Plant Sample Collection and Shipment for Multi‐omic Analyses and Phytosanitary Evaluation

Abstract

AbstractPlant sample preparation for analyses is a fundamental step in high‐throughput omics strategies. Especially for plant metabolomics, quenching of hydrolytic enzymes able to affect metabolite concentrations is crucial for the accuracy of results. Given that DNA is usually less labile than metabolites, most sampling and shipment procedures able to preserve the metabolome are also suitable for preventing the degradation of plant DNA or of DNA of pathogens in the plant tissue. In this article, we describe all the steps of sample collection, shipment (including the phytosanitary issues of moving plant samples), and processing for combined genomics and metabolomics from a single sample, as well as the protocols used in our laboratories for downstream approaches for crop plants, allowing collection of multi‐omic datasets in large experimental setups. The protocols have been adjusted to apply to both freeze‐dried and fresh‐frozen material to allow the processing of crop plant samples that will require long‐distance transport. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Preparation of freeze‐dried leaf disks for multiplexed PCR or DArT‐Seq genotypingBasic Protocol 2: Medium‐throughput preparation of pathogen‐free nucleic acids for most genotyping‐resequencing applications or pathogen detectionAlternate Protocol: Low‐throughput extraction of high‐quality DNA for resequencing using commercial kitsSupport Protocol: DNA quality controlBasic Protocol 3: Preparation of freeze‐dried plant material for metabolomicsBasic Protocol 4: Preparation of fresh‐frozen plant material for metabolomicsBasic Protocol 5: Preparation and shipment of metabolite extracts for metabolomic analysesBasic Protocol 6: Sample shipping and long‐term storage