Data from: Evaluating transgenic Darling 54 American chestnuts for reintroduction: Insights from survivorship, growth, and respiration in a common garden
Data files
Dec 22, 2025 version files 419.39 KB
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AugustGrowth_Dryad.csv
37 KB
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AugustRespforR_Dryad.csv
170.56 KB
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CG_Survival.csv
15.70 KB
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CGarden_Total_Dryad.csv
21.58 KB
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CGRespforR_Dryad.csv
166.95 KB
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README.md
7.60 KB
Abstract
Transgenic Darling 54 chestnuts, engineered with an OxO gene for blight tolerance, retain the native American chestnut’s genome and offer a potential restoration solution for this functionally extinct tree species. We compared the performance of three-year-old trees in a common garden experiment featuring nearly 500 trees across five chestnut types, including Darling 54 transgenic (OxO+, n = 198) and non-transgenic (OxO-, n = 201) full-siblings, hybrid chestnuts (B3F3 backcross hybrids, n = 34; F1 hybrids, n = 17), and Chinese chestnuts (n = 55). We measured survivorship, growth, crown morphology in August 2024 and dark respiration rates in May and August 2024 to determine the suitability of Darling 54 transgenic trees for ecological restoration. Statistical analyses assessed the effects of transgene status and maternal lineage on growth performance and respiration. Darling 54 OxO+ trees exhibited strong survivorship and a favorable growth form comparable to related non-transgenic chestnuts, despite reduced growth rate and survival. Elevated leaf respiration was observed in OxO+ trees during late-season measurements, suggesting a potential metabolic cost associated with transgenesis. Overall, Darling 54 OxO+ chestnuts maintain desirable traits, but reduced growth and intermittently higher respiration rates may indicate a trade-off. Although OxO+ chestnuts show promise as restoration trees, additional research is needed to assess blight tolerance, long-term performance under competitive forest conditions, and whether growth constraints persist over time.
Dataset DOI: 10.5061/dryad.ht76hdrvt
Description of the data and file structure
This dataset was collected during a common garden experiment designed to evaluate the performance of transgenic and non-transgenic American chestnuts (Castanea dentata) alongside hybrid and Chinese chestnut controls. Nearly 500 trees were planted and monitored over three years to assess survivorship, growth, crown morphology, and leaf respiration. The data were used to test the effects of transgene status and maternal lineage on growth and physiology, with the aim of determining the suitability of Darling 54 transgenic chestnuts for forest restoration.
Files and variables
File: CG_Survival.csv
Description: Dataset of original common garden plantings in 2021 used to assess survivorship in 2024 across the five chestnut types. Note: N/A means "not planted," and thus this variable is not applicable.
Variables
- Row: Alphabetic location of trees (A through S)
- Pos: Numeric location of trees (1 through 28)
- TreeID: Unique tree identifier
- Type: Chestnut type (5 variables: OxO-, OxO+, B3F3, Chinese, F1)
- Mother: Maternal line (13 variables)
- Status: Survival status (1 = alive, 0 = dead)
File: AugustGrowth_Dryad.csv
Description: Dataset collected in August 2024 and used to evaluate tree grown and morphology
Variables
- Row: Alphabetic location of trees (A through S)
- Pos: Numeric location of trees (1 through 28)
- TreeID: Unique tree identifier
- Type: Chestnut type (5 variables: OxO-, OxO+, B3F3, Chinese, F1)
- Mother: Maternal line (13 variables)
- Height: Total tree height in 2023 in meters (m)
- NewHeight: Total tree height in 2024 in meters (m)
- HeightDiff: NewHeight minus Height in meters (m)
- CrownHeight: Height of tree crown in meters (m)
- CrownWidth: First width of crown in meters (m)
- CrownWidth2: Second width of crown measured perpendicular from CrownWidth in meters (m)
- Crown: Average of CrownWidth and CrownWidth2 in meters (m)
- Diamwidth: First basal diameter in centimeters (cm)
- Diamwidth2: Second width of crown measured perpendicular to DiamWidth in centimeters (cm)
- BasalDiam: Average of Diamwidth and Diamwidth2 in centimeters (cm)
- 1stOrderBranch: Not analyzed
- DomLeader: Not analyzed
File: CGarden_Total_Dryad.csv
Description: Dataset collected in December 2023 and used to evaluate tree heights
Variables
- Plot: Common Garden
- TreeID: Unique tree identifier
- Type: Chestnut type (5 variables: OxO-, OxO+, B3F3, Chinese, F1)
- Mother: Maternal line (13 variables)
- Row: Alphabetic location of trees (A through S)
- Pos: Numeric location of trees (1 through 28)
- Height: Total tree height in 2023
File: AugustRespforR_Dryad.csv
Description: Foliar respiration dataset generated by an open gas exchange system (LI-6400) in August 2024 for 100 OxO full-sibling American chestnut trees
Variables
- Row: Alphabetic location of trees (A through S)
- Pos: Numeric location of trees (1 through 28)
- TreeID: Unique tree identifier
- Family: Maternal line (13 variables)
- Type: Transgene status (2 variables: OxO-, OxO+)
- Obs: Order of respiration measurements
- HHMMSS: Hour/minutes/seconds
- PhotoAreaNeg: Respiration on an area basis expressed as a negative number (μmol CO2 m -2 s -1)
- PhotoArea: Respiration on an area basis corrected to a positive number (μmol CO2 m -2 s -1)
- PhotoMass: Respiration on a mass basis (nmol CO2 g -1 s -1)
- Cond: Conductance to H2O (mol H2O m -2 s -1)
- Ci: Intercellular CO2 concentration (μmol CO2 mol -1)
- Trmmol: Transpiration rate (mmol H2O m -2 s -1)
- VpdL: Vapor pressure deficit based on Leaf temp (kPa)
- CTleaf: Computed leaf temp (C)
- Area: Total leaf surface area
- SLA: Specific leaf area (cm2g -1)
- StmRat: Stomatal ratio
- BLCond: Total boundary layer conductance for the leaf (includes stomatal ratio) (mol m -2 s -1)
- Tair: Temperature in sample cell (C)
- Tleaf: Temperature of leaf thermocouple (C)
- TBlk: Temperature of cooler block (C)
- CO2R: Reference cell CO2 (μmol CO2 mol -1)
- CO2S: Sample cell CO2 (μmol CO2 mol -1)
- H2OR: Reference cell H2O (mmol H2O mol-1)
- H2OS: Sample cell H2O (mmol H2O mol -1)
- RH_R: Relative humidity in the reference cell (%)
- RH_S: Relative humidity in the sample cell (%)
- Flow: Flow rate to the sample cell (μmol s -1)
- PARi: In-chamber quantum sensor (μmol m -2 s -1)
- PARo: External quantum sensor (μmol m -2 s -1)
File: CGRespforR_Dryad.csv
Description: Foliar respiration dataset generated by an open gas exchange system (LI-6400) in May 2024 for 100 OxO full-sibling American chestnut trees
Variables
- Row: Alphabetic location of trees (A through S)
- Pos: Numeric location of trees (1 through 28)
- TreeID: Unique tree identifier
- Family: Maternal line (13 variables)
- Type: Transgene status (2 variables: OxO-, OxO+)
- Date: Date of measurements
- Obs: Order of respiration measurements
- HHMMSS: Hour/minutes/seconds
- PhotoAreaNeg: Respiration on an area basis expressed as a negative number (μmol CO2 m -2 s -1)
- PhotoArea: Respiration on an area basis corrected to a positive number (μmol CO2 m -2 s -1)
- PhotoMassNeg: Respiration on a mass basis expressed as a negative number (nmol CO2 g -1 s -1)
- PhotoMass: Corrected positive respiration on a mass basis (nmol CO2 g -1 s -1)
- Cond: Conductance to H2O (mol H2O m -2 s -1)
- Ci: Intercellular CO2 concentration (μmol CO2 mol -1)
- Trmmol: Transpiration rate (mmol H2O m -2 s -1)
- VpdL: Vapor pressure deficit based on Leaf temp (kPa)
- CTleaf: Computed leaf temp (C)
- Area: Total leaf surface area (cm2)
- SLA: Specific leaf area (cm2g -1)
- StmRat: Stomatal ratio
- BLCond: Total boundary layer conductance for the leaf (includes stomatal ratio) (mol m -2 s -1)
- Tair: Temperature in sample cell (C)
- Tleaf: Temperature of leaf thermocouple (C)
- TBlk: Temperature of cooler block (C)
- CO2R: Reference cell CO2 (μmol CO2 mol -1)
- CO2S: Sample cell CO2 (μmol CO2 mol -1)
- H2OR: Reference cell H2O (mmol H2O mol -1)
- H2OS: Sample cell H2O (mmol H2O mol -1)
- RH_R: Relative humidity in the reference cell (%)
- RH_S: Relative humidity in the sample cell (%)
- Flow: Flow rate to the sample cell (μmol s -1)
- PARi: In-chamber quantum sensor (μmol m -2 s -1)
- PARo: External quantum sensor (μmol m -2 s -1)
Code/software
The data files are provided in comma-separated values (.csv) format, which can be opened using any free or open-source software such as R (R Core Team, 2025), or more generally in spreadsheet programs.
All analyses for this project were conducted in R version 4.4.3 (R Core Team, 2025). Within R, I primarily used the tidyverse collection of packages (Wickham et al., 2019), including readr for importing CSV files, dplyr for data wrangling, and ggplot2 for visualization. Additional packages used were lme4, emmeans, car, doBy, grid, gridExtra, and multcomp.
The workflow involved importing each CSV file into R using read.csv(), performing data cleaning and transformation steps, conducting statistical analyses (e.g., ANOVA and Tukey’s HSD tests), and generating figures.