Additional file 3 of Sparse Phenotyping and Haplotype-Based Models for Genomic Prediction in Rice

Additional file 3: Table S2. Genomic prediction accuraciesof days to headingand plant heightin the three rice populations using three prediction modelswith different missing rates of environment-specific best linear unbiased estimatesof genetic effects of lines in the training set. The genetic effect was respectively described by SNP genotypes, haplotype using complete blocks, and short haplotypes containing two SNPsand three SNPswithin a haplotype block. The missing rate zeroindicates the training set holds complete environment-specific BLUEs. The asterisk and pound sign indicate the prediction accuracies of haplotype-based approaches were statistically significantlyhigher and lower than those of the marker-based approach.