Table 2.
CAPs markers conversion.
| SNP-ID | Primer forward | Primer reverse | Reads ratio | Enzyme | Product size (bp) | Restriction site (bp) | "RomanescoC3" restriction produts | "Altilis 41" restriction products | Segregation pattern | Linkage groups |
|---|---|---|---|---|---|---|---|---|---|---|
| 211-167 | TCAACCCAATCTCGTCAGTG | CTTCATAGTGGCAGCCTGGT | 10/30 | EcoRV | 372 | 162 | 372 | 372,210,162 | Test cross | LG Alt_1a |
| 4977-209 | AAATCCCACATATGGAAATAGC | TCATGACACAAGGTGGAGACA | 28/45 | XmnI | 360 | 176 | 360 | 360,176,184 | Test cross | LG Alt_2 |
| 5548-175 | AATGCACAAACCAAGTGCAA | TGAGCTCATTCGGAGGAAAT | 5/17 | XmnI | 248 | 110 | 138,110 | 248,138,110 | Test cross | New LG Alt_22 |
| 5983-127 | TTGGTGGGTTTTAGACACCTTT | GTTAAACCCCCTGGATTGCT | 3/5 | TaqI | 179 | 118 | 179 | 179,61,118 | Test cross | LG Alt_1b |
| 13671-168 | TCTGGAGCATAAGAGGTAGGG | TTCAGTCGACTTCAAGGGAAC | 13/20 | FokI | 243 | 88 | 243 | 243,155,88 | Test cross | LG Alt_1a |
| 14488-152 | AAAGCTTTTTCCCCTTTCC | AAGTGCGTATTTGATTGATTGA | 22/51 | MseI | 388 | 150 | 388 | 388,238,150 | Test cross | LG Alt_6 |
| 14600-111 | AAAAACACGCTCCTTCCATA | TGTCATCCCCATGAAAAAGC | 7/12 | BccI | 290 | 97 | 290 | 290,193,97 | Test cross | New doublet |
| 20149-154 | CCAGATGCAAATTGATACGTTG | GGATCTGCATTGAAACCTTGA | 10/21 | EcoRV | 262 | 153 | 153,109 | 264,153,109 | Test cross | LG Alt_1b |
| 22767-99 | CGGCACAACTAAGAGACAATCT | TTGGAGTATGTCTCGGGCTA | 8/15 | BccI | 315 | 88 | 315 | 315,227,88 | Test cross | LG Alt_18 |
| 25124-86 | ACAAGGCCGGACCCTAAAC | TGGAACAGGAAGGACAGGTT | 7/15 | DraI | 288 | 71 | 288 | 288,217,71 | Test cross | LG Alt_9 |
| 25294-169 | GAGGAAACTTTTCCCCATCG | CCGTTGTTGTATGCCTCAAA | 4/11 | XbaI | 327 | 159 | 212,159 | 327,212,159 | Test cross | LG Alt_4 |
| 25584-143 | ATTCGCCATGGAACAAGG | GCAGTCTAATGCTTCAACTGGT | 12/29 | TaqI | 272 | 89 | 183,89 | 272,183,79 | Unclear | - |
| 26480-171 | CGACAAACTCCCTCCATGTT | TGTGGTATTGATGGGGAACC | 3/6 | EcoRV | 320 | 153 | 320 | 320,172,153 | Test cross | LG Alt_2 |
| 26420-81 | ACATCAACGCCAGCAAAGAT | TTCTTGTTTGAATCTCAAGTGC | 5/18 | XmnI | 281 | 76 | 205,76 | 281,205,76 | Missing cut | - |
| 36002-194 | GCACAGGAAAATGTTGGTGTTA | GTCTTTGCAATTCCAATCAGA | 5/16 | DraI | 369 | 152 | 217,152 | 369,217,152 | Test cross | LG Alt_14 |
| 36199-225 | TGACCAGGTTTCAGGTATGTG | AACGTACAAATTCAAAGCACGA | 7/11 | BamHI | 398 | 221 | 221,177 | 398,221,177 | Test cross | LG Alt_8 |
| 38377-214 | AGAACCCGAAAACGTCTCCA | AGGACCTAATGCAGGTTCTGA | 16/22 | NdeI | 451 | 203 | 451 | 451,248,203 | Test cross | LG Alt_4 |
| 38382-111 | CAGGGAGAATCCCTCTCTCA | CATATATTGGATGATCCCTTGG | 4/9 | DraI | 305 | 99 | 206,99 | 305,206,99 | Unclear | - |
| 40917-80 | TGCTTCCCAATAGCCTCTAA | TGTGGTGATTTTGGACGTGT | 7/13 | FokI | 306 | 70 | 306 | 306,236,7 | Test cross | LG Alt_1a |
| 43124-62 | TGATTATGCATCACCCCAAA | CACTTTTAATCCCAAAACAACC | 9/19 | TaqI | 309 | 52 | 257,52 | 309,257,52 | Test cross | LG Alt_4 |
| 43867-147 | TGCATTTCTTCCTTGTGGTTC | ATGCTCCGTGAGGTTCGTAG | 10/19 | EcoRV | 314 | 138 | 176,138 | 316,176,138 | Unclear | - |
| 45558-111 | GGGAGAAGACCACGTAATTTGA | GTTTATTTCCGTCCCCAGGT | 10/19 | FokI | 294 | 122 | 172,122 | 294,172,122 | Test cross | LG Alt_5 |
| 45893-190 | TCATTGGTCTTGCAGTTGGA | ACTTGGGCTGTAGCTTGACG | 8/13 | TaqI | 344 | 176 | 176,168 | 344,176,168 | Test cross | LG Alt_18 |
| 45900-239 | GGACAGTTTTGAGAAATGGTCT | TCACACGGTTTTGCAATCTC | 2/6 | EcoRV | 306 | 203 | 306 | 306,203,103 | Missing cut | - |
CAPs markers conversion of 24 RAD loci randomly selected among CcRAD2. SNP-ID identifies the RAD contig name and the original SNP position, respectively separated by "-". Reads ratio refers to the number of occurrence of a nucleotide differing from the consensus sequence. Bands present only in the "Altilis 41" parental line are underlined. Linkage groups are reported according to the reference map of cultivated cardoon [12].