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Data.zip (38.4 MB)

Supplemental Material for Adak et al., 2023

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posted on 2024-04-29, 14:52 authored by Alper AdakAlper Adak, Aaron J. DeSalvio, Mustafa A. Arik, Seth C. Murray

  

Supplementary files were stored in the "Data.zip" file containing necessary files to reproduce the prediction codes.


  • FPCA.code.txt:      Contains the FPCA R code for a combination of growing locations (Pop1:      2018, 2019 and Pop2: Drought and optimal trials in 2020, and drought trial      in 2021), and two different flight durations (flights until flowering      time, and full flights).
  • CSV files:


  • Files named FP.location.csv (e.g.,       FP.2018.csv) represent the results of flight-Pedigree interaction in       equation 2 for each VI in each growing location.
  • Files named       FP.location.FPCA.until_flowering.csv (e.g.,       FP.2018.FPCA.until_flowering.csv) contain the results of FPCA analysis       using the flight information of each VI until flowering times in each       growing location. These files contain the first two FPCAs of each VI for       each hybrid.
  • Files named       FP.location.FPCA.full_flights.csv (e.g., FP.2018.FPCA.full_flights.csv)       present the results of FPCA analysis using all flight information of each       VI in each growing location. These files also contain the first two FPCAs       of each VI for each hybrid.
  • GAPIT.Genotype.Numerical Pop1.txt and      GAPIT.Genotype.Numerical Pop2.txt: These files      comprise the numeric genomic data of Population 1 and 2, respectively.
  • PHT.csv and Yield.csv:      These files contain the plant height (cm) and grain yield (t/ha) BLUEs      values for Pop1 and Pop2 grown in 2018, 2019, drought, and optimal trials      in 2020, as well as the drought trial in 2021. They were utilized as      predicted variables in the M1 to M5 prediction models.


  • PHT.for.multitrait.csv and      Yield.for.multitrait.csv: These files      contain the plant height (cm) and grain yield (t/ha) BLUEs values, along      with the FPCA1 value of VARI as a secondary trait for Pop1 and Pop2 grown      in 2018, 2019, drought, and optimal trials in 2020, along with the drought      trial in 2021. These data were used as predicted variables in the M6      prediction model.
  • Prediction code M1 to M5.txt and      Prediction code M6.txt: These files contain the      prediction codes for M1 to M5 and M6 prediction models, respectively.

History

Article title

Field-Based High-Throughput Phenotyping Enhances Phenomic and Genomic Predictions for Grain Yield and Plant Height Across Years in Maize