wheat: Wheat dataset

Description Usage Format Source References

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:

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.

Replicated and Un-replicated data.

The CRAN version includes the wheatHTP dataset containing (un-replicated) 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 GitHub (development) version of the SFSI R-package (https://github.com/MarcooLopez/SFSI) includes also the wheatHTP dataset plus wheatHTP.E1,...,wheatHTP.E4 datasets containing replicated (adjusted) phenotypic and reflectance data for all four environments, respectively.

Cross-validation partitions.

One random partition of 4-folds is provided for the un-replicated data (wheatHTP dataset) containing 776 individuals and 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 from the un-replicated data (wheatHTP dataset) containing 776 individuals. 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 30,000 iterations discarding 5,000 runs for burning. A marker-derived relationships matrix as in VanRaden (2008) was used to model between-individuals genetic effects; both between-traits genetic and residual covariances were assumed unstructured.

Genetic and residual 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

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  data(wheatHTP)
  # data(wheatHTP.E1) # GitHub version
  # data(wheatHTP.E2) # GitHub version
  # data(wheatHTP.E3) # GitHub version
  # data(wheatHTP.E4) # GitHub version

Format

Replicated data (wheatHTP.E1,...,wheatHTP.E4 datasets):

Un-replicted data (wheatHTP dataset):

Source

International Maize and Wheat Improvement Center (CIMMYT), Mexico.

References

Perez-Rodriguez P, de los Campos G (2014). Genome-wide regression and prediction with the BGLR statistical package. Genetics, 198, 483–495.

VanRaden PM (2008). Efficient methods to compute genomic predictions. Journal of Dairy Science, 91(11), 4414–4423.


SFSI documentation built on Oct. 1, 2021, 1:08 a.m.