Table 4. List of the Top 10 Significant Candidate Genes for Each QTL Ranked by LOD Effect.
| Phenotype | QTL | %Var | Candidate Genes (Ordered by P Value) |
|---|---|---|---|
| LA.plast | 1@3 | (−) 3.13 | |
| RGR.dry | 1@12 | (−) 3.30 | |
| LA.dry | 1@32 | (−) 3.48 | |
| FT.wet | 1@84 | (+) 3.95 | AT1G65490, FAS1 |
| ABA.dry | 2@16 | (−) 5.16 | AT2G03140, AT2G04380**, ALDH6B2, AT2G04170*, UGT73B5, AT2G05915 |
| Roll.dry | 2@74 | (−) 6.23 | ACX5*, AT2G36460, CTF2A, GLTP1* |
| Proline.dry | 2@74 | (+) 24.8 | AT2G38800*, P5CS1, PROT1* |
| Proline_plast | 2@74 | (+) 13.6 | |
| WUE.dry | 2@74 | (+) 3.6 | |
| WC.dry | 2@87 | (−) 3.34 | MAC3B, ATTI3, AT2G43210, AT2G46220, IQD14, AT2G46100**, AT2G38800, AT2G32150, AT2G42490, AT2G32160 |
| GR.dry | 3@4 | (−) 4.56 | |
| GR_plast | 3@4 | (−) 4.38 | |
| WUE.wet | 3@18 | (+) 3.12 | CBSDUFCH1, RPL18AC*, AT3G18530, AT3G14595 |
| RMR.dry | 3@19 | (+) 19.7 | UGT88A1, AT3G14360**, AT3G18535, AT3G18530, CYP77A5P |
| LA.plast | 3@27 | (−) 4.18 | |
| RGR.dry | 3@30 | (−) 3.81 | |
| RDM.dry | 3@33 | (+) 19.2 | AT3G16750, AT3G25240, BRT1 (UGT84A2) |
| Proline.dry | 3@50 | (−) 4.91 | AT3G43230, AT3G28080, AT3G27250, ATCSLC04, AT3G30300*, AT3G26670*, PRODH, CAF1-9*, ATMYB30, |
| RGR.wet | 3@54 | (−) 6.69 | AT3G44430, emb2076, AT3G43430, AT3G43670, ATIVD (IVD), ATMLO3 (MLO3)*, AT3G45555 |
| WUE.dry | 3@58 | (−) 3.76 | |
| WUE.wet | 3@65 | (−) 5.14 | HR4, ABC2 Homolog 1 (ATATH1)*, scpl48, ALDH2B4**, AT3G47580, IVD, AT3G53730*, ATEXLA1, AT3G51470**, CSR1 |
| LA.dry | 3@90 | (+) 3.30 | |
| RMR.dry | 4@1 | (+) 15.9 | ATSTE24, SAM-2* |
| Wilt.dry | 4@2 | (−) 4.01 | |
| FT.wet | 4@3 | (−) 59.1 | AT4G00740, FRI, ECA2 |
| Proline.dry | 4@3 | (−) 3.46 | AT4G01130, SAM-2*, ATSTE24, AT4G00270, AT4G02540, MLO1 |
| WUE.wet | 4@4 | (−) 7.09 | FRI |
| WUE.plast | 4@4 | (+) 3.47 | |
| WUE.wet | 4@42 | (−) 2.59 | |
| GR.plast | 4@60 | (−) 4.82 | CRK22, CRK21, AT4G22990, AT4G24050, ISU1, AT4G21910, ATSBT3.12, TOM1* |
| FT.wet | 4@62 | (−) 5.19 | CRK22, CRK23, AT4G24340 |
| FT.wet | 5@15 | (−) 1.83 | CSA1, CHS3, AT5G18950, AT5G16890, AT5G17680, PAT1(TRP1), GDH1**, ATCBR* |
| WUE.wet | 5@37 | (−) 3.49 | |
| FT.wet | 5@72 | (+) 4.24 | ATATG18F, AT5G55180, AT5G54710, AT5G54720, PORA*, ATM2 |
| WUE.dry | 5@84 | (+) 3.53 | XYL4**, AGL62, AT5G61660, ABA1, LECRK110, AT5G62350, DAR5, AT5G55180, KCA2 |
| WUE.wet | 5@89 | (+) 6.33 | AT5G54710, AT5G55180, AT5G54720*, ARF2*, ATATG18F, AT5G63020, AT5G53700, SNRK2-3, AT5G60160**, AT5G61660 |
The QTL-specific percentage of variance explained is presented and is preceded by the direction of the QTL effect. Positive values indicate a higher mean of the TSU allele. Candidate genes for QTL with confidence intervals that spanned >25 cM are not listed. Bold font indicates those genes discussed in the text. Genes without DNA sequence or with neither DNA sequence nor protein divergence between TSU and KAS alleles are marked by one asterisk or two asterisks, respectively.