*4.8. QTL Validation*

Three approaches were applied to validate QTL identified by GWAS. The first approach was to compare our QTL with previously identified QTL as described above. The same QTL was inferred if two QTL were mapped to the same recombination block or haplotype block. The second approach tested the significance of difference of phenotypes between two contrasting haplotype pairs of a QTL in the populations. Statistically significant differences served to validate significant QTL. Both *t* and Wilcox non-parametric tests were performed using the R functions "t.test" and "wilcox.test" for each QTL in the merged and individual populations and in different year/location environments. To test the positive correlations of a trait upon pyramiding of QTL, a simple regression of the number of positive-effect QTL on phenotypic values of a trait was calculated. A positive-effect QTL in an individual meant that this individual possessed a positive effect allele for the QTL. The last approach was to perform genome-wide selective sweep scans to confirm QTL associated genomic regions as described below.
