Supplemental Material for Belamkar et al., 2018
datasetposted on 25.06.2018 by Vikas Belamkar, Mary J. Guttieri, Waseem Hussain, Diego Jarquín, Ibrahim El-basyoni, Jesse Poland, Aaron J. Lorenz, P. Stephen Baenziger
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
File S1 contains supplementary Tables S1-S2 and Figures S1-S7.
File S2 has details of the preliminary yield trials (F3:6) and advanced yield trials (F3:7) grown in 2012-2015 and 2013-2016. The experimental design, number of locations, number of replicates per location, heritability for yield within and across locations is provided.
File S3 contains the R script developed for analyzing preliminary yield trials (F3:6) grown in an augmented design. Mixed models incorporated both experimental design and spatial variation.
File S4 provides an example phenotypic dataset for utilizing the R script provided in File S3.
File S5 shows the SNP calling accuracy of 20 lines genotyped by genotyping-by-sequencing at least twice (biological replicates) over the years. The accuracy is presented as sequential pairwise comparisons of 20 unique samples.
File S6 contains the yield data (best linear unbiased predictors) of the preliminary yield trials (F3:6) grown in 2012-2015 used for genomic selection.
File S7 contains the SNP marker data of 26,925 SNPs on the 1,110 F3:6 lines grown in 2012-2015. The homozygous major, homozygous minor, and heterozygous genotypes are coded as 1, 0, and 0.5 in the genotype matrix.
File S8 shows the Akaike Information Criterion (AIC) values and the residual plots for each of the mixed models tested for the yield data collected on the preliminary yield trial (F3:6) grown in McCook, NE in 2014.