Table 1 Pea carbohydrate metabolism candidate genes, primer sequences for fragment amplification and fragment characterisation
Gene, EC number, (GenBank accession, locus), Genus and species | Primer(s) | Primer sequences (5′ to 3′ direction) | PopSet alignmenta (location on accession) | Alignment length (bp) |
|---|---|---|---|---|
Hexokinase, EC 2.7.1.1 (XM_003630659), Medicago truncatula | Ps_2048 (S), Ps_2049 | F: CGGTTTTACGTTCTCGTTCC R: ATCTGCCTCCAGCCAATGT | 694,184,588 (1003–1079) | 291 |
Hexokinase, EC 2.7.1.1 (XM_003630659), M. truncatula | Ps_2050 (S), Ps_2051 | F: AAGCGGAGTTTTTCGGAGAT R: ACCGCGATAAGCAACAATG | 694,183,180 (1446–1545) | 244 |
Phosphoglucomutase (plastidial), EC 5.4.2.2 (AJ250770, rug3), Pisum sativum | Ps_1321 (S), Ps_1322 (S) | F: GTCAACGCCAGCCGTTTC R: GGGTGTTTCCGTAAATCTTGTC | 694,186,924 (566–636, 637–658) | 471 |
Phosphoglucomutase (plastidial), EC 5.4.2.2 (AJ250770, rug3), P. sativum | Ps_1325, Ps_1328 (S) | F: AGGGTCTTGCACGATCAATG R: GGCTTCTCTCTCCCTGTGAA | 694,182,794 (1651–1674, 1675–1752, 1753–1834) | 374 |
Sucrose synthase, EC 2.4.1.13 (AJ012080, rug4), P. sativum | Ps_0685 (S), Ps_0689 | F: TGACTGATGGTGCATTTGGT R: CGTTGGCCACAAGTAGTTCC | 694,182,614 (376–401, 402–594) | 378 |
Second sucrose synthase, EC 2.4.1.13, (AJ001071, Sus2), P. sativum | Ps_0076 (S), Ps_0079 | F: ATATGTTGCTCAGGGGAAAGG R: ATTAACACGGACATACTCCCAAAC | 694,184,180 (297–337) | 374 |
Sucrose phosphatase, EC 3.1.3.24 (AY651774), M. sativa | Mt_0208 (S), Mt_0211 | F: GAACCAGAAATGGGACAAGG R: TGCCACTGCAGTAATTCCTCT | 694,182,434 (289–373) | 235 |
Sucrose phosphate synthase, EC 2.4.1.14 (Z56278), Vicia faba | Ps_1581, Ps_1583 (S) | F: ACAGGAAATAGAAGAACAGTGGCGCT R: AGGACGGCATTCTCCAAACGCT | 694,186,708 (1292–1409, 1410–1442) | 569 |
Cell wall invertase, EC 3.2.1.26 (AF063246, bfruct1), P. sativum | Ps_0276 (S), Ps_0280 | F: TGATCCTCAACTTCTGTGTAGTC R: TGCTAATGTAGGATAAACTCTGG | 694,183,574 (1466–1560, 1561–1602) | 303 |
Invertase inhibitor, putative (XM_004508064), Cicer arietinum | Ps_2042 (S), Ps_2043 | F: TTAAATGAACCCCCACCAGA R: TCCAGAAGCACTTTCCCATC | 694,182,042 (162–556) | 411 |
ADP glucose pyrophosphorylase L1, EC 2.7.7.27 (X96766, rb), P. sativum | Ps_0036 (S), Ps_0039 | F: GGGAGCTGACTATTACCAAACTGA R: CTTGATACCTTCACACACTCAACC | 694,185,424 (1507–1567, 1568–1730) | 374 |
ADP glucose pyrophosphorylase S2, EC 2.7.7.27 (X96765), P. sativum) | Ps_0057 (S), Ps_0065 (S) | F: GGCTACTGGGAAGACATTGGTA R: GATTCTCGCGTTCTTGTCAAC | 694,187,965 (1149–1269, 1270–1368) | 559 |
UDP-glucose pyrophosphorylase, EC 2.7.7.9 (AF435969), Amorpha fruticosa | Ps_1557 (S), Ps_1562 | F: AGTTGGAAATTCCTGATGGAGCCGT R: AAGAAGACAACCAGCAAGGCCTCA | 694,187,311 (1529–1610) | 201 |
UDP-glucose pyrophosphorylase, EC 2.7.7.9 (XM_003616133), M. truncatula | Ps_1556 (S), Ps_1561 | F: CCGCTACCGCTACCAACCTCG R: GCAACCCATAGTTGTCCCCAAGCC | 694,186,492 (254–303, 304–397) | 507 |
α-1,4-glucan phosphorylase L, EC 2.4.1.1 (Z36880), V. faba | Ps_1495 (S), Ps_1499 | F: AGCTGTTGCACACGATGTCCCC R: GCTCTGGGATGCACAAAGTTGGGT | 694,186,062 (994–1095, 1096–1181) | 491 |
Starch synthase II, EC 2.4.1.21 (X88790, rug5), P. sativum | Ps_1315 (S), Ps_1317 (S) | F: ACAGCATTCCTGGATTGGAA R: TTGCGAAATATTGGACTGTCA | 1,206,484,033 (587–969) | 521 |
Starch synthase II, EC 2.4.1.21 (X88790, rug5), P. sativum | Ps_1320 (S), Ps_1319 (S) | F: TTATCGCGATCATGGTTTGA R: TTGGTATTTGGCAGCAACAA | 694,183,776 (1809–2299) | 491 |
Granule bound starch synthase, EC 2.4.1.21 (X88789, lam), P. sativum | Ps_0251, Ps_0255 (S) | F: GGGTAGAAACGCCTTTTCAG R: CCTCCAGTACCTCGATTTGC | 694,186,276 (1067–1191, 1192–1369) | 389 |
Granule bound starch synthase Ib, EC 2.4.1.21 (AJ345045), P. sativum | Ps_0499 (S), Ps_0503 | F: AGAAAAGTCCGCTTCTTCCA R: TTGGTCAGGGAGATTGAGAAG | 694,187,140 (534–626, 627–690, 691–756) | 546 |
Starch branching enzyme II, EC 2.4.1.18 (X80010), P. sativum | Ps_2070 (S), Ps_2071 | F: AGATTTGCTGCTCCCTACGA R: AACTTTGGCCCACATCAAAG | 694,185,214 (709–844) | 244 |
Isoamylase, isoform 1, EC 3.2.1.68 (DQ092413), P. sativum | Ps_1512 (S), Ps_1516 | F: AGGGGGAGTTTGTCAGTGCCTCA R: AGACCATGCCACTGCAGCCT | 694,187,747 (1906–1959, 1960–2040, 2041–2105) | 441 |
Isoamylase, isoform 2, EC 3.2.1.68 (DQ092414), P. sativum | Ps_0155, Ps_0152 (S) | F: GATCCTTATGTCAATAGGTCAGGTG R: CCTGAGGCTATCCAAAATCAAA | N/A b 1056–1135 | 142 |
Isoamylase, isoform 3, EC 3.2.1.68 (DQ092415), P. sativum | Ps_1479 (S), Ps_1483 | F: TGCTTCCCACACCCCCAACA R: TCGTAGGACCACTCTCAAGTAGAGCTT | 694,184,796 (2220–2509) | 511 |
Pullulanase 1, chloroplastic-like, EC 3.2.1.41 (XM_004496070), C. arietinum | Ps_1471, Ps_1472 (S) | F: TGGTGGGACACCCGTTGCTT R: TCCTGCATCTCTCAGCTACACCGA | 694,182,256 (2170–2226) | 291 |
Pullulanase 1, chloroplastic-like, EC 3.2.1.41 (XM_004496070), C. arietinum | Ps_1469 (S), Ps_1473 | F: ACACTGGACCATCGTTGGCTTATGG R: GCACTCGCATCAGATTTTCCTTGGC | 694,184,384 (2657–2717, 2718–2817, 2818–2846) | 360 |
Beta-amylase 1-like, EC 3.2.1.2 (XM_004503530), C. arietinum | Ps_1518 (S), Ps_1521 | F: CTGTGCTGCGTGGGCGTTCT R: TGGCATGTTCCAAGAGCCACCC | 694,185,636 (762–810, 811–909, 910–996) | 481 |
Beta-amylase-like, EC 3.2.1.2 (XM_003593956), M. truncatula | Ps_1523 (S), Ps_1525 | F: GCTGTTCATGCTGAACCGATCAGAG R: TCTTTGTAACACTGTCCCGACCGA | 694,183,376 (436–717) | 501 |
Beta-amylase-like, EC 3.2.1.2 (XM_003593956), M. truncatula | Ps_1475 (S), Ps_1476 | F: GCGGTCCACACGATGTGCCT R: TTCATGTCTTACACTGCTTGCATGCTC | 694,185,848 (1179–1699) | 521 |
Beta-amylase like, EC 3.2.1.2 (XM_004513491), C. arietinum | Ps_1602 (S), Ps_1606 | F: TGCTGCTGAACTCACTGCTGGA R: TGAATCCCAAGGGAACGGCACT | 694,182,984 (1347–1596) | 481 |
4-α glucanotransferase, EC 2.4.1.25 (XM_003602434), M. truncatula | Ps_1596 (S), Ps_1601 | F: TGGGTTTGGAGGTGGTCCCG R: TTGAGCAACGGAAGCCAGCG | 694,185,004 (1547–1611, 1612–1655) | 311 |
Phosphoglucan water dikinase, chloroplastic-like, EC 2.7.9.5 (XM_004497365), C. arietinum | Ps_1575 (S), Ps_1578 | F: GCTCTTCAACCCTTGCCGCTCA R: GCATGCCTATTGGGACGGTGGT | 694,183,978 (912–956, 957–1040) | 268 |
Phosphoglucan water dikinase, chloroplastic-like, EC 2.7.9.5 (XM_004497365), C. arietinum | Ps_1573 (S), Ps_1579 | F: TCCAGCGCCAATGTGGAGGA R: AGGTTGGGGCCTTGTCTGAACA | 694,187,529 (3119–3629) | 511 |