Table 2.
List of orthologous markers used for validation in pepper.*
| Marker name | Linkage group | Map unit (cM) | Marker type | (d)CAPS enzyme | Forward primer | Reverse primer | |
|---|---|---|---|---|---|---|---|
| 1. | C2At1g05385 | 3 | 41.5 | dCAPS | AccI | ACGAACAGCTGATGCAGCAAAGG | GACCAGATGAAACAAACTCAGGTAG |
| 2. | C2At2g47580 | 3 | 46.5 | CAPS | Hpy188I | TAGCGGCGGCGAAGTTCCAC | ATCAAACACTACCCACGCCTGTCC |
| 3. | C2At4g03200 | 3 | 50.9 | CAPS | RsaI | TGGGGCTGAGCCTTCAGGGAA | GCCAGCATATCTGCTGCACAGCAC |
| 4. | C2At5g42740 | 3 | 53 | PCR | NA | AGCACCATTTGAGAAAAATATACCTG | ATCCAAGGAATGAAACATTCCACAC |
| 5. | TG517 | 3 | 55.1 | dCAPS | BclI | CTTCTTCTGCTCAGCAGCAACATCATGA | TTTATCGGCTCTCGTTTTGC |
| 6. | C2At4g18593 | 3 | 59.3 | CAPS | AluI | AGGTGATTGTTATAATCGTGGAGAAAG | TTCACAATGCGCACATAAAAGCTTG |
| 7. | C2At1g64770 | 3 | 61.4 | CAPS | BstBI | TCCGGAGCTGTACTTATTGCACACATC | AGCCCAAACGTATTATCCTAAAGAAGAG |
| 8. | C2At3g13180 | 3 | 61.4 | dCAPS | RsaI | TATTGTTGATCCACAGCCTGGTGAG | AGGGAATATGGTGCTTGTATTGAAGG |
| 9. | C2At5g62390 | 3 | 63.3 | CAPS | TaqI | TGCTACTAACTGTTGATGCCATTGAG | TTGGGGGTCGATAACATCAAGC |
| 10. | C2At3g63530 | 3 | 67.1 | dCAPS | CfoI | CTTGTGTTAGCATTTAGAAAAACTGCG | AACATGTGTGCACAAGGTAAAGTGGTC |
| 11. | C2At5g23880 | 3 | 71.1 | CAPS | RsaI | AGCTAACCTAATCCTTGATACAACACC | ACCATCAGAACGACCTTCGAAGTCC |
| 12. | C2At1g51160 | 3 | 75.1 | CAPS | DraI | TCTTCGGAGGATCAGAGATCAGTCC | AACGAACATCCTTGTCCAGGTAATTG |
| 13. | C2At5g17170 | 3 | 91.9 | dCAPS | RsaI | TTCAAGGGCTATCATTACAAGAGGC | CTTGCGAGAAATTCTCTAATAAGTGGT |
| 14. | C2At3g03100 | 3 | 94.1 | CAPS | AflII | TGGTGCAACACTTGTTGGTGTGG | TGGAGCCAGCCATGCCATTC |
| 15. | C2At5g41040 | 3 | 95.8 | CAPS | HinfI | AGAAGGGGCTGTCTTTGTTGAGGC | TCGCGCTTTCCAGACGAAAGCTG |
| 16. | C2At5g52820 | 3 | 109.5 | CAPS | AseI | TGGGATCTAAATACCCAGACACC | ACAGAAAGAACCCAATTTCTGTGC |
| 17. | C2At5g49970 | 3 | 114.4 | CAPS | EcoRV | AATTGGCAGGCTTGAGTGTTGC | TCCCACCATTGTTACCAGGACCAC |
| 18. | C2At5g23060 | 3 | 119.2 | CAPS | AseI | ACTTAGAGCTTCTTCAGCCACCGC | ATGCCAGCACTCTGCATTGCCTC |
| 19. | C2At1g18660 | 3 | 123.9 | CAPS | TaqI | ACCCTGTGCTTAAAGTTATTATATGAACC | ACTGTTCGGCACAATGGACATCTG |
| 20. | C2At1g80170 | 3 | 125.3 | CAPS | PvuII | TTTAACTTTCCACAAATGCAACAACC | TCTTTATTCTAACCCCGTTCTCAGTG |
| 21. | C2At3g47640 | 3 | 126.7 | CAPS | AvaII | AGCTGCTCGATTTGTAAAGGACATGC | TGGCCATACATCATTTGGAGTGGG |
| 22. | C2At1g16180 | 3 | 128 | CAPS | RsaI | TTCTTGTCTTGCGTCATGCTGTGC | ACCAGCAAATGATTTTCATCATCC |
| 23. | C2At5g42950 | 4 | 139.6 | dCAPS | SspI | CTCTTCTGGAACACATTATCGTCCCAA | ACATTTTTGGCACTTGCACCAGTGAC |
| 24. | C2At1g75350 | 4 | 140.6 | CAPS | HincII | AATGTCGCTCCTCCTTCATTCTCC | ATGTATATCCTTCTTCCTGCAGCTCC |
| 25. | C2At1g63610 | 4 | 142.8 | CAPS | BsiHKAI | TGATGACTGGATATATGTTTAGGAATGC | ACGATTCAATTCCTCCACTTCTGCTTC |
| 26. | C2At1g20575 | 4 | 145 | CAPS | TaqI | AGACACTACTTTGGCCGGGTGTATC | ATGATGTCTTCTAGTGCAGACTTCTGG |
| 27. | C2At1g42990 | 4 | 147.2 | CAPS | DpnII | ATGACCCCGTCGATAAGAAGCG | ACCTCACAGCTGCATCTCTATTCCTC |
| 28. | C2At1g76080 | 4 | 158.6 | CAPS | AluI | TAGTATGGAGGAATTGGATGAAGC | TCTTCTCTGCTGTGGAGCTGCAC |
| 29. | C2At4g25650 | 5 | 0 | dCAPS | EcoRV | AGCGCAAGCTAAAGGAAATTGG | AAGTCTGTACTGAACAATCTAGCAAGATA |
| 30. | C2At3g52155 | 5 | 7.3 | dCAPS | StyI | TTCTCATACCCCACTTGTGAGATTCCA | AAGTTGTCCAGATCTACTCAAAGGACG |
| 31. | T0635 | 5 | 11.1 | CAPS | PstI | TCAACCAACAACAAGGGTCA | CCAGGAGCATCACAGTCAAA |
| 32. | C2At2g39580 | 5 | 14.9 | CAPS | BsaHI | AGATAACTGGTTTGACGAAGTTCCTGG | TGAAGCTTCTACCCATACATATTCTGG |
| 33. | C2At1g08630 | 5 | 18.3 | CAPS | BslI | TATTCTCGGTGATTATTCCCATATCC | AGACCATACTTCTTTGCTAGCTCTCC |
| 34. | C2At1g60560 | 5 | 19.4 | CAPS | BclI | TAGGGAACATAGTGTACAGCATTTGGG | TCAGACTATATGATGATTCACATCTTGG |
| 35. | T0707 | 5 | 34.1 | CAPS | DpnII | TCGTGGATTATGGGCTTCTT | TCAAAGTTTTATTGATGATGTTCGAC |
| 36. | C2At3g17040 | 5 | 36.8 | CAPS | AseI | TGGGGTTGGATGGAGTGGAAAG | AGTAGAGGTTACGAATTTCCTCTGC |
| 37. | C2At3g51010 | 5 | 39.4 | CAPS | HindIII | TCCAAACAATCCCAATGAAGGAAG | ACGCTCTACTCGCTTAATCATTTTC |
| 38. | C2At1g33970 | 5 | 44.6 | CAPS | BstXI | TGGAAGTGCAATAAGTGATGATTGGG | TCGTTTCCAACAAATTCAGGTTCAG |
| 39. | C2At2g01770 | 5 | 49.8 | dCAPS | TaqI | ACCATGTATGAAAGGAGTTGTACCTCG | AATTTACAGCAACTTGCATATGGAGA |
| 40. | C2At1g27385 | 5 | 53.1 | CAPS | HinfI | ACCGTGCATGATGATTCAACTAATGAG | AGTACCAATAGCTGTAAAGCCTCTTTC |
| 41. | C2At2g46580 | 5 | 56.4 | dCAPS | TaqI | TGCTGGTATTTCACTGAAACTTGGG | TGTTCATCTAGAGAAGGAAGCCCTCG |
| 42. | C2At3g10920 | 5 | 70.9 | dCAPS | AflII | TGGCTTGGTGTGGACAAAGAGC | GATGAGCACTCATGAAAGTTGGACTTA |
| 43. | U221402 | 5 | 72.1 | PCR | NA | AAGCCTCCTTGACAAATGCATATAG | AGATATAGCTACAGTGGCAGCTTCATC |
| 44. | C2At3g55800 | 5 | 74.5 | CAPS | TaqI | ATGCTTGTTCTGAGGAAGTTCCTGAG | AGTTCGTGTCCACAATACTAGAACCATC |
| 45. | C2At3g06440 | 5 | 76.8 | CAPS | BstNI | TCGTTAGGATTGATGAAGTTCTATCTAGC | GATTCACAACCGGCATTGTAAAATCT |
| 46. | C2At4g12590 | 5 | 82.1 | dCAPS | HinfI | ACATGGCTATGGATATGATGAAGAAG | ACCAAGCTCTTAATATTGACAAAGAAT |
| 47. | C2At4g01900 | 6 | 0 | dCAPS | MseI | GAGTTTTAGTGCATCGGACTGCTTTA | TGGGCGCCAAAACCACGAAC |
| 48. | C2At1g72030 | 6 | 2.7 | CAPS | AvaII | AATGTTGCTGCTGTTCAAGCTGAAGC | ATCACCTGAAACTACTATATAACCTGCAT |
| 49. | C2At2g39690 | 6 | 8.8 | dCAPS | SspI | TGGTCTTGAATATCCAGAACCTAATG | CTCTGTCTGTTAAATTTGACGAAAAT |
| 50. | C2At3g25120 | 6 | 36.8 | CAPS | HinfI | CCTTCCTCGGATCGAAAACATT | AGCACTTGGATAGGCGACCATTC |
| 51. | C2At2g30100 | 6 | 41.2 | PCR | NA | CAAACTATTTCAGATTTACACTTAAATG | ACCGTTCAAGTTGGCTCTTCACAACAG |
| 52. | C2At3g46780 | 6 | 46.7 | CAPS | ApoI | TGGAGTTTCTGACCTTGGTGCTGC | TCTGCATCTTGAAATGATGATGCAAC |
| 53. | C2At2g29630 | 6 | 47.6 | CAPS | TaqI | TCTGAGACCTGGTTCAATTTATGATGC | TGGTACGTGTCCAGGCCCTTCATTC |
| 54. | C2At3g56130 | 6 | 48.5 | dCAPS | CfoI | CTATCTTGTGTATGCCTTGTGAGCAG | AGAGGATTTTCAAGACTTCTCCAGCC |
| 55. | C2At3g56040 | 6 | 49.5 | CAPS | AccI | TCGCTATTGGATATAATGCGTAATGC | AACTCAGCAACCTCTATTAGCAACTC |
| 56. | C2At1g06110 | 6 | 55.9 | CAPS | EcoRV | TTGACTTATCTTCTCCAATTGACCC | AGAGAACCCTAGTAGGTAGAGGCAG |
| 57. | C2At1g44760 | 6 | 62.2 | CAPS | EcoRI | TTCTTCATCTGCTGCTCATCTTGC | AGAGGGTTTTTTCTGACCCAAGAC |
| 58. | C2At1g03150 | 6 | 80.6 | dCAPS | AluI | TGCCAGTTTCCTGCCGGATTA | AACAATCAACATTACAAATCATATTAGC |
| 59. | C2At1g79810 | 6 | 90.4 | CAPS | BanII | ATATGAACCAGAACTTGATGCTTTTC | ACGAGCCCATATATATTGACCACCAAC |
| 60. | C2At1g73885 | 6 | 94.4 | dCAPS | TaqI | TGGTGCACCATCCACAAGGCCA | AGAAAACAAATATAAGTTTTCCCTCGT |
| 61. | C2At5g07960 | 6 | 98.4 | CAPS | RsaI | AAGATCTTCCTATAGATTACTCCG | TGAATATAATAGCAAGCCACGAGC |
| 62. | C2At1g24360 | 6 | 103 | CAPS | HaeIII | TCCGGTTGTTATTGTCACTGGAGC | TGGAAACTTCTTCTGCCTCCTTTG |
| 63. | C2At2g43360 | 6 | 110.3 | PCR | NA | TCGATCTCCTCTTTCATGGCG | TTGAGGACAATACGAACAATCTTC |
| 64. | C2At2g27450 | 11 | 91.9 | dCAPS | RsaI | TCAAGATGATGGACTTGATTCTCG | AGAGAAAATGTTACATTTGCTAGTA |
| 65. | C2At3g44600 | 11 | 99.2 | CAPS | CfoI | TCCTTTATACCGACTTGAAGCTATTG | AGATTCTATGTTTCTTGAAAGCACAGC |
| 66. | C2At3g44890 | 11 | 102.7 | CAPS | SpeI | ATTGGGCAAAGCTCAAATTGTGAC | AGCCTCAATTTTCTCGTCTTCCATC |
| 67. | C2At5g60540 | 11 | 106.2 | PCR | NA | TGCTGTTTTCATCCGTGCTCC | AGTTAATTCGGGATGAAAAGCAG |
| 68. | C2At5g11550 | 11 | 108.2 | CAPS | MspI | ATTGCCCCTCCTGTTTTGTACAC | CACCGGATTCGGAACAAGTGAATG |
| 69. | C2At2g28250 | 11 | 110.2 | CAPS | HinfI | AGACTTCATCATCGTCATGTGGTTCCG | TTTGGAGGTGCTTTGCCATACCAAG |
| 70. | C2At4g22260 | 12 | 0 | CAPS | ScrFI | TCCTCTAACGGTCTAGAGAAATGGG | AGGAACTCTTGCAATTGTTTCCAGAAC |
| 71. | C2At1g79260 | 12 | 1.7 | dCAPS | CfoI | CCATCATGTTATCAGATTTTTAGATGC | CTTCATGAATGCACCCATAAAATAAG |
| 72. | C2At3g52640 | 12 | 3.3 | CAPS | CfoI | TACCTTGGCAGTAGAAGATTTCTTCTTG | AACCCTTTCCAACTGATCCAATTTC |
| 73. | C2At5g16630 | 12 | 7.5 | CAPS | SspI | TAAATGCAATCACTGATGGAGAGCA | TGCCAATACTGCATCCCACCAAAT |
| 74. | C2At5g16710 | 12 | 12.7 | PCR | NA | TGATGAGCTGACAGCTTTCAATGAT | AGTGAATCTGGAATAGACCAATTCTTAT |
| 75. | T0408 | 12 | 17.9 | CAPS | NsiI | GCTGCTGGACTCACAGTTGA | TTCTCGGCACCCATTCTAAC |
| 76. | C2At3g60830 | 12 | 27.4 | CAPS | DpnII | ATGCTGGTTCTAAATTTCTCAAAGC | ATATGCGTCCAACTGCATAAAGCG |
| 77. | C2At3g54840 | 12 | 28.9 | dCAPS | SspI | CATGTTCTTATATCATGTAACGTTTAA | TGTGCTTTGGCAAAAGACTCAGGAC |
| 78. | C2At2g28600 | 12 | 36.4 | dCAPS | HinfI | AGCGATGATTCCATTCAGAGAAGG | TTCACGACAATTATTTTCTTTATTGA |
| 79. | C2At4g15010 | 12 | 40.8 | CAPS | DpnII | ACATCCCAATTTGGTTACTGCCCTG | AGGGGACAATGGACCAACTTCTTCATC |
| 80 | C2At5g64730 | 12 | 45.6 | PCR | NA | GATCGACAAGTATTTTATTGGGATGT | GTAGTCGTCGTTGATTGAGGCATAAT |
| 81. | C2At5g09880 | 12 | 50.4 | CAPS | MseI | AAAACATGTTTGATCCTGCAACTGAG | CCTTTGAACTTGGCATCATATTCAT |
| 82. | C2At3g24490 | 12 | 52.4 | CAPS | Hpy188I | AGGAGAAGATGAAGTTTGCAGAGACTG | ATTCTTGCAATTTCTGCCTGAGC |
| 83. | C2At4g39660 | 12 | 56.5 | CAPS | SspI | ACAGGGAGCCACTACTGGGGTTT | ACATAACCAACAAATAAGGTGCACG |
| 84. | C2At4g39870 | 12 | 56.5 | CAPS | TaqI | AGACTTAACCAATGCTTCTGTTGGC | AACTAGCCCACCAAACACAGCACC |
| 85. | C2At1g79790 | 12 | 57.3 | CAPS | ApoI | ATATTCCTACCTTGAAGGTGTTGAAG | AGAGTTTTAGCTCGTCCTCAATCATC |
| 86. | C2At1g65230 | 12 | 57.3 | dCAPS | HindIII | TTACAGGACGAGACAAGTACAAGAGACC | TTATAATTTGAAAACAGGGTAAAAAGC |
*
Source: Wu et al., 2009.