Table 2.
Cloned phenylpropanoid pathway gene fragments in common bean.
| Enzyme | Gene | PCR primers | Common bean clone | ||||
|---|---|---|---|---|---|---|---|
| Source | Position (bp) | Sequence (5′-3′) | Size (bp) | BLASTn E-value | GenBank accession | ||
| GENERAL PHENYLPROPANOID PATHWAY | |||||||
| Phenylalanine ammonia lyase | PAL1 | P. vulgaris | 1060–1628 | GGATCTGCTGAAAGTGGTTGACA | 486 | 0.0 | CV670758 |
| M11939 | TCCGGCTTTCCATGTAGATTTG | 506 | CV670759 | ||||
| PAL2 | P. vulgaris | 1612–3729 | CCCACCGCCGTACCAAACAA | 399 | 5E-24 | CV670734 | |
| P19142 | GCAACTCAAAGAACTCAGAACCAA | ||||||
| PAL3 | P. vulgaris | 630–1373 | GTGCAAACTCCAACAGGCAAA | 298 | 1E-49 | CV670735 | |
| P19143 | GCAGCAATGTAGGACAGAGGAA | ||||||
| Cinnamate 4-hydroxylase | C4H | P. vulgaris | 716–1074 | GTTCATTCAGGCCACGAGGTT | 359 | 0.0 | CV670736 |
| Y09447 | CCAACTCAGCTATTGCCCATT | ||||||
| 4-coumarate: CoA ligase | 4CL1 | G. max | 903–1447 | GCGTTGGTTAAGAGCGGAGAGA | 545 | 0.0 | CV670737 |
| AF279267 | CCTACAACGGCAGCATCAGAAA | ||||||
| 4CL2 | G. max | 870–1271 | CTCCTTGCTTGCTCTCATTCA | 402 | 5E-64 | CV670738 | |
| AF002259 | CCTTTCATAATCTGGTCGCCTCT | ||||||
| LIGNIN/LIGNAN BRANCH | |||||||
| Cinnamoyl CoA reductase | CCR | G. max | 129–575 | CTGGTGGCTTCATCGCCTCT | 338 | E-130 | CV670739 |
| BI426824 | CAGCCTTCCCATAGCAATACCAA | ||||||
| Cinnamyl alcohol dehydrogenase | CAD1 | M. sativa | 855–1160 | GACACAATATCTGCTGCTCATT | 306 | 1E-54 | CV670740 |
| L46856 | GGCCACATCAATCACAAACCGAT | ||||||
| 4-coumarate-3 hydroxylase | C3H | S. indicum | 325–871 | GACTTGATTTGGTCCGATTATGG | 386 | 2E-97 | CV670754 |
| AY065995 | CGATAACGGTGTCATCACTGAG | 468 | E-147 | CV670755 | |||
| Caffeate O-methyltransferase | COMT | M. sativa | 388–779 | GATGGTGTATCCATTTCTGCTCTT | 401 | 6E-98 | CV670741 |
| M63853 | CCACCAACATGCTCAACTCCT | ||||||
| Ferulate 5-hydroxylase | F5H | G. max | 67–534 | AGCGGGTCCAACAAGAGCTG | 468 | E-135 | CV670742 |
| BM527849 | CGAACACGTCACCCATGTCC | ||||||
| Laccase | LAC | G. max | 2937–3980 | CCACTCCCTGCTTACAACGACA | 489 | E-142 | CV670743 |
| AF527604 | CCCGAAACCCTCTGCAACAA | ||||||
| Lignin peroxidase (PER) | FBP1 | P. vulgaris | 224–982 | CGATAGTGAGCGAGCAAGAAG | 513 | 9E-63 | CW652094 |
| AF149277 | CCAAAGTAGCCAATCCAGCAGA | ||||||
| FBP4 | P. vulgaris | 133–827 | TGACGGTTCTGTTCTCATTTCC | 496 | 0.0 | CW652095 | |
| AF149279 | TGCCCATCTTCACCATAGCATTT | 495 | 0.0 | CW652096 | |||
| FLAVONOID/ANTHOCYANIN BRANCH | |||||||
| Chalcone synthase | CHS | P. vulgaris | 194–971 | GTGAGCACATGACCGACCTCA | 585 | 0.0 | CV670744 |
| X06411 | CCAGGGTGTGCAATCCAGAA | ||||||
| Chalcone isomerase | CHI | P. vulgaris | 950–1826 | CGTCACTCGCCACCAAGTGGAA | 215 | E-176 | CV670745 |
| Z15046 | GCCTTTGGCTTCAGCATCACCAT | ||||||
| Chalcone reductase | CHR | G. max | 52–489 | TGCCTTTGAGGTTGGCTACAGA | 579 | 6E-55 | CW652099 |
| BU578179 | ACAGCAGGAGGGATGGTTGC | 465 | 2E-78 | CW652100 | |||
| Rhamnosyl transferase | 3RT | P. coccineus | 53–303 | TGGGTGTTGAGGGTTCATCG | 251 | 2E-79 | CV670748 |
| CA914524 | CACTCGCGCATTTATCCCTTG | ||||||
| Flavanone 3-hydroxylase | F3H | M. sativa | 2119–2856 | GCAAGAAGATTGTGGAGGCTT | 590 | E-119 | CW652103 |
| X78994 | CCTGGATCTGTGTGGCGTTT | ||||||
| Flavonoid 3′-hydroxylase | F3′H | G. max | 242–1082 | GGCTTCGTCGATGTCGTGGT | 486 | E-128 | CV670760 |
| AB061212 | GGTGGGCCAAGTCCTCTTCTTT | 508 | E-139 | CV670761 | |||
| Anthocyanin 5-O-glucosyltransferase | UF5GT | P. coccineus | 6–340 | CCAAGGCGTAATCCAAGTCCA | 221 | E-103 | CV670749 |
| CA914529 | GGGTTTCAGGCTCTCCATGA | ||||||
| Anthocyanidin reductase | ANR | M. truncatula | 369–778 | GTGTTGAAAGCATGTGTAAGAGCA | 576 | 5E-80 | CW652104 |
| AY184243 | GCCCGACAAATATCCTCGACAT | 590 | 6E-80 | CW652105 | |||
| Anthocyanin 5-acyltransferase | AAT | P. coccineus | 166–572 | GGGTGTCTCTTCACCACTCCA | 407 | 0.0 | CV670746 |
| CA900148 | GAAATGGCGGCGAAAGTGTT | ||||||
| Glutathione S-transferase | GST1 | P. acutifolius | 202–802 | GCTTCTCAAATACAACCCAGTTCA | 487 | 2E-85 | CW652097 |
| GAAACGCAATGGTAACTAACAGCA | 502 | 0.0 | CW652098 | ||||
| GST2 | AY220095 | 509 | E-179 | CV670756 | |||
| 498 | 0.0 | CV670757 | |||||
| Vacuolar transporter | VT | P. coccineus | 3–455 | TGGAAGTGGATGGCAAGCAG | 451 | 0.0 | CV670747 |
| CA907034 | TCACATACTTGTGCTGACAGTGAA | ||||||
| ISOFLAVONOID BRANCH | |||||||
| 2-hydroxyisoflavanone synthase | IFS | G. max | 573–1325 | GGCGAGGCTGAGGAGATCAGA | 507 | E-139 | CV670762 |
| AF195818 | CTGGGAGTGGTGGGTGCATT | 506 | E-154 | CV670763 | |||
| Isoflavanone reductase | IFR | M. sativa | 906–1581 | GGAAGACACATAGTTTGGGCAAGT | 268 | E-139 | CV670750 |
| U17436 | CGGTAAAGGCGTGGCAACAA | ||||||
| 7-O-methyltransferase | IOMT | M. sativa | 234–637 | GGTAACGTGCGGCGTCTCAT | 456 | 0.0 | CV670751 |
| AF000975 | GCAGTTGTTCCAGTTCCACCA | ||||||
| REGULATORY GENES | |||||||
| KAP-2 (CHS) | KAP2 | P. vulgaris | 504–1007 | GAAGGCACAAAGGAAGAGCAA | 504 | 0.0 | CV670752 |
| AF293344 | CCAGTGAGAAGTGGATAAGGGAA | ||||||
| Myb AtMyb4 (PAL) | Myb4 | P. coccineus | 92–406 | AAGATGGGAAGAGCTCCTTGTT | 544 | 4E-64 | CW652106 |
| CA902489 | ATCTCATTATCTGTTCGTCCTGGT | ||||||
| Homeodomain protein GL2 like1/ANL2 | HD | P. coccineus | 3–326 | GTCGGTGGAGACCGTGAACA | 324 | 8E-95 | CV670753 |
| CA902455 | CGAACCACCACCCTTGCCTA | ||||||
| ZINC finger WIP (TT1) | WIP | P. coccineus | 2–496 | GGGCCTCATTCACATGCAA | 534 | 4E-70 | CW652101 |
| CA902512 | CGTGGGTGGTCGATGTTGTT | ||||||
| LIM domain protein WLIM1 (lignin) | LIM | G. max | 27–569 | GGCATTTGCAGGAACAACTCAG | 458 | 0.0 | CW652092 |
| BU764417 | GCACTCTTCTCATGGTCACCTTC | 489 | 0.0 | CW652093 | |||
| Myb AtMYB15 | Myb15 | P. coccineus | 39–452 | GAGTGATGGCGTGCGGAGTA | 519 | E-162 | CW652102 |
| CA902486 | CCCAGCGTCTCATGCAGCTT | ||||||