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Table 5 Published functional candidate genes potentially involved in grapevine seed and/or berry development colocalized with QTLs detected

From: New stable QTLs for berry weight do not colocalize with QTLs for seed traits in cultivated grapevine (Vitis vinifera L.)

Grapevine 12X gene ID Gene name LG position in 12X putative homologous gene and/or function In the CI of a QTL of the present study1 Reference
GSVIVT01011687001 - 1 5123090 5124512 ZmCNR2 involved in tissue growth activity in maize RESN, MSFW [60]
GSVIVT01018839001 VvAP3.2 = TM6 4 19395438 19397804 MIKC gene expressed in flowers and berries MSN, TSFW [61]
GSVIVT01025701001 - 8 12843442 12845830 ethylene signalling protein preferentially expressed in flb mutant vs WT MBW - RESFW [62]
GSVIVT01025700001    12845836 12854444    
- - 8 13327417 cell number regulator 8-like MBW, RESN, RESFW -
13332631
GSVIVT01032681001 EXP2 13 1578645 1580497 expansin EXP8 (A. thaliana) with expression linked to berry development MBW, RESFW (in Syrah) [63]
GSVIVT01016525001 EXP3 13 3120277 3122170 expansin EXP4 (A. thaliana) with expression linked to berry development MBW, RESFW (in Syrah) [63]
GSVIVT01016276001 AQ2 = PIP2;1 13 5602025 5605019 Plasma membrane intrinsic protein 2B (PIP2B); aquaporin PIP2.2 (A. thaliana) with expression linked to berry development RESFW [63]
GSVIVT01008122001 - 17 5600143 5602650 Cytochrome P450 78A-like protein in Solanum lycopersicum (tomato), harboring the causal SNP of a berry weight QTL MBW-RESN-RESFW [58]
GSVIVT01008046001 - 17 6316168 6320317 WRKY transcription factor 72-like, regulation of skin and flesh ripening MBW, RESN, RESFW [64]
GSVIVT01008034001 - 17 6455525 6456835 transcription factor bHLH135-like, regulation of pre-véraison processes in the pericarp MBW, RESN, RESFW [64]
GSVIVT01007987001 EXPA 17 6888373 6890086 Alpha-expansin with expression linked to berry development MBW2, RESN2, RESFW2 [65]
GSVIVT01009791001 VvBG1 18 11286578 11293205 beta-galactosidase (cell-wall modifying enzyme expressed during berry development) MBW, RESN, RESFW [66]
GSVIVG01009815001 VvAP3 18 11506514 11512366 Apetala 3 (Arabidopsis), MADS box flower development MBW, RESN, RESFW [67]
expressed highest in young fruit   [68]
expressed almost exclusively in inflorescences   [61]
GSVIVT01009865001 - 18 11920498 11929437 auxin response factor 5-like, transcript variant 1, includes an EST of hypothetical transcription factor preferentially expressed in WT vs flb mutant RESFW [62]
GSVIVG01025945001 VvAGL11 = VvAG3 = MADS5 18 26888677 26896544 Agamous like 11 (Arabidopsis), MADS box ovule identity (MIKC gene expressed in flowers and berries) MBW, RESN, MSN, TSFW, MSFW,%SDM [30, 67]
  1. Candidate genes colocalized with QTLs detected in the present study. Gene numbers were obtained from the automatic annotation provided with the Genoscope 12X whole genome sequence release of PN40024 (http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/[1]).
  2. 1MBW: mean berry weight; MSN: mean seed number; TSFW: total seed fresh weight; MSFW: mean seed fresh weight; %SDM: seed dry matter percentage; RESN: residual berry weight unexplained by seed number; RESFW: residual berry weight unexplained by total seed fresh weight.
  3. 2In QTL confidence interval but not within 3 cM of LOD peak position.