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Table 3 Colocation between QTLs and candidate genes related to kernel desiccation and ABA biosynthesis

From: QTLs and candidate genes for desiccation and abscisic acid content in maize kernels

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  
  1. 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.