Simplified sample collection protocols amenable to use by non-specialized personnel

One of the main tasks of a Research Infrastructure dedicated to plant genetic resources (PGR) is to provide advanced scientific services to the scientific community and end-users of the resources available within the infrastructure. Without these services, PGR lose a significant part of their value. Additionally, these scientific services are essential for the efficient and high-quality operation of the members of the distributed infrastructure (such as genebanks, in situ PGR collections), which often have limited technological capacities.

In this context, the PRO-GRACE project aims to identify and validate genomic, metabolomic, bioinformatic and phytosanitary technologies and scientific services useful for collection holders, the scientific community and end-users.

Plant sample preparation for analyses is a fundamental step in high-throughput omics strategies. Deliverable 3.1 focused on developing and demonstrating sample collection and shipment protocols to simplify their usage by non-specialized personnel operating in genebanks. These protocols are intended for the application of DNA barcoding, cytogenomic, metabolomic and phytosanitary characterization methods. They facilitate the processing of samples for combined genomics and metabolomics analysis, enabling the collection of multi-omic datasets in large experimental setups. The developed protocols include:

  • Sampling for DNA flow cytometry
  • Sampling for genomic analyses 
  • Protocol 1: Preparation of freeze-dried leaf disks for multiplexed PCR or DArT-Seq genotyping
  • Protocol 2: Medium throughput preparation of pathogen-free nucleic acids for most genotyping-resequencing applications or pathogen detection
  • Alternate Protocol 1: DNA extraction using a kit 
  • Support Protocol 1: DNA quality control
  • Sampling for metabolomics analyses 
  • Protocol 3:  Preparation of freeze-dried plant material for metabolomics
  • Protocol 4: Preparation of fresh frozen plant material for metabolomics
  • Protocol 5: Preparation and shipment of metabolite extracts for metabolomic analyses
  • Protocol 6: Sample shipping and long-term storage

Deliverable D3.1 was led by MPG in collaboration with ENEA, WORLDVEG, UNITO, UEB

For more information, download the Deliverable report.