A comparison of methods for training set optimization in genomic selection to discover the most favorable genotypes from a candidate population

The dataset was used in the article "A comparison of methods for training set optimization in genomic selection to discover the most favorable genotypes from a candidate population".In the dataset, inside each file, the file name containing kinship is the kinship matrix, the file name containing PC is the principal components matrix, the file name containing subpop is a vector represents the subpopulation of each individuals, and the file name containing pheno is the phenotype data.The tropical rice dataset is originally from Spindel et al. (2015) [1], The wheat dataset is originally from Kristensen et al. (2019) [2], The sorghum dataset is originally from Fernandez-Gonzalez et al. (2022) [3], and soybean dataset is originally from Stewart-Brown et al. (2019) [4]. Spindel J, Begum H, Akdemir D, Virk P, Collard B, et al. (2015) Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLoS Genet 11: e1004982.Kristensen PS, Jensen J, Andersen JR, Guzmán C, Orabi J, Jahoor A (2019) Genomic prediction and genome-wide association studies of flour yield and alveograph quality traits using advanced winter wheat breeding material. Genes 210(9): 669.Fernandez-Gonzalez et al. (2022) A comparison of methods for training population optimization in genomic selection. Theor and Appl Genet 136:30Stewart-Brown, B. B., Song, Q., Vaughn, J. N., and Li, Z. (2019). Genomic selection for yield and seed composition traits within an applied soybean breeding program. Genes|Genomes|Genetics 9, 2253–2265.