wheat: Wheat dataset
In SFSI: Sparse Family and Selection Index

Wheat data set

R Documentation

Wheat dataset

Description

The dataset consists of 1,092 inbred wheat lines grouped into 39 trials and grown during the 2013-2014 season at the Norman Borlaug experimental research station in Ciudad Obregon, Sonora, Mexico. Each trial consisted of 28 breeding lines that were arranged in an alpha-lattice design with three replicates and six sub-blocks. The trials were grown in four different environments:

E1: Flat-Drought (sowing in flat with irrigation of 180 mm through drip system)
E2: Bed-2IR (sowing in bed with 2 irrigations approximately 250 mm)
E3: Bed-5IR (bed sowing with 5 normal irrigations)
E4: Bed-EHeat (bed sowing 30 days before optimal planting date with 5 normal irrigations approximately 500 mm)

1. Phenotypic data.

Measurements of grain yield (YLD) were reported as the total plot yield after maturity. Records for YLD are reported as adjusted means from which trial, replicate and sub-block effects were removed. Measurements for days to heading (DTH), days to maturity (DTM), and plant height (PH) were recorded only in the first replicate at each trial and thus no phenotype adjustment was made.

2. Reflectance data.

Reflectance data was collected from the fields using both infrared and hyper-spectral cameras mounted on an aircraft on 9 different dates (time-points) between January 10 and March 27th, 2014. During each flight, data from 250 wavelengths ranging from 392 to 850 nm were collected for each pixel in the pictures. The average reflectance of all the pixels for each wavelength was calculated from each of the geo-referenced trial plots and reported as each line reflectance. Data for reflectance and Green NDVI and Red NDVI are reported as adjusted phenotypes from which trial, replicate and sub-block effects were removed. Each data-point matches to each data-point in phenotypic data.

3. Marker data.

Lines were sequenced for GBS at 192-plexing on Illumina HiSeq2000 or HiSeq2500 with 1 x 100 bp reads. SNPs were called across all lines anchored to the genome assembly of Chinese Spring (International Wheat Genome Sequencing Consortium 2014). Next, SNP were extracted and filtered so that lines >50% missing data were removed. Markers were recoded as –1, 0, and 1, corresponding to homozygous for the minor allele, heterozygous, and homozygous for the major allele, respectively. Next, markers with a minor allele frequency <0.05 and >15% of missing data were removed. Remaining SNPs with missing values were imputed using the mean of the observed marker genotypes at a given locus.

Adjusted un-replicated data.

The SFSI R-package includes the wheatHTP dataset containing (un-replicated) only YLD from all environments E1,...,E4, and reflectance (latest time-point only) data from the environment E1 only. Marker data is also included in the dataset. The phenotypic and reflectance data are averages (line effects from mixed models) for 776 lines evaluated in 28 trials (with at least 26 lines each) for which marker information on 3,438 SNPs is available.

The full (replicated) data for all four environments, all traits, and all time-points can be found in the repository https://github.com/MarcooLopez/Data_for_Lopez-Cruz_et_al_2020.

Cross-validation partitions.

One random partition of 4-folds was created for the 776 individuals (distributed into 28 trials). Data from 7 entire trials (25% of 28 the trials) were arbitrarily assigned to each of the 4 folds. The partition consist of an array of length 776 with indices 1, 2, 3, and 4 denoting the fold.

Genetic covariances.

Multi-variate Gaussian mixed models were fitted to phenotypes. Bi-variate models were fitted to YLD with each of the 250 wavelengths from environment E1. Tetra-variate models were fitted for YLD from all environments. All models were fitted within each fold (provided partition) using scaled (null mean and unit variance) phenotypes from the remaining 3 folds as training data. Bayesian models were implemented using the 'Multitrait' function from the BGLR R-package with 40,000 iterations discarding 5,000 runs for burning. A marker-derived relationships matrix as in VanRaden (2008) was used to model between-individuals genetic effects. Between-traits genetic covariances were assumed unstructured, while residual covariances were assumed diagonal.

Genetic covariances between YLD and each wavelength (environment E1) are storaged in a matrix of 250 rows and 4 columns (folds). Genetic and residual covariances matrices among YLD within each environment are storaged in a list with 4 elements (folds).

Usage

  data(wheatHTP)

Format

Y: (matrix) phenotypic data for YLD in environments E1, E2, E3, and E4; and columns 'trial' and 'CV' (indicating the 4-folds partition).
M: (matrix) marker data with SNPs in columns.
X_E1: (matrix) reflectance data for time-point 9 in environment E1.
VI_E1: (matrix) green and red NDVI for time-point 9 in environment E1.
genCOV_xy: (matrix) genetic covariances between YLD and each reflectance trait, for each fold (in columns).
genCOV_yy: (4-dimensional list) genetic covariances matrices for YLD among environments, for each fold.
resCOV_yy: (4-dimensional list) residual covariances matrices for YLD among environments, for each fold.