DOI: 10.5061/dryad.x95x69pth
title: Data from: A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation

description: 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.
description: 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
 (T<sub><em>t</em></sub><sup>em-ti</sup>) in order to develop an index for sensed photoperiod (<em>DL</em><sup>s</sup>); (D3) envirotype <em>DL</em><sup>s</sup> 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 <em>et</em> <em>al</em>., 2020 and Rogers <em>et</em> <em>al</em>., 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 T<sub><em>t</em></sub><sup>em-ti</sup> 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 <em>et al.</em>, 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 <em>DL</em><sup>s</sup> 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 <em>DL</em><sup>s </sup>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 <em>per</em> <em>se</em> 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 <em>et</em> <em>al</em>., 2005) was assembled from previous experiments (File S5). These lines were observed across a maximum of three SD environments (maximum photoperiod &lt;12.3 h) and 16 long-day (LD) environments (minimum photoperiod of &gt;14.5 h) spanning 18.00° N to 42.76° N latitude.
description: # Data from: A reaction norm for flowering time plasticity reveals
 physiological footprints of maize adaptation
 [https://doi.org/10.5061/dryad.x95x69pth](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](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.