Data for: Multi-trait/environment sparse genomic prediction using the SFSI R-package
Data files
May 19, 2025 version files 70.80 MB
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README.md
3.04 KB
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wheat_data.tar.gz
70.80 MB
May 19, 2025 version files 70.80 MB
-
README.md
3.05 KB
-
wheat_data.tar.gz
70.80 MB
Abstract
This data set is from CIMMYT’s Global Wheat Program and includes adjusted phenotypic records of grain yield (ton/ha) from n=3,731 wheat (Triticum aestivum) lines evaluated at four environmental conditions (B2I, B5I, MEL, and LHT), and marker data for 9,045 SNPs. This dataset is a subset, corresponding to the lines that have data in the four environments, from a full dataset containing 29,484 lines evaluated at six environments.
Dataset DOI: 10.5061/dryad.vx0k6dk3p
Data set overview
This data set is from CIMMYTs Global Wheat Program and includes adjusted phenotypic records of grain yield (ton/ha) from n=3,731 wheat (Triticum aestivum) lines evaluated at four environmental conditions (B2I, B5I, MEL, and LHT), and marker data for 9,045 SNPs. This data set is a subset, corresponding to the lines that have data in the four environments, from the full data set described and analyzed by Perez-Rodriguez et al. (2017) and Lopez-Cruz & de los Campos (2021).
Data structure
The data set consists of two .csv files:
pheno.csv: Phenotypic data file consists of a matrix with grain yield records for 3,731 wheat lines (in rows) evaluated at four environments (B2I, B5I, MEL, and LHT) in columns.geno.csv: Genotypic data (geno.csv) is a matrix with 9,045 SNP markers (in columns) for all the 3,731 wheat lines (in rows)
Full data description
Experimental data
The original data set comprised a total of 29,484 lines derived from years 2009 through 2016 evaluated at the CIMMYTs experimental station in Ciudad Obregon, Mexico. Lines were evaluated under six environmental conditions representing a combination of planting system (bed vs. flat, the later referred to as melgas), number of irrigations (2, 5 irrigations or drip irrigation), and sowing date (optimum, late or early planting):
- B2I: bed planting and two irrigations
- B5I: bed planting and five irrigations
- MEL: melgas flat planting and five irrigations
- LHT: late heat
- DRB: bed planting and drip irrigation
- EHT: early heat
Grain yield trials were established in an alpha-lattice design with three replicates into incomplete block. Moisture-standardized grain yield (ton/ha) was measured as the total yield plot.
Adjusted means. Least-square means for each line within environmental condition were obtained using mixed-effect models that include a fixed intercept and the random effects of trial, block (within trial), and replicate (within trial).
Genotypic data
Lines were were genotyped using GBS (Genotyping-by-sequencing) technology which produced 42,706 SNP markers. SNPs were filtered by removing those with more than 70% of missing values and those with minor allele frequency (MAF) lower than 5%. A total of 9,045 SNPs were retained after applying these filters. Markers scores that were missing were imputed with the sample mean of lines at the corresponding loci.
References
Perez-Rodriguez, P., Crossa, J., Rutkoski, J., Poland, J., Singh, R., Legarra, A., Autrique, E., Campos, G. de los, Burgueño, J., & Dreisigacker, S. (2017). Single-Step Genomic and Pedigree Genotype x Environment Interaction Models for Predicting Wheat Lines in International Environments. The Plant Genome, 10(2), 115.
Lopez-Cruz, M., & de los Campos, G. (2021). Optimal breeding-value prediction using a Sparse Selection Index. Genetics, 218(1), 110.
The original data set includes phenotype data from 29,484 wheat lines that were derived from years 2009 through 2016 evaluated at the CIMMYT’s experimental station in Ciudad Obregon, Mexico. Lines were evaluated under six environmental conditions representing a combination of planting system (bed vs. flat, the later referred to as melgas), number of irrigations (2, 5 irrigations or drip irrigation), and sowing date (optimum, late or early planting). Each year, grain yield trials were established in an α-lattice design with three replicates into incomplete blocks. Moisture-standardized grain yield (ton/ha) was measured at each plot. Least-square means by line and environmental condition were obtained using mixed-effects models with a fixed intercept and the random effects of trial, block (within trial), and replicate (within trial).
Lines were genotyped using GBS (Genotyping-by-sequencing) for 42,706 SNP markers. SNPs with more than 70% of missing values and those with minor allele frequency lower than 5% were removed, leading to 9,045 filtered SNPs. The remaining markers that were missing were imputed with the sample mean of lines at the corresponding loci.