Jul 25, 2023
Version 4
Plant material collection protocol for eastern hemlock (Tsuga canadensis) to assess chemical and expression profiles associated with HWA resistance V.4
- Vidya Vuruputoor1,
- karlfetter 1,
- victoriaburton 1,
- Jill Wegrzyn1
- 1UConn
- PlantCompGenomics
Protocol Citation: Vidya Vuruputoor, karlfetter , victoriaburton , Jill Wegrzyn 2023. Plant material collection protocol for eastern hemlock (Tsuga canadensis) to assess chemical and expression profiles associated with HWA resistance. protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vzbryrvx1/v4Version created by Vidya S Vuruputoor
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 24, 2023
Last Modified: July 25, 2023
Protocol Integer ID: 85430
Keywords: plant material collection protocol for eastern hemlock, transcriptomic assessment, terpenoid profiling, stem sample, stem samples for each individual, hwa resistance, plant material collection protocol, branch tissue from eastern hemlock, tsuga canadensi, pcg team for sampling needle, hwa resistance this protocol, rna, sampling needle, eastern hemlock, likely hwa, sample, terpenoid
Abstract
This protocol was developed by the PCG team for sampling needle and branch tissue from eastern hemlock (Tsuga canadensis) for terpenoid profiling, as well as transcriptomic assessment (RNA-Seq). This study is a time-course assessment comparing known HWA-resistant (lingering) individuals from the New Jersey bullet-proof population (NJ3 and NJ4) to likely HWA-susceptible individuals. The plots assessed include those described in Kinahan et al. 2020 (https://www.mdpi.com/1999-4907/11/3/312). Sampling occurs once per month and includes deeper sampling (more bulletproof population members) at the Arnold Arboretum. Non-targeted LC/MS and GC/MS assessment is underway with Tim Cernak and Roland Kersten at the University of Michigan. RNA-Seq will be conducted at UConn on a subset of the individuals collected. This protocol describes the collection of three tubes worth of needle/stem samples for each individual (two for terpenoids and one for RNA-Seq), to be conducted on a monthly basis across all plots.
Image Attribution
The image was taken by Dr. Karl Fetter
Materials
Trimmers
Sterile latex gloves
Sterile 10ml cryotubes with internal threads
Sterile 5ml cryotubes with internal threads
Spray bottle of RNAase
Spray bottle of ethanol
1 dewer with liquid nitrogen
Dry ice
2 styrofoam boxes for overnight shipping
TreeSnap Observation
TreeSnap is a mobile application that can run on both Apple OS and Android that utilizes the phone’s GPS to collect location information and present a set of standardized questions to the collector on basic traits of the tree, including image data. This is the application of choice for this project to record this information, including local identifiers associated with the tree. The application will record the coordinates even if cell service is limited or absent in that region.
Note
Please download TreeSnap prior to sampling https://treesnap.org/
Pop-up box displaying the levels of infestation of HWA to record
Use the comment field to enter: EHS present OR EHS absent to record the hemlock scale.
highlighting where to place additional notes on individual sampled. EHS is important to log.
Take at least 3 photos with TreeSnap. This includes at least one of the trees itself, one photo of the tree tag if that is present, and one photo of the collection vial with the label as well.
Geolocation will be recorded automatically but TreeSnap can also connect with a more precise external GPS device.
Note DBH in appropriate column
Note any other observation you may have- including plant condition (Excellent/Good/Poor), and placement of individual (lower canopy, full sun, etc.)
Prepare sampling sheet
The sample sheet would look like this:- Link to spreadsheet
Collection
You will collect two sets of samples from each tree. One for RNA extraction for transcriptomics and one for metabolomics. The first needs less material so we will use the 5ml tubes. The latter needs more material and will use the 10ml tubes (you'll do this for two tubes). The first should include two branches that are approximately 5 cm in length. The second should include four branches, ideally taken from different locations around the tree.
Safety information
For RNA collections- please use gloves, and spray RNase on gloves and trimmers (separate vial- 5ml cryovial)
Metabolomics- You would use 2 10ml vials. You will be able to fit 4 branches (5cm) in each tube- so sample from one direction of the tree, then collect the three other branches from the other sides of the tree (you would ideally try to sample around the individual).
Note
Per individual- you will use TWO 10 ml vials.
RNA- You would use one 5ml vial. For this, 2 branches would be more than sufficient to fit into the vial. Ideally, you would want to sample from 2 different locations of the individual.
Note
RNA degrading enzymes occur on your skin and on the surfaces and act quickly to denature the sample. It is important to spray the shears and gloves with RNAse before sampling and to swap gloves after each tree.
In total- THREE vials per individual. TWO for terpenoids/metabolomics, and ONE for RNA.
Placing in Liquid Nitrogen
Close cryovials, and place the vial slowly into the LN dewar. Be wary of LN splashing out, and wear appropriate gear, and stay at a distance.
Safety information
Use appropriate wear while handling liquid nitrogen
Cleaning before sampling from new individual
Clean trimmers between trees with ethanol (spray bottle).
Note
For the collection of RNA- spray clippers and gloves with ethanol first, followed by RNase
Use a clipboard to manually record notes on a pre-printed spreadsheet with sample names.
After returning from the field, ensure that notes are consistent with TreeSnap entries. These entries can be amended after collection as needed.
Post-sampling and Pre-shipping
Remove all vials from the dewar (cross-check with the sample sheet). Samples must be stored at -80C or should be on dry ice during transport.
Cross-check all samples at this stage with your sample sheet.
Shipping
Shipping instructions will be provided via email. Shipments must be sent on dry ice that is contained inside a styrofoam box insert. You will be shipping separate parcels for the Metabolomics and RNA samples.
Note
Please separate the RNA and terpenoid vials before shipment
Log all data and samples in a Google sheet, or send over sample sheet so that we log your data