DOI: 10.5061/dryad.fttdz08nq
title: Two reproductive traits show contrasting genetic architectures in Plantago lanceolata

description: In many species, temperature-sensitive phenotypic plasticity (i.e., an
 individual's phenotypic response to temperature) displays a positive
 correlation with latitude, a pattern presumed to reflect local adaptation.
 This geographic pattern raises two general questions: 1) Do a few
 large-effect genes contribute to latitudinal variation in a trait? 2) Is
 the thermal plasticity of different traits regulated pleiotropically? To
 address the questions, we crossed individuals of Plantago lanceolata
 derived from northern and southern European populations. Individuals
 naturally exhibited high and low thermal plasticity in floral reflectance
 and flowering time. We grew parents and offspring in controlled cool- and
 warm-temperature environments, mimicking what plants would encounter in
 nature. We obtained genetic markers via genotype-by-sequencing (ddRADseq),
 produced the first recombination map for this ecologically-important
 non-model species, and performed QTL mapping of thermal plasticity and
 single-environment values for both traits. We identified a large-effect
 QTL that largely explained the reflectance plasticity differences between
 northern and southern populations. We identified multiple smaller-effect
 QTLs affecting aspects of flowering time, one of which affected flowering
 time plasticity. Results indicate that the genetic architecture of thermal
 plasticity in flowering is more complex than for reflectance. One
 flowering time QTL showed strong cytonuclear interactions under cool
 temperatures. Reflectance and flowering plasticity QTLs did not
 colocalize, suggesting little pleiotropic genetic control and freedom for
 independent trait evolution. Such genetic information about the
 architecture of plasticity is environmentally important because it informs
 us about the potential for plasticity to offset negative effects of
 climate change.
description: 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.
description: <strong>Readme.txt</strong>
 <strong>Data:
 REF_FT_Phenotypic_Data.xlsx</strong><br> - Phenotypic data for
 all individuals as summarized in Table 1 organized into 5 tabs.<br>
 - 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<br> - 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<br> - 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<br> - 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<br> - 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  <strong>Script: PVE.R - R Script
 for performing PVE calculations</strong><br>
 <strong>Data: PVE_Data.CSV - Raw data of genotypic means for parent
 and F2 genotypes.</strong><br> - Columns: 'Genotype'
 - Genotype of measurement, 'Generation' - South or North for F0
 parents, F2 for F2 genotypes<br> - Columns: Data columns indicate
 trait and environment (or plasticity) as Trait.Environment;
 'Reflectance.Cold', 'Reflectance.Warm',
 'Reflectance.Plasticity, 'FT.Cold', 'FT.Warm',
 'FT.Plasticity'<br> - 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.<br>  <br> <strong>Script:
 Recombination_Mapping.R</strong><br> <strong>Data:
 Recombination_Mapping.txt </strong>- 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.
 <strong>Script: qtl_FT.R</strong><br>
 <strong>Script: qtl_Reflectance.R</strong><br>
 <strong>Data: ALL_DATA.qtl.csv</strong>; File structure is as
 required by qtl package that runs in R. <br> - Columns:
 'Genotype'- F2 Genotype, 'Cytoplasm' - N or S
 cytoplasm, <br> - Columns: Data columns indicate trait and
 environment (or plasticity) as Trait.Environment;
 'Reflectance.Cold', 'Reflectance.Warm',
 'Reflectance.Plasticity, 'FT.Cold', 'FT.Warm',
 'FT.Plasticity'<br> - Columns: '393',
 '99', '493', etc.: These are the DNA markers from the
 recombination map (As in Figure 5). <br> <strong>Data:
 ALL_DATA.qtl_N.csv</strong>; Same as ALL_DATA.qtl.csv except F2s
 with Southern cytoplasm (S) are excluded. <br> <strong>Data:
 ALL_DATA.qtl_S.csv</strong>; Same as ALL_DATA.qtl.csv except F2s
 with Northern cytoplasm (N) are excluded.