Two reproductive traits show contrasting genetic architectures in Plantago lanceolata
Citation
Marshall, Matthew M.; Remington, David L.; Lacey, Elizabeth P. (2020), Two reproductive traits show contrasting genetic architectures in Plantago lanceolata, Dryad, Dataset, https://doi.org/10.5061/dryad.fttdz08nq
Abstract
Methods
Floral reflectance was measured as the average of % light reflected at 850nm for two spectral scans conducted on a single pre-flowering spike using a spectrophotometer with an integrating sphere.
Flowering time was the number of days from induction (day 168) to the complete emergence of the first flowering spike.
Usage Notes
Readme.txt
Data: REF_FT_Phenotypic_Data.xlsx
- Phenotypic data for all individuals as summarized in Table 1 organized into 5 tabs.
- Tab 'Parents.REF' - Reflectance Data from F0 Parent clones, and mean values. Columns 'Genotype' - A (Italy), B (Denmark), C (France), J (Sweden); 'Clone' - Clone Number or MEAN; 'Temperature' - Cool, Warm, or Mean; 'Cool' - Reflectance value in Cool; 'Warm' - Reflectance value in Warm; 'Plasticity' - Plasticity Value
- Tab 'F1.REF' - Reflectance Data from F1 genotypes. Columns 'Genotype'- BA and CJ are F1-parents; 'Family' - Parents listed as female x male, as in Figure 2; 'Generation' - F1; 'Temperature' - Cool, Warm; 'F1_ref' - Single environment genotypic mean calculated as the average of clonal replicates; 'Plast_REF' - Mean plasticity calculated as mean warm value - mean cool value
- Tab 'F2.REF' - Reflectance Data from F2 genotypes. Columns 'Genotype'- Individual; 'Cytoplasm' - N or S; 'Generation'- F2; 'Cool Reflectance' - Cool environment genotypic mean calculated as the average of clonal replicates; 'Warm Reflectance' - Warm environment genotypic mean calculated as the average of clonal replicates; 'PlasticityF2' - Mean plasticity calculated as mean warm value - mean cool value
- Tab 'Parents.FT' - Flowering Time Data from F0 Parent clones, and mean values. Columns 'Genotype' - A (Italy), B (Denmark), C (France), J (Sweden); 'Clone' - Clone Number or MEAN; 'Temperature' - Cool, Warm, or Mean; 'Cool' - Flowering Time value in Cool; 'Warm' - Flowering Time value in Warm; 'Plasticity' - Plasticity Value
- Tab 'F1_F2.FT' - Flowering Time Data from F1 and F2 genotypes. Columns 'Genotype'- BA and CJ are F1-parents; 'Family (for F1s) Cytoplasm (for F2s)' - Parents listed as female x male for F1s, Cytoplasm N or S for F2s (See Fig 2); 'Generation'- F1 or F2; 'Temperature' - Cool, Warm; 'F1_FT'- Flowering Time genotypic mean calculated as the average of clonal replicates of F1s; 'F2_FT'- Flowering Time genotypic mean calculated as the average of clonal replicates of F2s; 'Plast_FT' - Mean plasticity calculated as mean warm value - mean cool value
Script: PVE.R - R Script for performing PVE calculations
Data: PVE_Data.CSV - Raw data of genotypic means for parent and F2 genotypes.
- Columns: 'Genotype' - Genotype of measurement, 'Generation' - South or North for F0 parents, F2 for F2 genotypes
- Columns: Data columns indicate trait and environment (or plasticity) as Trait.Environment; 'Reflectance.Cold', 'Reflectance.Warm', 'Reflectance.Plasticity, 'FT.Cold', 'FT.Warm', 'FT.Plasticity'
- Values indicate mean trait value. For F0 genotypes mean trait value represents mean of a single clone. For F2 genotypes mean trait value represents mean of all clonal values. See methods for details.
Script: Recombination_Mapping.R
Data: Recombination_Mapping.txt - Raw data of 323 genetic markers for 104 F2 individuals with highest sequencing coverage. File structure is as required by OneMap 2.0-4 package that runs in R.
Script: qtl_FT.R
Script: qtl_Reflectance.R
Data: ALL_DATA.qtl.csv; File structure is as required by qtl package that runs in R.
- Columns: 'Genotype'- F2 Genotype, 'Cytoplasm' - N or S cytoplasm,
- Columns: Data columns indicate trait and environment (or plasticity) as Trait.Environment; 'Reflectance.Cold', 'Reflectance.Warm', 'Reflectance.Plasticity, 'FT.Cold', 'FT.Warm', 'FT.Plasticity'
- Columns: '393', '99', '493', etc.: These are the DNA markers from the recombination map (As in Figure 5).
Data: ALL_DATA.qtl_N.csv; Same as ALL_DATA.qtl.csv except F2s with Southern cytoplasm (S) are excluded.
Data: ALL_DATA.qtl_S.csv; Same as ALL_DATA.qtl.csv except F2s with Northern cytoplasm (N) are excluded.
Funding
National Science Foundation, Award: DEB 0236526