Cocoa pods, Venezuela. Photo: C.Lanaud ©CIRAD
Arabica coffee, Ethiopia. Photo: ©Jean-Pierre Labouisse
Yams in Benin. Photo: J-L Pham ©IRD
Rice harvest, Guinea. Photo: J-L Pham ©IRD
Maize corn. Photo: ©Brigitte Gouesnard

DNA bank and genotyping/sequencing laboratories

This platform will provide: (1) a laboratory for low to high throughput extraction of plant DNAs of diverse species, adapted to genotyping and sequencing analyses and that will feed a national DNA Bank, (2) a pre-NGS laboratory with all the GBS techniques suited for all the high-speed NGS sequencer systems available or under development, (3) a SNP laboratory with innovative, low to medium speed technologies to address the complex genomic situations of orphan or polyploid species.

DNABank

This bank will provide purified DNA associated with each live sample stored in BRCs, which allows exchanging PGR between partners under lower regulatory constraints, especially regarding technical and health issues, and carrying out all the traceability needed for good BRCs' management systems. It is based on: (1) Extraction/purification of nucleic acids, through a robotized line. It includes an automated DNA extraction robot such as Oktopure, highly automated DNA purification robots such as KingFisher, and robotic pipettor such as Beckman FX. Its productivity will be approximately 200 to 400 DNAs/24 hours, (2) Quality control of purified DNAs. The DNAs is controlled by electrophoresis, spectrophotometric and spectrofluorometric dosages, functional analyses by PCR or qPCR. (3) Secure storage of DNA samples. The produced DNAs is stored securely, under practical and accessible conditions for medium term use (freezer at -28°C) and under conditions of high biochemical stability and security, for the reference samples, using Imagene® metallic capsules. (4) Samples traceability system. The phases of DNA extraction is followed by laboratory tracking tools and the DNA samples managed using databases.

A pre-NGS laboratory

This laboratory is equipped for all the manipulations required for DNA preparations for GBS analyses: fractionation of DNA, sizing of the fragments, elaboration of DNA library and quality control. In addition, a NGS sequencer allow validating a series of original GBS technical adjustments, adapted to plants with little known or complex genomes, before developing large GBS programs supported by the sequencers of national or private genomic platforms.

A SNP laboratory

For medium throughput and flexible SNP genotyping, the choice was made to invest in a nanofluidic quantitative PCR analysis line such as Fluidigm. Fluidigm's technology is based on the use of micro-plates of PCR amplification consisting of 96 channels in rows where the DNA samples are deposited and 96 channels in columns where the reaction media with the PCR primers specific to a locus, are deposited. Each intersection of these 96x96 channels constitutes a reaction chamber of very low volume where a simplex amplification reaction is possible. This system is able to follow the 9,216 reactions simultaneously.

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