--- title: "Targeted Genotyping (SPET)" search_description: "IGATech’s targeted genotyping services provide customized SNP discovery and flexible panel design, ideal for genomic selection, GWAS, and local adaptation studies. Achieve high reproducibility and precision with tailored enrichment solutions." published: 2025-10-29 08:06:09.939495+00:00 locale: "it" --- # Targeted Genotyping \(SPET\) [Contact us for panel availability and new designs](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. ![AVITI Element Biosciences](/media/images/0.width-500.png) ### AVITI Element Biosciences The AVITI System by Element Biosciences is a benchtop sequencer designed for high performance, cost efficiency, and flexibility. It features dual independent flow cells for parallel or independent operation, enabling flexibility in throughput from low to full. The system utilizes Avidity Sequencing™ technology, ensuring over 90% of reads exceed Q30 quality, with minimal errors, low duplication rates, and reduced AT/GC bias. It supports easy data conversion to FASTQ files, offers compatibility with numerous assays, and provides cost-effective sequencing. This is our ideal companion for dedicated and fast-turnaround run set-up. For more detailed information, you can visit their website directly at [https://www.elementbiosciences.com/products/aviti](https://www.elementbiosciences.com/products/aviti). ![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*.* ![Hybridization-based enrichment](/media/images/Hybridization-based_enrichment.width-500.png) ### Hybridization-based enrichment In order to sequence only an exome, a limited set of genes, or any defined panel of loci, the template DNA must be enriched for fragments derived from them. One way to accomplish such task is to use a set of probes \(ssDNA or RNA\) to capture by hybridization the regions of interest. Probes, usually attached to biotin moieties, are pulled down with biotin-coated metal beads. See [Exome sequencing](https://igatechnology.com/genomics-research-services/plantanimal/exome-sequencing/) - [target genotyping](https://igatechnology.com/genomics-research-services/plantanimal/target-genotyping-by-sequencing/) - [clinical genotyping](https://igatechnology.com/genomics-research-services/clinical-genotyping/). ![Primer-extension enrichment](/media/images/Primer-extension_enrichment.width-500.png) ### Primer-extension enrichment As an alternative to hybridization-based enrichment, single-primer extension enrichments provides a very convenient system to enrich for target regions. The main advantage of such system is a much quicker workflow coupled with a higher performance in the enrichment efficiency \(i.e. reads that belongs to the desired target\). See [target genotyping](https://igatechnology.com/genomics-research-services/plantanimal/target-genotyping-by-sequencing/) - [clinical genotyping](https://igatechnology.com/genomics-research-services/clinical-genotyping/) ## Features and benefits 1. Reproducibility and transferability 2. Genotyping and discovery in one experiment 3. Maximized flexibility and panel customization 4. **Scale from thousand to hundred thousand loci** ## Tailored support 1. Expert assistance on panel design 2. Support for SNP mining on external data 3. Batch data aggregation 4. Assistance on GWAS , QTL and population structure analyses ## Full control of your experiment **GOODBYE ASCERTAINMENT BIAS** Either choosing hybridization-based systems or primer extension, the sequencing information will always provide additonal and off-target data, eliminating errors in diversity estimation caused by closed genotyping experiments as in arrays. Several scenarios and specific analyses require moving from random markers \(for which ddRAD is our system of choice\) to targeted regions when performing genotyping experiments. Focusing on a specific set of SNPs, genes or genomic locations is a crucial factor to cope with tasks such as genomic selection, local adaptation studies, TILLING, eco-TILLING, fine mapping, GWAS, genomic selection and many others. IGATech have optimized protocols for both hybridization-based and primer-based enrichment procedures. ### ![SPET](/media/images/SPET.width-1500.png) ### Single primer enrichment technology - Allegro IGATech, in collaboration with Tecan Genomics, have implemented a targeted genotyping system based on single primer enrichment technology \([Allegro, Tecan Genomics](https://lifesciences.tecan.com/allegro-targeted-genotyping-v2)\), which provides a very efficient approach to specifically target SNPs of interest. Every enriched read will be useful to the genotype calling of one selected SNP site. Nonetheless the technology allows to discover novel alleles by leveraging the sequencing information ensuring no restriction of transferability of each panel to other populations or even species. Sequencing read length can be scaled depending on the need of unknown \(rare\) variants versus the cost-effectiveness of focused genotyping. **Allegro provides highest reproducibility in the sequencing-based genotyping panorama while maintaining flexibility of continuous customization**. ## Publications & Webinars ![The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units](/media/images/The_FORGENIUS_genomic_resources.width-300.png) - [The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units](https://www.biorxiv.org/content/10.1101/2025.08.08.669074v1.full.pdf) ![Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize](/media/images/SPET_annals-of-botany.width-300.png) - [Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821380/) ![\[YOUTUBE\] SPET Webinar 1](/media/images/youtube_spet1.width-300.png) - [\[YOUTUBE\] SPET Webinar 1](https://www.youtube.com/watch?v=QWNkX8bppwo&t=962s) ![Development and application of Single Primer Enrichment Technology \(SPET\) SNP assay for population genomics analysis and candidate gene discovery in lettuce](/media/images/tripodi_SPET_lettuce.width-300.png) - [Development and application of Single Primer Enrichment Technology \(SPET\) SNP assay for population genomics analysis and candidate gene discovery in lettuce](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10471991/) ![Genetic dissection of fruit maturity date in apricot \(P. armeniaca L.\) through a Single Primer Enrichment Technology \(SPET\) approach](/media/images/cirilli_SPET_apricot.width-300.png) - [Genetic dissection of fruit maturity date in apricot \(P. armeniaca L.\) through a Single Primer Enrichment Technology \(SPET\) approach](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580121/) ![Single Primer Enrichment Technology \(SPET\) for High-Throughput Genotyping in Tomato and Eggplant Germplasm](/media/images/spet_barchi.width-300.png) - [Single Primer Enrichment Technology \(SPET\) for High-Throughput Genotyping in Tomato and Eggplant Germplasm](https://pmc.ncbi.nlm.nih.gov/articles/PMC6693525/) ![Fostering Conservation via an Integrated Use of Conventional Approaches and High-Throughput SPET Genotyping](/media/images/SPET_fostering.width-300.png) - [Fostering Conservation via an Integrated Use of Conventional Approaches and High-Throughput SPET Genotyping](https://pmc.ncbi.nlm.nih.gov/articles/PMC7381301/) ![Construction of a high density linkage map in Oil Palm using SPET markers](/media/images/oilpalm_spet.width-300.png) - [Construction of a high density linkage map in Oil Palm using SPET markers](https://pmc.ncbi.nlm.nih.gov/articles/PMC7305113/) ![Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant](/media/images/spet_eggplant_mangino.width-300.png) - [Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant](https://pmc.ncbi.nlm.nih.gov/articles/PMC8940277/) ![The giant diploid faba genome unlocks variation in a global protein crop](/media/images/favabean_genome_spet.width-300.png) - [The giant diploid faba genome unlocks variation in a global protein crop](https://pmc.ncbi.nlm.nih.gov/articles/PMC10033403/) ![The Jan Sjödin faba bean mutant collection: morphological and molecular characterization](/media/images/fava_collection.width-300.png) - [The Jan Sjödin faba bean mutant collection: morphological and molecular characterization](https://pmc.ncbi.nlm.nih.gov/articles/PMC11457391/) ![Epistatic QTLs for yield heterosis in tomato](/media/images/zamir_apistasis_spet.width-300.png) - [Epistatic QTLs for yield heterosis in tomato](https://pmc.ncbi.nlm.nih.gov/articles/PMC10083602/) ![Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions](/media/images/genetic_control_monforte_spet.width-300.png) - [Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions](https://pmc.ncbi.nlm.nih.gov/articles/PMC9027731/) > HIGH-SCALE MULTIPLEX GENOTYPING For small amounts of loci \(tens up to hundred\) in very large scale experiments \(thousands of samples\) IGATech can deploy a customized multiplex PCR panel to run massive genotyping based on simple amplicon sequencing, providing a high-throughput and cost-effective platform. The panel can be easily modified and increased in markers over the time without an impact on costs. ## PRE-DESIGNED SPET PANELS ## ## Fruits, vegetables and crops ![fruitsveggies-1620x600-1](/media/images/fruitsveggies-1620x600-1.width-1500.jpg) ### Maize \(Zea mais\) - 50k loci The 50k maize panel was generated with the collaboration of IGA and IGATech within the framework of the [Novabreed](https://cordis.europa.eu/project/id/294780/it) project. It has been highly curated as the results of a two tier approach where the 50k probes have been selected over a pilot panel of about 100k probes. This design has been largely tested in the genotyping of a MAGIC population in collaboration with the [Crop Genetics Group](https://www.capitalisegenetics.santannapisa.it/) of Scuola Superiore Sant'Anna \(Pisa\). See our [webinar](https://www.labroots.com/webinar/automation-aided-targeted-genotyping-allegro-maize-breeding-study-qtl-analysis-magic-mapping-populat) in collaboration with Tecan Genomics on the genotyping of MAGIC lines and the [seminal paper](https://academic.oup.com/aob/article/124/4/543/5424191) on SPET technology where we presented the benchmark of the maize panel against the Illumina Infinium chip. ### Fava bean \(Vicia faba\) - 90k loci Developed in collaboration with [Department of Molecular Biology and Genetics](https://pure.au.dk/portal/en/persons/stig-uggerhoej-andersen(dbcd376b-110b-489a-8f6d-85dd2268277d).html), Aarhus University and the [Department of Crop Science](https://www.reading.ac.uk/crop-science/our-staff/Donal-Osullivan), Reading University ### Grape \(Vitis vinifera\) - 60k loci The 60k grape panel has been originally delevoped in collaboration with Institute for Adriatic Crops and Karst Reclamation. It mostly cover all genes of the grape genome with homogeneous distribution. Given the high veriability of the genome and to maitain reusability also in wild species, probes have been mainly designed on coding regions while allowing to sequence also more variable regions such as introns. ### Tomato \(Solanum lycopersicum\) - 10k loci Developed in collaboration with [ISI Sementi](https://isisementi.com/it/) and CREA - Centro di Ricerca in Orticoltura e Florovivaismo , [Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia](https://www.crea.gov.it/web/orticoltura-e-florovivaismo) ### Tomato \(Solanum lycopersicum\) - 5k loci Developed in framework of the [G2P-SOL](http://www.g2p-sol.eu/) project the Tomato 5k has been used to genotype more than 16000 accessions to characterize worldwide genebanks. It is the result of the selection from a pilot design from which the most informative loci were selected. ### Eggplant \(Solanum melongena\) - 5k loci Developed in framework of the [G2P-SOL](http://www.g2p-sol.eu/) project the Eggplant 5k has been used to genotype more than 4000 accessions to characterize worldwide genebanks. It is the result of the selection from a pilot design from which the most informative loci were selected. ### Pepper \(Capsicum annuum\) - 12k loci Developed in collaboration with [Volcani Institute](https://www.agri.gov.il/en/home) \([Alexander Goldshmidt](https://www.agri.gov.il/en/author/alexg)\) from a selection of 16 reference genome assemblies and a 8 SRA accessions. ### Peach \(Prunus persica\) - 30k loci Developed in collaboration with University of Milano, [Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia](https://www.unimi.it/it/ugov/person/laura-rossini). Half of the selected loci have overlap with SNPs present in the Peach 18K SNP array \([link](https://air.unimi.it/handle/2434/693139)\). ### Apricot \(Prunus armeniaca\) - 25k loci Developed in collaboration with University of Milano, [Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia](https://www.unimi.it/it/ugov/person/laura-rossini)\). ### Lettuce \(Lactuca sativa\) - 40k loci The 40k lettuce panel was developed in collaboraton with [The European Cooperative Programme for Plant Genetic Resources \(ECPGR\)](https://www.ecpgr.cgiar.org/). ### Lemon \(Citrus lemon\) - 30k loci Developed in collaboration with University of Catania, [Dipartimento di Agricoltura, Alimentazione ed Ambiente](https://www.di3a.unict.it/docenti/mario.diguardo). ### Coffee \(Coffea arabica\) - 50k loci The 50k Coffea arabica genotyping platform was built on the purpose of a collaborative effort with [Illycaffè S.p.A](https://www.illy.com/it-it/landing/strategie-coffee-design-futuro-caffe-arabica). with the purpose of analyzing the genetic basis of resistance genes to coffea leaf rust. Probes are uniformily spread across the genome and can provide segregation analysis in both Coffea eugenioides and Coffea canefora sub genomes in the tetraploid Coffea arabica genome. ### Barley \(Hordeum vulgare\) - 90k loci A design developed by **Council for Agricultural Research and Economics \(CREA\)**. The first manuscript about this design is in preparation. To know about availability to use this design on service please contact [agostino.fricano@crea.gov.it](mailto:agostino.fricano@crea.gov.it) ## ## Forest trees ![INFORMA-Opinion-piece-image-940x667](/media/images/INFORMA-Opinion-piece-image-940x667.width-1500.png) ### Black poplar \(Populus nigra\) - 5k loci A selection of 5k higly informative loci utilized in the [Epidiverse](https://cordis.europa.eu/project/id/764965)project and extracted from the first prototype of SPET technoogy \(50k panel\) within the [Watbio](https://cordis.europa.eu/project/id/311929)project. The panel has been designed taking into account the whole diversity of European populations. ### FORGENIUS-Aalb10K European silver fir \(Abies alba\) - 10k loci The 10k Abies alba panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/) project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-Phal10K Aleppo pine \(Pinus halepensis\) - 10k loci The 10k Pinus halepensis panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp60K European black pine \(Pinus nigra\) - 10k loci The 10k Pinus nigra panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp60K European crab apple \(Malus sylvestris\) - 10k loci The 10k Malus sylvestris panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp60K European yew \(Taxus baccata\) - 10k loci The 10k Taxus baccata panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp60K European ash \(Fraxinus excelsior\) - 10k loci The 10k Fraxinus excelsior panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp60K European white birch \(Betula pendula\) - 10k loci The 10k Betula pendula panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp60K Wild cherry \(Prunus avium\) - 10k loci The 10k Prunus avium panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp50K Norway Spruce \(Picea abies\) - 10k+ The 10k Picea abies panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp50K European beech \(Fagus sylvatica\) - 10k+ The 10k Fagus sylvatica panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp50K Wild service tree \(Torminalis glaberrima\) 10k The 10k Torminalis glaberrima panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### FORGENIUS-MultiSp50K Oak \(Quercus spp.\) 10k+ The 10k+ Quercus spp. panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). It has been designed on Q. robur and Q. ilex genomes. ### FORGENIUS-MultiSp50K Sweet chestnut \(Castanea sativa\) 10k The 10k Castanea sativa panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### Common juniper \(Juniperus communis\) 10k The 10k Juniperus communis panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). ### Pine \(Pinus spp.\) 10k The 10k Pinus spp. panel was generated in the framework of the [FORGENIUS](https://www.forgenius.eu/)project in collaboration with [CNR-IBBR](https://www.ibbr.cnr.it/ibbr/). Pinus heldreichii, P. tabuliformis, P. pinaster were used in the design. ### European beech \(Fagus sylvatica\) - 90k loci We thank Henning Wildhagen \(HAWK Hochschule für angewandte Wissenschaft und Kunst Hildesheim/Holzminden/Göttingen, Germany\) and Oliver Gailing \(Georg-August-Universität Göttingen, Germany\) for sharing the 90k SPET panels of *Quercus petraea* and *Fagus sylvatica*, developed within the DroughtMarkers project \(funding provided by FNR-Waldklimafonds - 2218WK43A4 and 2218WK43B4\), which we used to design the probes for *Quercus robur* and *Fagus sylvatica*.” Grigoriadou-Zormpa et al. \(2024\): [https://doi.org/10.21203/rs.3.rs-4559673/v1](https://doi.org/10.21203/rs.3.rs-4559673/v1) Tost et al. \(2025\): [https://doi.org/10.1101/2025.04.08.647712](https://doi.org/10.1101/2025.04.08.647712) ### Oak \(Quercus robur and Quercus petraea\) - 90k loci We thank Henning Wildhagen \(HAWK Hochschule für angewandte Wissenschaft und Kunst Hildesheim/Holzminden/Göttingen, Germany\) and Oliver Gailing \(Georg-August-Universität Göttingen, Germany\) for sharing the 90k SPET panels of *Quercus petraea* and *Fagus sylvatica*, developed within the DroughtMarkers project \(funding provided by FNR-Waldklimafonds - 2218WK43A4 and 2218WK43B4\), which we used to design the probes for *Quercus robur* and *Fagus sylvatica*.” ## 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)