Table 3.
Colocation between QTLs and candidate genes related to kernel desiccation and ABA biosynthesis
| QTL name | Class | Bin | Position | From-to | Candidate gene |
|---|---|---|---|---|---|
| DW_80_2 *** | Growth | 1.04 | 250-273 | Rab17-EST (241) | |
| FW_80_1 * | Desiccation | 255 | 245-277 | ||
| Water_60_1 * | Desiccation | 333 | 305-344 | NCED2 (310) | |
| %DW_60_2 | Desiccation | 1.06 | 338 | 323-386 |
Aquaporin (314) AIP3 (323) |
| DW_80_3 | Desiccation | 460 | 455-464 | ||
| FW_80_2 *** | Desiccation | 1.08-1.09 | 460 | 457-463 | NCED1 = Vp14 (465) |
| Water_80_1 *** | Desiccation | 460 | 455-463 | ||
| ABA_embryo_30_1 | ABA content | 222 | 215-232 | ZEP1 (227) | |
| ABA_embryo_40_2 *** | ABA content | 2.04 | 226 | 219-234 | |
| ABA_endosperm_40_1 *** | ABA content | 230 | 224-237 | TIP2;1 (236) | |
| Slope_1 ** | Desiccation rate | 237 | 235-241 | ||
| Slope_3 | Desiccation rate | 3.05 | 220 | 212-244 | Vp1 (209) |
| Slope_4 | Desiccation rate | 82 | 66-97 | PM37 (82) | |
| FW_30_1 * | Desiccation | 4.03 | 92 | 79-109 | |
| FW_80_4 | Desiccation | 130 | 124-142 | WSI724 (132) | |
| Water_80_3 *** | Desiccation | 4.04-4.05 | 132 | 124-132 | |
| %DW_30_2 | Desiccation | 4.06 | 173 | 161-189 | PIP1;2 PIP1;4 (161) |
| ABA_endosperm_60_2 | ABA content | 4.10 | 340 | 329-346 | ABI2 (334) |
| %DW_80_2 * | Desiccation | 44 | 33-58 | ZEP-EST(41) | |
| DW_30_2 | Growth | 5.01 | 48 | 40-61 | |
| ABA_embryo_80_1 | ABA content | 96 | 77-115 | CCD-EST (81) | |
| %DW_60_4 * | Desiccation | 5.02 | 102 | 83-122 | Rab28 (132) |
| %DW_80_3 | Desiccation | 312 | 304-322 | ||
| ABA_embryo_40_3 * | ABA content | 5.07 | 302-322 | NCED5 (311) | |
| DW_60_4 | Growth | 317 | 304-327 | TIP2;2 (320) | |
| %DW_60_5 | Desiccation | 6.05 | 148 | 136-175 | Rab17-EST (138) |
| Water_60_4 ** | Desiccation | 136-201 | Emb5 (138) | ||
| Water_60_5 | Desiccation | 167 | 163-173 | PIP1;5 (164) | |
| ABA_endosperm_30_2 ** | ABA content | 7.02 | 183 | 179-189 |
PIP2;1 (164) PIP2;4 (164) PIP2;6 (164) |
| ABA_endosperm_80_1 | ABA content | 7.03 | 244 | 236-288 | PSY3 (241) |
| ABA_embryo_30_3 | ABA content | 7.05 | 383 | 365-402 | Rehydrin (380) |
| Rate_30_40_2 *** | Desiccation rate | 370-396 | |||
| %DW_80_5 ** | Desiccation | 9.04 | 125 | 108-140 | Rab17-EST (150) |
| ABA_embryo_60_1 | ABA content | 135 | 120-149 | ||
| ABA_endosperm_80_2 | ABA content | 9.07 | 279 | 262-294 | CCD-EST (271) |
| %DW_80_6 **** | Desiccation | 291 | 269-314 | ||
To compare with gene positions, QTLs mapped on the LHRF_F3:4 segregating population (Additional file 1) were projected on the REFMAP050110 map [32] using Biomercator [34]. Distances on REFMAP050110 are expressed in pcM and are shown in parentheses for gene candidates. Genes in bold were mapped by PCR in this study (Tables 4 and Additional file 1). Genes involved in kernel drying and located in the vicinity of the QTL confidence interval, are indicated in grey. ABI2: ABA-insensitive protein phosphatase 2C 2; AIP3: ABI3-interacting protein 3; Emb5: Embryogenic-ABA-inducible LEA 5; PM37: seed maturation protein; PSY3: phytoene synthase 3; Vp1: Viviparous1; WSI724: dehydrin. The asterisks behind each QTL represent the genomewide risk P (for definition see legend of Table 2) with * P < 0.25, ** P < 0.10, *** P < 0.05 and **** P < 0.01.