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Average predictive ability estimated with different numbers of SNPs fitted into the model. (DOCX 136Â kb)

ANOVA of predictive ability with SNP genomic location and SNP number as sources of variation. (DOCX 62Â kb)

Mean and standard deviation of predictive ability estimated with the five relative sizes of Training Set/Validation Set expressed in proportions and numbers of individuals. (DOCX 89Â kb)

Mean and standard deviation of predictive ability estimated with the five relative sizes of Training Set/Validation Set expressed in proportions and numbers of individuals. (DOCX 89Â kb)

Mean and standard deviation of predictive ability with the five prediction methods for the eight traits. (DOCX 96Â kb)

Average accuracy of SNP imputation methods with increasing proportions of missing data. SNPs on chromosomes 6 and 8 were randomly removed from the dataset to generate specific missing data proportions. Accuracy between imputed and true SNP genotypes were subsequently calculated with the different methods. (DOCX 1714Â kb)

Decay of linkage disequilibrium (LD) with physical distance estimated with SNPs in different genomic locations. (a) A comparison of the decay of LD with physical distance in four classes of SNPs located with coding, genic, intergenic and all regions, respectively. Dots of pairwise LD versus physical distance and the LD decay for SNPs located in all regions (b), coding region (c), genic region (d) and intergenic region (e), respectively. (DOCX 1375Â kb)

ANOVA of predictive ability with SNP genomic location and SNP number as sources of variation. (DOCX 62Â kb)

Average predictive abilities estimated using SNP sets located in different genomic regions. (DOCX 82Â kb)

ANOVA analysis of sources of variation affecting the predictive ability. (DOCX 48Â kb)