Table 2.
The sequence and annotations of the 48 InDel markers that were developed and used in this study.
| InDels Primer | Sequence from 5′ to 3′ | Contig | Annotation | bp difference | Location |
|---|---|---|---|---|---|
| Indel-001- F | AATTCGAGGGTGCTGAAATG | [0016] | Metallothionein, type 2 | 6 bp | 3′ non-coding |
| Indel-001-R | TCAAGGATGCAGCAAGACAC | ||||
| Indel-002_F | GCTCAACCGGTTCCAGAATA | [0023] | Allergen II | 5 bp | 3′ non-coding |
| Indel-002_R | AGGCAATGCCATAAAAGCAC | ||||
| Indel-003_F | GGCCCATGACAAAAGGACTA | [0031] | Peroxidase | 6 bp | 3′ non-coding |
| Indel-003_R | GAACTGTGACTGCCACGCAC | ||||
| Indel-004_F | GCCTGTAACTGCCTCAAAGC | [0038] | LTP | 18 bp | 3′ non-coding |
| Indel-004_R | CATACAAAGACTACAAGAGGARAGG | ||||
| Indel-005_F | CAAGCCAGGCTATTGACTCC | [0041] | Isoprene synthase | 3 bp | Coding |
| Indel-005_R | TCGTGAAATGACCATCATTG | ||||
| Indel-006_F | AGCTTAACGGCATCCTCTCA | [0055] | Glyceraldehyde-3-phosphate dehydrogenase | 10 bp | 3′ non-coding |
| Indel-006_R | GCTTAACAAGTGTAGTGGTAATAGTAG | ||||
| Indel-007_F | ACCGTGCTGTGACAAATTCA | [0047] | Hyoscyamine-6-dioxygenase | 22 bp | 3′ non-coding |
| Indel-007_R | GCACCTCTACATGAAGGTGAAC | ||||
| Indel-008_F | ACGTCTGACCCATGAAATCC | [0061] | Catalase | 30 bp | 3′ non-coding |
| Indel-008_R | CGTACACGCGGACAGATTTAG | ||||
| Indel-009_F | GCCTTATCAACYCTTTCACCCTC | [0057] | Gibberellin 2-oxidase | 15 bp | 5′ coding |
| Indel-009_R | AGCGGCAAGGAGAAGAATTT | ||||
| Indel-010_F | AGAGCATTAAGGAGAAAGCTGC | [0100] | LEA 4 | 3 bp | Coding |
| Indel-010_R | ATGTTGTCCGGTTGTGGAAT | ||||
| Indel-011_F | CTGCAAATTCGACAAGAGCA | [0059] | Cysteine proteinase | 5 bp | 3′ non-coding |
| Indel-011_R | GCAGAACATTTCACAGCATACATG | ||||
| Indel-012_F | CACATAGTGGGGCCTGATCT | [0113] | 1-Cys peroxiredoxin | 3 bp | 3′ non-coding |
| Indel-012_R | AACCATATTTAGATTTGTGAGATAGC | ||||
| Indel-013_F | CCACCCCCAGAGTACATCAC | [0110] | Vacuolar processing enzyme | 69 bp | Coding |
| Indel-013_R | GATGGATGCAGGATCGAAGC | ||||
| Indel-014_F | GGCACAGAGCAAAGTGAACA | [0115] | F-box protein | 3 bp | Coding |
| Indel-014_R | TTCTCAGAACCCCACAAAGG | ||||
| Indel-015_F | AGAGAAGCTGTGGGATGACG | [0276] | Auxin repressed protein | 2 bp | 3′ non-coding |
| Indel-015_R | CCACAGACCAAACAAGCAGA | ||||
| Indel-016_F | TCCTCATCAGGAACTGGGATA | [0160] | Alkaline alpha galactosidase | 19 bp | 3′ non-coding |
| Indel-016_R | TGCAGCAATAGGACTTCTGG | ||||
| Indel-017_F | GTGGAGGAGTGTACGGAGGA | [0137] | Drought induced protein | 7 bp | 3′ non-coding |
| Indel-017_R | CACACAAGAATGAAAGTGTAAAACC | ||||
| Indel-018_F | AGCTGGAAAGCAAGAGCAAG | [0177] | Arachin Ahy-3 | 12 bp | Coding |
| Indel-018_R | GCTGTTTGCGTTCATGTTGT | ||||
| Indel-019_F | CACCGACAACCTAGGCGTAT | [0285] | Lipid binding protein | 26 bp | 3′ non-coding |
| Indel-019_R | GAGCAATAGTGACCTTGCATTG | ||||
| Indel-020_F | CATTTTCAAACATTACACTCACTCATC | [0294] | Plant lipid transfer protein | 5 bp | 3′ non-coding |
| Indel-020_R | CAACACATGCAATGCAACAA | ||||
| Indel-021_F | CCGATTCCTTCAGATAGCAC | [0296] | 40S ribosomal protein | 2 bp | 3′ non-coding |
| Indel-021_R | GAGAAAATTGAAATTCAACTTCATC | ||||
| Indel-022_F | GCGGTGAAATCAACTCATCA | [0315] | Cell wall N rich protein | 6 bp | Coding |
| Indel-022_R | CTTTGTTGAAGCCACCGTTG | ||||
| Indel-023_F | CATCCGACATGTTACAATACTGAG | [0326] | bZip Transcription factor | 26 bp | 3′ non-coding |
| Indel-023_R | CCATTGATAGAGTGATTACAATTTCTC | ||||
| Indel-024_F | GTTGTGTTGATCCTTTCATTCGG | [0421] | Glutamate binding | 12 bp | 5′ non-coding |
| Indel-024_R | AGACGGTGATGGAGGATACG | ||||
| Indel-025_F | GACTCCATAATCGGAATCCAAG | [0495] | Vesicle membrane protein | 18 bp | 5′ non-coding |
| Indel-025_R | GCTTGAGCGCTGGAAGTAAC | ||||
| Indel-026_F | TCGGCTTACTCTCCCCTGAAC | [0500] | Plastic protein | 3 bp | Coding |
| Indel-026_R | GTCAATCTCGCACCCAAATC | ||||
| Indel-027_F | GGCTATTGCAGGTGGAACAC | [0518] | Wound induced protein | 3 bp | Coding |
| Indel-027_R | GACCCCACGTGCTCAAATAC | ||||
| Indel-028_F | ACCAATGCATGTGGATCATGC | [0534] | Lipid binding protein | 3 bp | 5′ non-coding |
| Indel-028_R | GCAGTGCACAAACAAAGTGC | ||||
| Indel-029_F | TTCCTTTGCTTTCCACCATT | [1556] | Protease inhibitor | 5 bp | 3′ non-coding |
| Indel-029_R | GCATGATGAGGATTAAAAGATGATAG | ||||
| Indel-030_F | TTGAAGGCAGAGGAGGTAGC | [0522] | Remorin | 11 bp | 3′ non-coding |
| Indel-030_R | GAAAGGAACATTGAACTAAATTTTGC | ||||
| Indel-031_F | CGTCATATCCATCACCACCA | [0581] | Proline rich cell wall protein | 12 bp | Coding |
| Indel-031_R | GGAGGAGTCATGCCACAAGT | ||||
| Indel-032_F | AGGAGCAACCGGACACATAC | [0628] | Electron transporter/metal ion | 7 bp | 3′ non-coding |
| Indel-032_R | TGCACCTCATCAACCTCTCA | ||||
| Indel-033_F | CCTTTAGGCCCAAGGATTTC | [3275] | Salt tolerance protein | 3 bp | Coding |
| Indel-033_R | TGCCTCTAAGTCCCTTCTTATTG | ||||
| Indel-034_F | TGCAGCACGTAAGGATCAAG | [0898] | Unknown | 3 bp | 3′ non-coding |
| Indel-034_R | TTTGTAACGCAACCTTGCAC | ||||
| Indel-035_F | CGTGGGAGGGACAGAGATTA | [1457] | Arginine/serine splicing factor | 3 bp | 3′ non-coding |
| Indel-035_R | AGATCGTCCATCACGGCTAC | ||||
| Indel-036_F | ATTGGCTTGTGAAGCATTCC | [2962] | ATARLA, GTP binding | 3 bp | 3′ non-coding |
| Indel-036_R | CAGCTACATCAACAATGACATGA | ||||
| Indel-037_F | CACCCCAAGTTTGGAAAATG | [3189] | Unknown | 7 bp | 3′ non-coding |
| Indel-037_R | CACTTGATTGCAAGCTTGTACAAAT | ||||
| Indel-038_F | TGAAGTCAGTGACAGTGGTGAA | [3291] | Glycine dehydrogenase | 1 bp | 3′ non-coding |
| Indel-038_R | GCAGTCAAAGCACAAGACAAG | ||||
| Indel-039_F | ACTTCCAATTCCCAGCACAG | [3482] | Unknown | 6 bp | 5′ non-coding |
| Indel-039_R | CCCAATGAAAGCTTGAAGGA | ||||
| Indel-040_F | CTTAATAATTTGGATGAAGGATCATC | [3624] | Unknown | 6 bp | 5′ non-coding |
| Indel-040_R | CGGTGGTTCCAAAAAGAAGA | ||||
| Indel-041_F | AAGCTGCTGAGAGGGAAAGAC | [3694] | Unknown | 18 bp | 5′ non-coding |
| Indel-041_R | GCCCACACATGCATAGACAG | ||||
| Indel-042_F | GGGATTGAGCATGAACGATT | [3863] | Dihydroxy-acid dehydratase | 2 bp | 3′ non-coding |
| Indel-042_R | GATAACAAATGGGGGCAAGA | ||||
| Indel-043_F | GATATAGCACCAGCAGCATAGTTTC | [1258] | Unknown | 9 bp | 3′ non-coding |
| Indel-043_R | TTTTCAGTCAAATGATGGAAGC | ||||
| Indel-044_F | TTGAGGCCCTAAGAATGAGC | [2367] | Cyclin-dependent protein kinase | 12 bp | 3′ non-coding |
| Indel-044_R | TTTTTGTCCTCATGAAGAACTACG | ||||
| Indel-045_F | GAGGAGGCCAAGAAGGAGTT | [3274] | Frutose-bisphosphate aldolase | 2 bp | 3′ non-coding |
| Indel-045_R | TGGCTCCTAACTTATGGCAAA | ||||
| Indel-046_F | TGAACTCGAGCGAACATCAC | [1585] | Ran GTPase binding | 24 bp | Coding |
| Indel-046_R | TTTGTGCTTTGGCACCATTA | ||||
| Indel-047_F | GCGCCTTTCTTTCACAACTC | [1596] | YABBy-like transcription factor | 18 bp | 5′ non-coding |
| Indel-047_R | AACAAAGCTGTTCGGAAGGA | ||||
| Indel-048_F | CTCCACATTCTTATCCTCAGATCTG | [3076] | Omega-3 fatty acid desaturase | 9 bp | Coding |
| Indel-048_R | CTCATTGACCTCCATGGATCC |