Table 2. Overview of QTL Identified by GWAS for Enzyme Activity, Metabolites, and Colocalizing QTL.
| Trait | QTL ID | QTL Size | Gene (AGI) | Gene ID | Function | LOD1 | LOD2 | Var1 | Var2 |
|---|---|---|---|---|---|---|---|---|---|
| Enzyme cis-QTL | |||||||||
| AGP | 73 | 1 | AT5G19220 | APL1 | ADP-Glc PPase large subunit 1 | 1.8 | 4.3 | 1.8 | 4.9 |
| aINV | 3 | 24 | AT1G12240 | VAC-INV | β-Fructofuranosidase | 7.7 | 6.8 | 10.2 | 8.4 |
| Fumarase | 30 | 5 | AT2G47510 | FUM1 | Fumarase 1 (mitochondrial) | 3.5 | 3.0 | 4.0 | 3.2 |
| UGP | 32 | 19 | AT3G03250 | UGP1 | UDP-Glc PPase 1 | 8.6 | 12.5 | 11.2 | 16.7 |
| Enzyme trans-QTL | |||||||||
| aINV | 19 | 1 | AT1G62710 | BETA-VPE | Vacuolar-processing enzyme | 7.2 | 4.7 | 9.5 | 5.4 |
| Fumarase | 79 | 1 | AT5G46110 | TPT | Triose-P/phosphate translocator | – | 5.7 | – | 7.0 |
| nINV | 6 | 1 | AT1G27720 | TAF4B | TBP-associated factor 4B | 4.9 | – | 6.0 | – |
| nINV | 44 | 1 | AT3G49430 | SR34A | Pre-mRNA splicing factor SF2 | 6.5 | 3.1 | 8.5 | 2.8 |
| nINV | 78 | 1 | AT5G44560 | VPS2.2 | Vacuolar protein sorting 2-2 | 3.8 | 6.2 | 4.5 | 8.0 |
| NRVs | 67 | 1 | AT5G01550 AT5G01560 | LECRKA4.2 LECRKA4.3 | Lectin receptor kinase A4.2/4.3 | 5.3 | 3.3 | 6.4 | 3.5 |
| tPGI | 46 | 28 | AT3G58560 | CCR4A | Carbon catabolite repressor 4 | 4.1 | 4.2 | 5.2 | 4.4 |
| Metabolite level QTL | |||||||||
| Fum | 21 | 1 | AT1G68600 | – | Malate transporter | 3.9 | 4.9 | 4.1 | 5.5 |
| Mal | 42 | 1 | AT3G47520 | pMDH | MDH, plastidial | 4.3 | 4.5 | 4.9 | 4.9 |
| AA | 31 | 1 | AT2G47570 | RPL18e | Ribosomal protein L18e | 3.8 | 2.4 | 4.1 | 2.4 |
| Fru | 63 | 4 | AT4G23060 | IQD22 | Protein IQ-domain 22 | 4.6 | 5.7 | 5.7 | 6.3 |
| G6P | 27 | 2.5 | AT2G33150 | KAT2 | 3-Ketoacyl-CoA thiolase 2 | 5.8 | 4.0 | 7.3 | 4.4 |
| Colocalized QTL | |||||||||
| Fum, Mal | 83 | 12 | AT5G50950 | FUM2 | Fumarase 2 (cytosolic) | 4.1-2.4 | 3.2-3.6 | 4.6-2.4 | 3.4-3.7 |
| Glc, Suc, Starch | 72 | 1 | AT5G12080 | MSL10 | Osmolyte channel 10 | 2.9-NA-4.5 | NA-2.9-2.6 | 3.2-NA-5.2 | NA-2.4-2.6 |
| Mal, MDH, GDH | 33 | 1 | AT3G07220 | FHA2 | SMAD/FHA domain protein | – | 4.4-3.9-3.1 | – | 4.7-4.3-3.2 |
| FW, Prot, AGP, UGP, tPGI | 48 | 1 | AT4G02500 | XXT2 | Xyloglucan 6-xylosyltransferase | 3.3 to 5.2 | – | 3.6 to 6.5 | – |
| FW, Prot, AA, Fum, G6P, | 56 | 68.2 | AT4G14400 | ACD6 | Ankyrin repeat-containing protein | 3.3 to 7.8 | 3.1 to 6.6 | 3.7 to 10.5 | 2.8 to 8.1 |
| aINV, nINV | |||||||||
| Fumarase, cPGI, tPGI, GDH |
Trait, QTL ID, QTL size in kilobases, candidate gene AGI code, gene ID, and function are shown. LOD = log10(P value) for Exp1 (LOD1) and Exp2 (LOD2) are included. Percentage of variation explained by the highest-LOD SNP is mentioned for each experiment separately (Var1 and Var2). A full description of gene function is available in Supplemental Data Set 5.