Table 4.
Markers associated with the QTL main effects and QTL by Environment (watering block) interaction for seed yield (SY) and other agronomic traits (DTF: Days to flower; PH: Plant height; SPAD: Chlorophyll content) using a doubled haploid population derived from BC1329/BC9102, in well-watered and water-deficit conditions under a rainout shelter (M: main effect; WW: well-watered block; WD: water-deficit block). The LOD scores (−log10 p-value), allelic effect, parental allele and percentage of genetic variance explained (R2) are also provided. The QTL by Environment interactions for each environment are in italics. Consistent markers that were associated with multiple traits are in bold font. The * QTL for corresponding traits were detected under field trials and a pot trial in rainout shelter conditions [15]; ≠Marker positions are approximate, as the DArTseq did not return significant hits for desired linkage group. NA: Unknown (marker sequence could not be mapped onto the reference sequence).
| Trait | Environment | Marker | Chromosome | Physical Map Position of ‘Top’ Marker on Darmor-bzh Genome Version 4.1 |
LOD | R 2 | Allelic Effect | Parental Allele |
|---|---|---|---|---|---|---|---|---|
| DTF | M | 4167999|F|0–65:C>G-65:C>G | A01 | 4,038,480 | 4.15 | 9.11 | 2.41 | BC1329 |
| DTF | M | 3127058|F|0–24:G>T-24:G>T | A08 | NA | 4.41 | 14.26 | −2.24 | BC9102 |
| *DTF | M | 3153720 | A09 | 29,356,333 | 4.31 | 17.81 | 2.19 | BC1329 |
| DTF | M | 3140774|F|0–65:T>A-65:T>A | A10 | NA | 3.15 | 17.58 | −2.44 | BC9102 |
| DTF | M | 3128614 | C02 | 9,287,096 | 3.88 | 13.04 | −2.25 | BC9102 |
| DTF | M | 3143291 | C02 | 45,636,489 | 9.95 | 26.7 | −3.31 | BC9102 |
| DTF | M | 3141556 | C06 | 27,740,738 | 12.17 | 39.12 | −4.13 | BC9102 |
| DTF | M | 3158874 | C09 | 46,623,311 | 16.66 | 48.55 | 5.06 | BC1329 |
| PH | M | 5150480|F|0–27:G>A-27:G>A | C03 | 23,396,698 | 2.82 | 3.36 | 3.46 | BC1329 |
| PH | M | ≠3097029|F|0–10:C>T-10:C>T/ 5034370|F|0–47:G>C-47:G>C |
C03 | NA 57,776,378 |
2.75 | 4.68 | 3.34 | BC1329 |
| PH | M | 27247510/≠3088657 | C09 | NA/48,143,335 | 3.3 | 6 | 3.76 | BC1329 |
| SPAD | M | 3089844|F|0–24:G>C-24:G>C | A01 | 7,826,453 | 2.61 | 11.05 | 0.77 | BC1329 |
| SPAD | M | 26680018 | A02 | 23,433,061 | 5.79 | 27.15 | −1.3 | BC9102 |
| SPAD | M | 3095732|F|0–21:C>A-21:C>A | A03 | 1,882,135 | 2.72 | 9.44 | −0.78 | BC9102 |
| SPAD | M | 3083376|F|0–17:A>G-17:A>G | A09 | 26,477,098 | 4.58 | 16.46 | 1.01 | BC1329 |
| SPAD | M | 3083310|F|0–11:A>T-11:A>T | A10 | 16,253,199 | 5.06 | 24.39 | −1.14 | BC9102 |
| SPAD | M | 27390133 | C05 | 539,869 | 4.72 | 19.51 | −0.98 | BC9102 |
| SPAD | M |
3101645|F|0–42:G>A-42:G>A/
≠3156841 |
C09 |
NA
48,490,657 |
3.48 | 14.94 | 0.87 | BC1329 |
| SY | WD | 3173313 | A02 | 19,738,340 | 2.76 | 1.13 | 3.91 | BC1329 |
| SY | WW | 3173313 | A02 | 19,738,340 | 2.76 | 1.13 | −12.86 | BC9102 |
| SY | M | 3140140 | A08 | 11,695,725 | 4.26 | 1.87 | 14.38 | BC1329 |
| *SY | M | 3153720 | A09 | 29,356,333 | 3.02 | 4.23 | −11.92 | BC9102 |
| SY | M | 3101614|F|0–46:C>T-46:C>T | C03 | 3,138,929 | 2.35 | 4.61 | 9.94 | BC1329 |
| SY | WD | 5121657/≠3079649 | C09 | NA/41,790,279 | 2 | 0.74 | −3.71 | BC9102 |
| SY | WW | 5121657/≠3079649 | C09 | NA/41,790,279 | 2 | 0.74 | 9.99 | BC1329 |