*2.6. QTL Effect Significance*

To validate the QTL, we tested statistical significance of difference of phenotypes between two contrasting haplotype pairs for each QTL in the merged and individual populations and in different year/location environments. QTL effect differences between two contrasting haplotype pairs for all 33 QTL were significant (Figure 4, Table S7). We also assessed relationship of the number of pyramiding positive-effect QTL in individuals with trait phenotypes. Significant linear relations for all eight traits which had two or more QTL identified in this study were observed, showing primarily additive or accumulative QTL effects (Figure 5).


**Table 3.** QTL and associated gene candidates.


**Table 3.** *Cont.*


confidence level.

*Int. J. Mol. Sci.* **2018**, *19*, x 10 of 27

**Figure 4.** Trait performance of two contrasting haplotype pairs for each of 33 QTL identified from 11 traits. A QTL is represented by the peak SNP identified in the association study. The numbers of QTL correspond to QTL No in Table 3. The BLUP values of the 11 traits in the merged population were used except for PLH/QTL 3 and DTM/QTL 7 for which BM population was used, DTM/QTL 8 for which EV population was used, and PAL/QTL 22, LIO/QTL 28 and LIN/QTL 31 for which SU population was used. The box width is proportional to the size of the subpopulations. Phenotype differences between two contrasting haplotype pairs for each QTL are shown by boxes' notches. For **Figure 4.** Trait performance of two contrasting haplotype pairs for each of 33 QTL identified from 11 traits. A QTL is represented by the peak SNP identified in the association study. The numbers of QTL correspond to QTL No in Table 3. The BLUP values of the 11 traits in the merged population were used except for PLH/QTL 3 and DTM/QTL 7 for which BM population was used, DTM/QTL 8 for which EV population was used, and PAL/QTL 22, LIO/QTL 28 and LIN/QTL 31 for which SU population was used. The box width is proportional to the size of the subpopulations. Phenotype differences between two contrasting haplotype pairs for each QTL are shown by boxes' notches. For any given QTL, boxes' notches that do not overlap indicate significant median differences at 95% confidence level.

any given QTL, boxes' notches that do not overlap indicate significant median differences at 95%

*Int. J. Mol. Sci.* **2018**, *19*, x 11 of 24

**Figure 5.** The relationship of phenotypes with the number of positive-effect QTL in individuals. Eight traits with two or more QTL identified were analyzed: (**a**) plant height (PLH), (**b**) days to maturity (DTM), (**c**) oil content (OIL), (**d**) iodine value (IOD), (**e**) palmitic acid content (PAL), (**f**) steric acid content (STE), (**g**) linoleic acid content (LIO), and (**h**) linolenic acid content (LIN). The BLUP values of the eight traits in the merged population were used. The correlation of phenotypes with the number of positive-effect QTL was calculated. \* and \*\* represent statistical significance at 0.05 and 0.01 probability level. **Figure 5.** The relationship of phenotypes with the number of positive-effect QTL in individuals. Eight traits with two or more QTL identified were analyzed: (**a**) plant height (PLH), (**b**) days to maturity (DTM), (**c**) oil content (OIL), (**d**) iodine value (IOD), (**e**) palmitic acid content (PAL), (**f**) steric acid content (STE), (**g**) linoleic acid content (LIO), and (**h**) linolenic acid content (LIN). The BLUP values of the eight traits in the merged population were used. The correlation of phenotypes with the number of positive-effect QTL was calculated. \* and \*\* represent statistical significance at 0.05 and 0.01 probability level.

#### *2.7. Pleiotropy of QTL 2.7. Pleiotropy of QTL*

Sixteen of the 33 QTL co-located at six genomic regions concerning nine traits (Figures 1 and 6, Table S8). QTL for PLH, DTH and YLD co-located on chr4. QTL for IOD, LIO and LIN co-located on chr4, 7 and 12. Chromosome 15 harbored QTL for OIL and PRO while chr5 had QTL for OIL and Sixteen of the 33 QTL co-located at six genomic regions concerning nine traits (Figures 1 and 6, Table S8). QTL for PLH, DTH and YLD co-located on chr4. QTL for IOD, LIO and LIN co-located on chr4, 7 and 12. Chromosome 15 harbored QTL for OIL and PRO while chr5 had QTL for OIL and PAL.
