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Table 4 Potential candidate genes a located within the SCL1, SCT4 and SCT5 intervals

From: Identification of QTLs affecting scopolin and scopoletin biosynthesis in Arabidopsis thaliana

No. Locus: Description ( TAIR ) Gene expression level ( Arabidopsis eFP Browser )
Relative level (Fold-change) Absolute level
Candidate genes selected from the QTL interval (SCT4) on chromosome 3: 9942057 to 10995480 nt.
1. AT3G27230: S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 1.18 210.15
2. AT3G27325: Hydrolases, acting on ester bond 1.20 40.38
3. AT3G27340: Molecular_function unknown; involved in oxidation reduction 1.62 83.80*
4. AT3G27890: Encodes NAD(P)H:quinone reductase 1.59 367.30
5. AT3G28200: Peroxidase superfamily protein 2.42 242.03
6. AT3G28480: Oxoglutarate/iron-dependent oxygenase 0.82 130.66
7. AT3G28740: Encodes a member of the cytochrome p450 family (CYP81D11) 3.35 35.84
Candidate genes selected from the QTL interval (SCT5) on chromosome 5: 4235132 to 5725918 nt.
8. AT5G13780: Acyl-CoA N-acyltransferases (NAT) superfamily protein 1.96 395.68
9. AT5G14130: Peroxidase superfamily protein 4.02 16.68
10. AT5G14240: Thioredoxin superfamily protein 2.49 397.36*
11. AT5G14340: Member of the R2R3 factor gene famil (MYB40) 5.16 28.41*
12. AT5G14390: Alpha/beta-Hydrolases superfamily protein 1.36 69.43
13. AT5G14430: S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 1.26 261.78
14. AT5G14750: Encodes a MyB-related protein containing R2 and R3 repeats (MYB66) 64.45 99.90*
15. AT5G15130: Encodes a member of WRKY Transcription Factor (WRKY72) 18.65 85.83*
16. AT5G15180: Peroxidase superfamily protein 36.11 287.14#
Candidate genes selected from the QTL interval (SCL1) on chromosome 5: 19414594 to 22027829 nt.
17. AT5G47950: HXXXD-type acyl-transferase family protein 11.16 68*
18. AT5G47980: HXXXD-type acyl-transferase family protein 28.79 66*
19. AT5G47990: Encodes a member of the CYP705A family of cytochrome P450 enzymes 40.50 168*
20. AT5G48000: Encodes a member of the CYP708A family of cytochrome P450 enzymes 221.82 189*
21. AT5G48020: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 1.22 177
22. AT5G48560: Basic helix-loop-helix (bHLH) DNA-binding superfamily protein 11.99 124
23. AT5G48930: Encode shikimate O-hydroxycinnamoyltransferase (HCT)b 1.70 757
24. AT5G49520: Encodes WRKY48, a member of the WRKY Transcription Factor 3.86 175*
25. AT5G49560: Putative methyltransferase family protein 2.95 71
26. AT5G49810: Methionine S-methyltransferase (MMT) 1.27 349
27. AT5G49950: Alpha/beta-Hydrolases superfamily protein 1.16 119
28. AT5G50890: Alpha/beta-Hydrolases superfamily protein 1.27 36
29. AT5G51130: S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 1.41 46.65
30. AT5G51880: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 0.99 291.46
31. AT5G52260: Encodes a member of the R2R3 factor gene family (MYB19) 4.83 30.21*
32. AT5G52400: Encodes a member of CYP715A 1.03 12.91
33. AT5G53560: Encodes a cytochrome b5 isoform that can be reduced by AtCBR 1.54 1845.23
34. AT5G53990: UDP-Glycosyltransferase superfamily protein 19.54 10.75#
35. AT5G54080: Homogentisate 1,2-dioxygenase (HGO) 1.53 254.15
36. AT5G54160: OMT1:A caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1)b 1.01 758.6
37. AT5G54230: Encodes a putative transcription factor (MYB49) 7.01 34.73*
  1. aThe list of potential candidate genes was compiled by searching TAIR (http://www.arabidopsis.org/) and Arabisopsis eFP Browser (http://bar.utoronto.ca/).
  2. bLoci known to be involved in coumarins biosynthesis.
  3. *Genes with the highest expression in roots of vegetative rosette.
  4. #Genes with relatively high expression in roots of vegetative rosette.
  5. The selected intervals are associated with scopolin (SCL1) and scopoletin (SCT4, SCT5) accumulation and are characterized by the highest percentage of phenotypic variance explained by each QTL and the highest LOD score values. Most of selected genes (except two highlighted with letter b) are novel loci.