## Less is more > We were able to make an excellent map to anchor our genome assembly. IGATech support was very helpful. Mark Aarts Associate Professor in Plant Genetics Wageningen University \(Netherlands\) One of the major benefits of low error rate provided by Illumina platform is their utilization for accurate SNP calling. However, for large scale experiments where cost-effectiveness has to cope with massive panel of samples \(breeding, ecology, association-studies, etc.\), whole genome sequencing remains an unaffordable option. One of the most effective techniques in the cutting down of such cost is **to reduce the genome to a fraction of its size before sequencing**. The method of choice adopted by IGATech for genotyping-by-sequencing is the so-called **ddRAD \(double digest Restriction Associated DNA\)**. The system provides complexity reduction by selecting genomic DNA fragments generated by cleavage by both restriction enzymes, one per side. This has the advantage of having **each genomic locus characterized by a specific size in the library of fragments**. Adopting in silico simulation it is possible to fine-tune the amount of genomic loci to be selected. **AN "OPEN SYSTEM"** Genetic variability is sampled unbiasedly ![ddrad](/media/images/ddrad.width-1500.png) This capability allows to accommodate the adequate sequencing yield to obtain effective coverage to most of loci and thus providing high and reproducible genotyping ratio across individuals also in large cohorts. Moreover, compared to array-based solutions, sequencing is an “open system”, meaning that genetic variability is sampled unbiasedly: this has a critical impact on experiments involving genetic backgrounds and haplotypes not exhaustively represented by the panel of markers used in an array or any previous experiment. | Sample number | Standard complexity \(avg. 4M reads/sample\) | High complexity \(avg. 12M reads/sample\) | Standard bioinformatics | | --- | --- | --- | --- | | 96 | 59 euro/sample | 80 euro/sample | 7 euro/sample | | 192 | 50 euro/sample | 70 euro/sample | 6 euro/sample | | 288-384 | 42 euro/sample | 60 euro/sample | 5 euro/sample | | 480-864 | 38 euro/sample | 50 euro/sample | 4 euro/sample | | 960+ | 34 euro/sample | 47 euro/sample | 4 euro/sample | > Over the past years we came to heavily rely on the excellent services provided by IGATech, whose expertise, efficiency, helpful and custom-oriented attitude accompanied us in our scientific growth in the field of genomics. A recent service extension is their double enzyme ddRAD Seq approach we are currently using with great success in several crop species. Prof. Mario Enrico Pè Director of the Institute of Life Science, Scuola Superiore Sant'Anna, Pisa \(Italy\) **Choosing the sequencing depth.** The **standard complexity** option \(avg. 4M reads per sample\) is generally suitable for genomes of standard size \(< 3 Gbp\) when the target outcome is in the range of 10,000–30,000 polymorphic loci. For large genomes \(> 3 Gbp\), or when a much higher number of polymorphic loci \(> 30,000\) is required, we recommend the **high complexity** option \(avg. 12M reads per sample\). It is worth noting that each locus corresponds to approximately 200 bp of sequence, so more than one SNP can be called per locus: in our experience, polymorphic loci typically yield 3 to 10 SNPs each, depending on the species and on the size and diversity of the population under study. ### ### Expertise IGATech has successfully conducted hundreds of genotyping-by-sequencing experiments on plants and animals, with genome size ranging from megabases to tens of gigabases. Despite such variability in genome size and complexity we manage to obtain effective complexity reduction and target more than 90% of sequencing data in loci with adequate coverage overall. Our internally developed protocol is also suitable for the finding of discriminatory marker for varietal identification and contamination levels estimation also in food substrates. Reproducible experiments and bioinformatics analyses are aimed to obtain high quality and comparable data. We provide tailored consultancy for every project to make sure the outcome will meet our customer expectations. Every genome and experimental design have its challenges: **we cover them all.** ### Selected Publications **ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.** *Genetic Selection Evolution* 54, Article number: 8 \(2022\). [https://doi.org/10.1186/s12711-022-00698-7](https://doi.org/10.1186/s12711-022-00698-7) **Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes.** *Commun Biol.* 2020 Jul 16;3\(1\):387. [doi: 10.1038/s42003-020-1098-7.](https://doi.org/10.1038/s42003-020-1098-7) **A RAD-based linkage map of kiwifruit \(Actinidia chinensis Pl.\) as a tool to improve the genome assembly and to scan the genomic region of the gender determinant for the marker-assisted breeding** *Tree Genetics & Genomes* 11, 115 \(2015\). [https://doi.org/10.1007/s11295-015-0941-3](https://doi.org/10.1007/s11295-015-0941-3) ## Terms and Conditions - [Privacy Information.pdf](/documents/12/Privacy_Information_rev00.pdf) - [Human samples clearance.pdf](/documents/13/__Human-samples_clearance.pdf) - [Shipping and Packaging Guidelines.pdf](/documents/9/SHIPPING_AND_PACKAGING_GUIDELINES.pdf) - [rev05 Terms and Conditions.pdf](/documents/137/__M12_01_rev05_Terms_and_Conditions.pdf)