Targeted Genotyping Panels (Allegro - SPET)

Speed up your research with readily available and validated genotyping panels

During the years, IGATech has collborated with several research groups and experts to build optimized targeted genotyping panels with the Allegro technology (also known as SPET). Similar to GBS but with the unique ability to target specific SNPs/loci or gene of interest. These panels have been specifically curated either by our team or by researchers with strong expertise in the genetics of the subject species. The panels listed below are readily available and can be used with a minimum order of one plate. Being already in stock, the turnaround times will be much faster as compared to new custom designs. 

Note that this is a sequencing-based genotyping and therefore panels are capable to retrieve also non-target polymorphisms. This makes the panels highly reusable also on populations that are far from those that were originally exploited to target specific SNPs. Each locus will be sequenced for hundreds of base pairs (usually about 300bp).

 

Crop Species

 

Maize (Zea mais) - 50k loci

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.

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 

 

Fruits and Vegetables

 

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.

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).

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) - 50k 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.

 

Forest Trees

 

Scots pine (Pinus sylvestris) - 8k loci

The 8k Pinus sylvestris panel was generated in collaboration with INIA, Forest Research Center (Chile).

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. 

European yew (Taxus baccata) - 10k loci

The 10k Taxus baccata panel was generated in the framework of the GenTree project.The goal of GenTree is to provide the European forestry sector with better knowledge, methods and tools for optimising the management and sustainable use of forest genetic resources (FGR) in Europe in the context of climate change and continuously evolving demands for forest products and services.

European black pine (Pinus nigra) - 10k loci

The 10k Pinus nigra panel was generated in the framework of the GenTree project.The goal of GenTree is to provide the European forestry sector with better knowledge, methods and tools for optimising the management and sustainable use of forest genetic resources (FGR) in Europe in the context of climate change and continuously evolving demands for forest products and services.

European silver fir (Abies alba) - 10k loci

The 10k Abies alba panel was generated in the framework of the GenTree project.The goal of GenTree is to provide the European forestry sector with better knowledge, methods and tools for optimising the management and sustainable use of forest genetic resources (FGR) in Europe in the context of climate change and continuously evolving demands for forest products and services.

Jerusalem pine (Pinus halepensis) - 10k loci

The 10k Pinus halepensis panel was generated in the framework of the GenTree project.The goal of GenTree is to provide the European forestry sector with better knowledge, methods and tools for optimising the management and sustainable use of forest genetic resources (FGR) in Europe in the context of climate change and continuously evolving demands for forest products and services.

Swiss stone pine (Pinus cembra) - 10k loci

The 10k Pinus cembra panel was generated in the framework of the GenTree project.The goal of GenTree is to provide the European forestry sector with better knowledge, methods and tools for optimising the management and sustainable use of forest genetic resources (FGR) in Europe in the context of climate change and continuously evolving demands for forest products and services.

 

Animals

 

Goat (Capra hircus) - 4k loci

A 4k (double-probe) panel designed in collaboration with University of Bari, Department of Veterinary Medicine. Most of the sites covers SNPs present in the GoatSNP50 chip, supplemented with coverage on caseine genes.

 

 

Documents & Reports

Human samples clearance

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Terms and Conditions v04.pdf

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Privacy Information

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Samples Spreadsheet v7.xlsx

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SPET seminal paper.pdf

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Genotyping Sample requirements guidelines v01.pdf

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