The 50k maize panel was generated with the collaboration of IGA and IGATech within the framework of the Novabreed 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 of Scuola Superiore Sant'Anna (Pisa). See our webinar in collaboration with Tecan Genomics on the genotyping of MAGIC lines and the seminal paper on SPET technology where we presented the benchmark of the maize panel against the Illumina Infinium chip.
Targeted Genotyping (SPET)
Technologies
Features and benefits
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Reproducibility and transferability
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Genotyping and discovery in one experiment
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Maximized flexibility and panel customization
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Scale from thousand to hundred thousand loci
Tailored support
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Expert assistance on panel design
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Support for SNP mining on external data
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Batch data aggregation
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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.
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), 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
HIGH-SCALE MULTIPLEX GENOTYPING
PRE-DESIGNED SPET PANELS
Maize (Zea mais) - 50k loci
Fava bean (Vicia faba) - 90k loci
Developed in collaboration with Department of Molecular Biology and Genetics, Aarhus University and the Department of Crop Science, 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 and CREA - Centro di Ricerca in Orticoltura e Florovivaismo , Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia
Tomato (Solanum lycopersicum) - 5k loci
Developed in framework of the G2P-SOL 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 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 (Alexander Goldshmidt) 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. Half of the selected loci have overlap with SNPs present in the Peach 18K SNP array (link).
Apricot (Prunus armeniaca) - 25k loci
Developed in collaboration with University of Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia).
Lettuce (Lactuca sativa) - 40k loci
The 40k lettuce panel was developed in collaboraton with The European Cooperative Programme for Plant Genetic Resources (ECPGR).
Lemon (Citrus lemon) - 30k loci
Developed in collaboration with University of Catania, Dipartimento di Agricoltura, Alimentazione ed Ambiente.
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. 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.
Black poplar (Populus nigra) - 5k loci
A selection of 5k higly informative loci utilized in the Epidiverse project and extracted from the first prototype of SPET technoogy (50k panel) within the Watbio project. The panel has been designed taking into account the whole diversity of European populations.
FORGENIUS-Aalb10K European silver fir (Abies alba) - 10k loci
FORGENIUS-Phal10K Aleppo pine (Pinus halepensis) - 10k loci
FORGENIUS-MultiSp60K European black pine (Pinus nigra) - 10k loci
FORGENIUS-MultiSp60K European crab apple (Malus sylvestris) - 10k loci
FORGENIUS-MultiSp60K European yew (Taxus baccata) - 10k loci
FORGENIUS-MultiSp60K European ash (Fraxinus excelsior) - 10k loci
FORGENIUS-MultiSp60K European white birch (Betula pendula) - 10k loci
FORGENIUS-MultiSp60K Wild cherry (Prunus avium) - 10k loci
FORGENIUS-MultiSp50K Norway Spruce (Picea abies) - 10k+
FORGENIUS-MultiSp50K European beech (Fagus sylvatica) - 10k+
FORGENIUS-MultiSp50K Wild service tree (Torminalis glaberrima) 10k
FORGENIUS-MultiSp50K Oak (Quercus spp.) 10k+
FORGENIUS-MultiSp50K Sweet chestnut (Castanea sativa) 10k
Common juniper (Juniperus communis) 10k
Pine (Pinus spp.) 10k
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
Tost et al. (2025): 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.”