Table 1. Location of QTL identified in this study and the amount of phenotypic variance they explain.
| Trait | Chr. | Position (cM) (1.5-LOD SI) | Nearest Marker | LOD Score | Genotype | % PVE | Total % PVE | Estimated Effect |
|---|---|---|---|---|---|---|---|---|
| Melanin | A | 15.6 (11.0, 29.8) | CNA03020 | 12.5 | na | 15 | 49 | a 2.9 |
| d 1.0 | ||||||||
| B | 15.0 (11.2, 18.8) | CNB03520 | 13.8 | na | 16 | a 1.9 | ||
| d 3.4 | ||||||||
| G | 3.6 (0.0, 9.6) | CNG01240 | 9.0 | A | 10 | a −3.9 | ||
| d −1.8 | ||||||||
| L | 0.0 (0.0, 7.2) | CNL03990 | 11.3 | na | 13 | a 61.1 | ||
| d −75.5 | ||||||||
| L | 9.4 (9.0, 9.8) | CNL06810 | 10.6 | na | 12 | a −49.0 | ||
| d −51.2 | ||||||||
| a:a −1.9 | ||||||||
| A:B | 15.6 (11.0, 29.8) | CNA03020 | 12.4 | AD:AD | 14 | d:a 6.1 | ||
| 15.0 (11.2, 18.8) | CNB03520 | a:d 5.7 | ||||||
| d:d 16.1 | ||||||||
| a:a −126.0 | ||||||||
| L:L | 0.0 (0.0, 7.2) | CNL03990 | 8.7 | A:A | 10 | d:a 151.2 | ||
| 9.4 (9.0, 9.8) | CNL06810 | a:d −125.0 | ||||||
| d:d 150.0 | ||||||||
| Cell Size | A | 35.7 (35.0, 37.6) | CNA06130 | 7.3 | AD | 8 | 51 | a −0.4 |
| d −0.7 | ||||||||
| A | 54.2 (52.4, 58.2) | CNA073100 | 10.3 | na | 8 | a 0.4 | ||
| d 0.7 | ||||||||
| A | 64.0 (61.0, 64.3) | CNA07990 | 12.8 | na | 14 | a 0.0 | ||
| d 0.1 | ||||||||
| D | 41.6 (15.6, 41.9) | RUM1 | 4.5 | AD | 5 | a 0.1 | ||
| d 0.4 | ||||||||
| F | 1.2 (0.0, 8.0) | CNF00290 | 11.9 | na | 13 | a 0.1 | ||
| d 0.2 | ||||||||
| I | 2.6 (0.0, 12.8) | CNI01350 | 7.9 | na | 8 | a −0.2 | ||
| d 0.3 | ||||||||
| a:a −0.2 | ||||||||
| A:I | 54.2 (52.4, 58.2) | CNA07310 | 5.5 | AD:AD | 5.7 | d:a −0.6 | ||
| 2.6 (0.0, 12.8) | CNI01350 | a:d −0.2 | ||||||
| d:d 0.3 | ||||||||
| a:a −0.2 | ||||||||
| A:F | 64.0 (61.0, 64.3) | CNA07990 | 10.8 | D:AD | 11.9 | d:a 0.4 | ||
| 1.2 (0.0, 8.0) | CNF00290 | a:d 0.6 | ||||||
| d:d −0.3 | ||||||||
| Cell wall size | A | 14.6 (3.8, 37.0) | CNA02700 | 4.3 | AD | 8 | 8 | a 0.01 |
| d 0.02 | ||||||||
| Capsule | A | 0.0 (0.0, 33.2) | CNA00050 | 4.1 | AD | 5 | 43 | a −0.05 |
| d 0.04 | ||||||||
| B | 0.6 (0.0, 3.0) | CNB00360 | 6.9 | na | 9 | a −0.02 | ||
| d 0.07 | ||||||||
| D | 41.9 (38.6, 41.9) | CND06160 | 7.9 | AD | 11 | a 0.02 | ||
| d 0.10 | ||||||||
| H | 0.0 (0.0, 8.4) | CNH00030 | 6.0 | na | 7 | a −0.06 | ||
| d 0.05 | ||||||||
| L | 2.2 (0.0, 10.2) | CNL04620 | 2.7 | AD | 3 | a 0.02 | ||
| d 0.08 | ||||||||
| a:a −0.03 | ||||||||
| B:D | 0.6 (0.0, 3.0) | CNB00360 | 5.8 | AD:AD | 7.0 | d:a −0.02 | ||
| 41.9 (38.6, 41.9) | CND06160 | a:d 0.02 | ||||||
| d:d 0.3 | ||||||||
| MIC on agar | A | 4.2 (3.0, 6.0) | CNA00290 | 25.2 | AD | 36 | 46 | a −1.0 |
| d 1.0 | ||||||||
| E | 7.8 (0.0, 26.0) | CNE01630 | 3.1 | AD | 3 | a −0.2 | ||
| d 0.5 | ||||||||
| N | 15.0 (1.8, 15.0) | CNN02060 | 3.8 | A | 4 | a 0.3 | ||
| d −0.4 | ||||||||
| MIC in broth | A | 4.2 (0.0, 6.0) | CNA00290 | 9.6 | A | 14 | 43 | a -1.5 |
| d 0.3 | ||||||||
| A | 59.8 (54.0, 64.3) | CNA07470 | 7.6 | AD | 11 | a −1.2 | ||
| d 0.9 | ||||||||
| C | 9.4 (0, 16.8) | CNC06110 | 3.2 | AD | 4 | a 0.7 | ||
| d 1.1 |
Positions of QTL (quantitative trait loci) are shown with 1.5–LOD support intervals. Genotype refers to the allele(s) for which the greatest phenotypic values were observed for the given trait, with “na” indicating the marker showing QTL effects in the model for interactive effects. For the estimated effects of each QTL, “a” refers to the additive effect and “d” refers to the dominance effect. For QTL that showed significant interaction these are denoted with a “:”. Chr., chromosome; LOD SI, logarithm of odds support interval; PVE, percent of phenotypic variance explained; MIC, minimal inhibitory concentration.