DOI: 10.5281/zenodo.14727773
title: SNP genotype and hyperspectral reflectance data from: Ensembles of genomic and hyperspectral imaging-based prediction enable selection for reduced deoxynivalenol content in wheat grains

description: SNP genotype and hyperspectral reflectance data from: Ensembles of genomic and hyperspectral imaging-based prediction enable selection for reduced deoxynivalenol content in wheat grains

 

Description of the SNP data and file structure

Eric Olson, Michigan State University, eolson@msu.edu

File name: AMAT_IMPUTED_NUMERIC_3117ind_15456snp_0.05MAF_0.70coverage_0.10het.csv

This is a .csv file of genotypic data used in genomic prediction of the mycotoxin DON in the publication "Ensembles of genomic and hyperspectral imaging-based predictions enable selection for reduced deoxynivalenol content in wheat grains".

SNPs were developed using a double digest RAD seq method. SNPs were initially filtered for 70% coverage on 3,117 individuals, 10% heterozygocity (as F4-derived and inbred lines were genotyped) and 5% minor allele frequency. Nucleotides were then coverted to numeric format. The genotype data is in numeric format with 1=major allele, -1= minor allele, 0=heterozygous. All filtering steps and conversion to numeric format was done in TASSEL5.

Missing numeric genotypes were imputed with the population mean using the A.mat function in the R package, rrblulp (Endelman, 2011).

Description of hyperspectral reflectance data and file structure

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Ensembles of Genomic and Hyperspectral Imaging-Based Prediction Enable Selection for Reduced Deoxynivalenol Content in Wheat Grains

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Hyperspectral Imaging (Phenomic) Data

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Hyperspectral Imaging Sensor: Specim IQ (Specim, Oulo, Finland)

Image Processing: Region of interest (seeds) were separated from the background in QGIS 3.10.2. Processed image was saved as ESRI shapefile (.shp)

Spectral reflectance value generation: Mean for each of the 2024 wavebands in the visible light to near infrared region was generated by averaging the spectral reflectance values from all the pixels in the region of interest. Mean spectral reflectance value was calculated using "raster" package in R.

Number of Trials: 2 (2021, 2022)

Total Number of Genotypes: 558 (2021: n=298, 2022: n=285)

Number of replicates (images) per genotype: two to three

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For individual trials, BLUEs (best linear unbiased estimates) across replicates (images) of the spectral reflectance values of each genotype

was generated using "lsmeans", and was fitted in linear model with genotype as fixed effect.

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Across trials (years), BLUEs across replicates (images) of spectral reflectance values of each genotype was generated using "lsmeans", and

was fitted in a mixed linear model using "lme4", with genotype as fixed effect, year (trial) as random effect, and genotype-by-year interaction as random effect.

| File Name | Description

|--------------------------------|----------------------------------------------------------------------------------------------------------|

| 2021_Phenomic_Data_VIS/NIR | Spectral reflectance values at the VIS/NIR (visible to near-infrared region), 397.2 nm to 1003.58 nm, |

| | of the 298 genotypes evaluated in 2021 for Deoxynivalenol content. Values are the mean (BLUEs) spectral |

| | reflectance values of two to three images (replicates) per genotype |

| | |

| 2022_Phenomic_Data_VIS/NIR | Spectral reflectance values at the VIS/NIR (visible to near-infrared region), 397.2 nm to 1003.58 nm, |

| | of the 285 genotypes evaluated in 2022 for Deoxynivalenol content. Values are the mean (BLUEs) spectral |

| | reflectance values of two to three images (replicates) per genotype |

| | |

| 2021-2022_Phenomic_Data_VIS/NIR| Spectral reflectance values at the VIS/NIR (visible to near-infrared region), 397.2 nm to 1003.58 nm, |

| | of the 558 genotypes evaluated in 2021 and 2022 for Deoxynivalenol content. Values are the BLUEs |

| | (best linear unbiased estimates) of the genotypes across years, with genotype as fixed effect, year as |

| | random effect, and genotype-by-year interaction as fixed effect. |