Data from: A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation
Data files
Jul 15, 2024 version files 737.28 KB
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File_S1.txt
53.34 KB
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File_S2.txt
6.05 KB
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File_S4.txt
55.21 KB
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File_S5.txt
602.40 KB
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File_S6.txt
12.51 KB
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README.md
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Nov 27, 2024 version files 840.30 KB
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File_S1.txt
53.34 KB
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File_S2.txt
6.05 KB
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File_S3.txt
101.27 KB
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File_S4.txt
55.21 KB
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File_S5.txt
602.40 KB
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File_S6.txt
12.51 KB
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README.md
9.51 KB
Abstract
Understanding how plant phenotypes are shaped by their environments is crucial for addressing questions about crop adaptation to new environments. This study focused on analyzing the genetic variability underlying genotype-by-environment interactions and adaptation for flowering time in maize. We developed the use of a physiological reaction norm for flowering time plasticity (PRN-FTP) modeled from multi-environment trial networks, with genotype-specific parameters putatively linked to different regulatory modules for flowering time. We show how genotype-specific differences in developmental responses to temperature fluctuations condition differences in photoperiod perceived among genotypes. This occurs not only across but also within common environments, as the perception of photoperiod is altered by variation in rates of development and durations for becoming sensitized to photoperiod. Using a new metric for envirotyping sensed photoperiods for maize, it was found that, at high latitudes, different genotypes in the same environment can experience up to hours-long differences in photoperiod. This emphasizes the importance of considering genotype-specific differences in the experienced environment when investigating plasticity. Modeling the PRN-FTP for global breeding material of maize showed that tropical and temperate germplasm occupy distinct territories of the trait space for PRN-FTP parameters, supporting that the geographical spread and adaptation of maize was differentially mediated by distinct pathways for flowering time regulation. Our results have implications for understanding crop adaptation and for future crop improvement efforts.
README: Data from: A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation
https://doi.org/10.5061/dryad.x95x69pth
Description of the data and file structures
File_S1. Estimates of thermal time from planting to male flowering (anthesis) for Genomes-To-Fields data used to compare temperature response functions.
Dataset D1: Contains metadata and best linear unbiased estimates (BLUEs) for days to anthesis (DTA) of 24 hybrids in 25-26 field environments. Field metadata and BLUEs for DTA were assembled from McFarland et al (2020) and Rogers et al. (2021) (see Main text). Three temperature response functions (Eq. S1-S3, Methods S1 of Main text) were used to estimate thermal times.
File_S1.txt (tab delimited); description of columns
env: environment code (year x location)
year: year of planting
lat: latitude of field environment
lon: longitude of field environment
hybrid: hybrid name
date_planted: planting date
BLUE_DTA : best linear unbiased estimate for days from planting to anthesis (DTA)
BLUE_DTA_date : date of best linear unbiased estimate (BLUE) for DTA
BLUE_DTA_Tt_EqS1 : thermal time of BLUE for DTA estimated by Eq. S1 (Methods S1 of Main text)
BLUE_DTA_Tt_EqS3 : thermal time of BLUE for DTA estimated by Eq. S2 (Methods S1 of Main text)
BLUE_DTA_Tt_EqS3 : thermal time of BLUE for DTA estimated by Eq. S3 (Methods S1 of Main text)
File_S2. Estimates of thermal time to tassel initiation for panel 1 used for modeling sensed daylength (DLs).
Dataset D2: Contains estimates for genotypes in panel 1 (284 inbred lines), measured under short-day conditions in the Phenoarch platform (phyllochron) and the field in Puerto Vallarta, MX (final leaf number).
File_S2.txt (tab delimited); description of columns
genotype: line name
BLUE_FLN: best linear unbiased estimate (BLUE) for final leaf number
BLUE_Ptip: BLUE for phyllochron, with thermal time estimated using Eq. S2 (Methods S1 of Main text)
Tt_em_ti: thermal time from crop emergence to tassel initiation estimated from BLUE_FLN and BLUE_Ptip using Eq. 1 (Materials and Methods of Main text)
File_S3. Metadata for 671 field environments and estimates of sensed photoperiod (DLs) envirotypes.
Dataset D3: Contains metadata for 671 environments used for envirotyping the DLs of three percentile-maturity groups (based on the 5th, 50th, and 95th percentiles of the BVP-ti distribution for panel 1; described in Main text).
File_S3.txt (tab delimited); description of columns
env: environment code (year x location)
lat: latitude of field environment
lon: longitude of field environment
date_planted: planting date
date_emerged: crop emergence date
project: project associated with data row
meteo_source: source of temperature data (satellite or field station)
meteo_website: website for source for meteo data (if NA, records were retrieved from a local contact)
date_DLs_05: date of DLs estimated for the 5th-percentile of the BVP-ti distribution for panel 1
date_DLs_50: ddate of DLs estimated for the 50th-percentile of the BVP-ti distribution for panel 1
date_DLs_95: date of DLs estimated for the 95th-percentile of the BVP-ti distribution for panel 1
daylength_DLs_05: civil twilight daylength (h) for date_DLs_05
daylength_DLs_50: civil twilight daylength (h) for date_DLs_50
daylength_DLs_95: civil twilight daylength (h) for date_DLs_95
File_S4. Data used for modeling the physiological reaction norm for flowering time plasticity (PRN-FTP) of seven genotypes.
Dataset D4: Contains metadata and estimates used for modeling the PRN-FTP, including the control groups used for latent variable adjustment and seven tropical lines used for fitting the bilinear function for the PRN-FTP (described in Main text).
File_S4.txt (tab delimited); description of columns
country: country of field environment
env: environment code (year x location)
year: year of planting
loc: location of planting
lat: latitude of field environment
lon: longitude of field environment
genotype: line name
set: indicator of photoperiod-insensitive control group used for latent variable adjustment vs. test genotype
project: project associated with data row
date_planted: planting date
date_emerged: crop emergence date
bvp_ti_platform: basic vegetative phase of tassel initiation (BVP-ti) calculated according to Eq.1 (see Main text)
BLUE_DTA: best linear unbiased estimate (BLUE) for days from planting to anthesis
SE_DTA: standard error for BLUE_DTA
BLUE_DTA_date: date corresponding to BLUE_DTA
BLUE_DTA_Tt_EqS2: thermal time from date_planted to BLUE_DTA_date (using Eq. S2 in Supplemental Information)
BLUE_DTA_em_Tt_EqS2: thermal time from date_emerged to BLUE_DTA_date (using Eq. S2 in Supplemental Information)
BLUE_DTA_em_Tt_EqS2_adjusted:latent variable-adjusted value for BLUE_DTA_em_Tt_EqS2 (see Materials and Methods of Main text)
date_DLs: date of DLs
doy_DLs: day of year of DLs
daylength_DLs: daylength at DLs (genotype-specific)
daylength_DLs_ref: daylength at DLs (common 50th-percentile reference)
diff_daylength_DLs: difference between the genotype-specific DLs and the 50th-percentile reference DLs
File_S5. Data used for estimating parameters of the physiological reaction norm for flowering time plasticity (PRN-FTP) in a diversity panel constituting separate breeding pools of maize.
Dataset D5: Contains metadata and estimates used for modeling the PRN-FTP, including the control groups used for latent variable adjustment and the remaining lines for applying the LD-SD method for modeling the PRN-FTP (see Materials and Methods in Main text).
File_S5.txt (tab delimited); description of columns
env: environment code (year x location)
year: year of planting
lat: latitude of field environment
lon: longitude of field environment
genotype: line name
set: indicator of photoperiod-insensitive control group used for latent variable adjustment vs. test genotype
breeding_pool: temperate, tropical, admixed, or NA
project: project associated with data row
date_planted: planting date
date_emerged: crop emergence date
BLUE_DTA: best linear unbiased estimate (BLUE) for days from planting to anthesis
SE_DTA: standard error for BLUE_DTA
BLUE_DTA_date: date corresponding to BLUE_DTA
BLUE_DTA_Tt_EqS2: thermal time from date_planted to BLUE_DTA_date (using Eq. S2 in Supplemental Information)
BLUE_DTA_em_Tt_EqS2: thermal time from date_emerged to BLUE_DTA_date (using Eq. S2 in Supplemental Information)
BLUE_DTA_em_Tt_EqS2_adjusted: latent variable-adjusted value for BLUE_DTA_em_Tt_EqS2 (see Materials and Methods of Main text)
date_DLs: date of DLs
doy_DLs: day of year of DLs
daylength_DLs: daylength at DLs
File_S6. Parameter estimates for the physiological reaction norm for flowering time plasticity (PRN-FTP) in a diversity panel constituting separate breeding pools of maize.
Contains estimates of flowering time per se (intercept) and photoperiod sensitivity (slope) based on the LD-SD method (see Materials and Methods in Main text) applied to panel 2.
File_S6.txt (tab delimited); description of columns
genotype: line name
set: indicator of photoperiod-insensitive control group used for latent variable adjustment vs. test genotype
breeding_pool: temperate, tropical, admixed, or NA
PRNFTP_LDSD_adjusted_intercept: parameter estimate for flowering time per se based on the LD-SD method with latent variable adjusted values
PRNFTP_LDSD_adjusted_slope: parameter estimate for photoperiod sensitivity based on the LD-SD method with latent variable adjusted values
no_env_LD: no of long-day environments in which the line was measured
no_env_SD: no of short-day environments in which the line was measured
Code/Software
Scripts and meteo data for fitting the PRN-FTP are available at https://github.com/maizeatlas/prnftp.
Version changes
Nov-2024:
File_S1: We revised the dataset to include a more balanced set of BLUE_DTA values for a common set of genotypes and environments. The file now contains 24 genotypes with BLUE_DTA values for 25 to 26 environments.
File_S2: We noticed that certain genotypes were attributed an incorrect value for final leaf number. Correcting this also resulted in new estimates for Tt_em_ti per genotype, which in turn resulted in new estimates for DLs in Files S3-S6 (noted for each of the revised files). In addition, due to a difference in genotype names when merging information, several genotypes were inadvertently filtered in the pervious version. This correction resulted in an increase from 239 to 284 genotypes.
File_S3: Nine of the original 680 environments (env) were filtered. These environments were defined by separate planting dates at common field locations within the same year. The values of date_DLs_05, date_DLs_50, date_DLs_95, daylength_DLs_05, daylength_DLs_50, and daylength_DLs_95 were changed because of the new values of Tt_em_ti used as an estimator of DLs.
File_S4: Values for date_DLs, doy_DLs, and daylength_DLs were changed after using new values of Tt_em_ti to estimate DLs. New information was added (columns daylength_DLs_ref and diff_daylength_DLs).
File_S5: Values for date_DLs, doy_DLs, and daylength_DLs were changed after using new values of Tt_em_ti to estimate DLs.
File_S6: Values for PRNFTP_LDSD_adjusted_intercept and PRNFTP_LDSD_adjusted_slope were changed after using new values of Tt_em_ti to estimate DLs.
Methods
Datasets (“D”) from multiple projects and experiments were assembled to: (D1) select a temperature response function for thermal time estimation; (D2) estimate variation in the thermal time duration between crop emergence and tassel initiation (Ttem-ti) in order to develop an index for sensed photoperiod (DLs); (D3) envirotype DLs in maize fields across the Northern Hemisphere; (D4) demonstrate methods for modeling a physiological reaction norm for flowering time plasticity (PRN-FTP); and (D5) compare the trait space of parameters estimated from the PRN-FTP in a diversity panel constituting separate breeding pools of maize. The current study focused on days to anthesis (male flowering) as the final characteristic.
(D1) Three temperature response functions (Methods S1, Eq. S1-S3) for measuring thermal time were compared using MET data with 24 hybrids tested in 25 to 26 field environments, spanning latitudes from 30.5371° N to 44.2089° N (File S1; data sourced from the Genomes-To-Fields Initiative). For each environment, the sowing date, field coordinates, and best linear unbiased estimates (BLUEs) for calendar days from sowing to anthesis were obtained from McFarland et al., 2020 and Rogers et al., 2021. Using temperature data, genotype-specific BLUEs for calendar days to anthesis were converted to thermal time.
(D2) A collection of 284 maize inbred lines (panel 1) was used to estimate Ttem-ti for each genotype using a physiological formalism (Eq. 1) based on experimental data for crop emergence, phyllochron, and final leaf number recorded in two experiments with short-day (SD) conditions that (File S2). Crop emergence and phyllochron were measured in a greenhouse phenotyping platform at the LEPSE of INRAE (PhenoArch, Montpellier, FR; Cabrera-Bosquet et al., 2016) under well-watered conditions, while final leaf number was recorded in a field experiment in Puerto Vallarta, MX, also in well-watered conditions. For both experiments, daylengths throughout the growth cycle never exceeded 12.5 h. Additional details for these experiments can be found in Supplemental Information (Methods S2).
(D3) Computational envirotyping of DLs was performed for fields across the Northern Hemisphere (latitudinal range of 13.7578° N to 54.2900° N) where maize was previously grown. For this, the geographical coordinates and planting dates of 671 field environments were assembled from past publications and ongoing projects (File S3).
(D4) To test modeling procedures for the PRN-FTP, anthesis data from 37 field trials were combined into a multi-environment trial (MET) dataset (File S4). This dataset maximized the number of field trials available for a common subset of genotypes also present in dataset D2 (so that genotype-specific values for DLs could be determined), including seven temperate inbred lines (B37, B73, M37W, Mo17, Oh43, LH123Ht, and 2369) and seven tropical inbred lines (CML10, CML258, CML277, CML341, CML373, Tzi8, and Tzi9). Still, representation of these lines across the 37 environments was not fully balanced. The temperate lines were present in a minimum of 15 and a maximum of 22 environments. The tropical lines were present in a minimum of 18 and a maximum of 37 environments.
(D5) To examine the relationship between PRN-FTP parameters associated with flowering time per se and photoperiod sensitivity, MET data for a collection of 111 temperate, 52 tropical, and 51 admixed inbred lines constituting separate breeding pools (panel 2; Flint-Garcia et al., 2005) was assembled from previous experiments (File S5). These lines were observed across a maximum of three SD environments (maximum photoperiod <12.3 h) and 16 long-day (LD) environments (minimum photoperiod of >14.5 h) spanning 18.00° N to 42.76° N latitude.