Table 2.
Loci and Corresponding PCR Primer Sequences of Chromosome-Specific Markers
| Marker name | Forward primer 5′–3′ | Reverse primer 5′–3′ | PCR size (bp) | Repeat | PCR conditions | Chromosome | Band assignment | Nomenclature Mellersh et al. 2000 |
| AHT K338 | ACAAAGCAATTTTTGCTACAAGC | TAATAGGTGTGGGACATTCGTT | 291 | (GT)12 | PCR55/4mM | CFA 1 | q11-q12 | CFA 1 |
| AHT H304Ren | CTCCTTGGTCCCCTCTTTTCTC | TATTCATTTCTCCCTGTGTCCAATC | 249 | – | TD61/2mM | CFA 1 | q37distal-q38 | CFA 1 |
| AHT H72Ren | TTTAGCATTTTCCTCTGGCTTT | ATCTGGTCTGTTTGCCTTCC | 172 | – | TD65/2mM | CFA 2 | q12.3-12.5 | CFA 2 + RH7 |
| LEI 1D6 | GCTCCATCCACATCATTGC | AGCAGCATCGACAATAGCC | 172 | (AC)15 | TD66/4.5mM | CFA 2 | q34distal-q35prox. | CFA 2 + RH7 |
| AHT H255Ren | GTCCCAAAGGCTTTCCAAAT | GATGGCTGGGTCCTGTCTTA | 168 | – | TD67/2mM | CFA 2 | q35prox. | CFA 2 + RH7 |
| AHT H291Ren | CAAATTCTGCCTGAATATACCACAA | TATCAAGCAGTCCTCCTTTGACAGA | 254 | – | TD61/2mM | CFA 3 | q21.1-q21.3prox. | CFA 3 |
| LEI 1E12 | GGAAATGCATGTAGATACATGTG | AGAATGGGAATTGGAAGTCAGG | 152 | (TG)13 | TD61/4.5mM | CFA 3 | q22.3 | CFA 3 |
| AHT H219Ren | CTATGAGTCAAGACTAGGGGCAGTG | AGAGCTGTCTCCCAGAGACGTTAAG | 296 | – | TD61/2mM | CFA 3 | q22.3distal | CFA 3 |
| AHT1.37 | AACTTTTATTTTTTCACTTA | GCTCTAATCAGAACAATCA | 389 | (GT)11 | TD45/3mM | CFA 4 | q22 | Synt. 1 |
| AHT H1.37Ren | ACTGCCCAGAGGAAGGAGAG | TGGTACATTTAGGGGCAACA | 202 | – | TD59/2mM | CFA 4 | q22 | Synt. 1 |
| AHT H142Ren | CATTGGGGTAAAAGCTGCAT | TTTGATGGGGACAGAGCTTC | 163 | – | TD65/2mM | CFA 4 | q33distal-q34.1 | Synt. 1 |
| AHT H68Ren | TGCTTTCTTTGCTTATTCCTATGAT | TGAGAGTCACTCCATTGCTTAGTTT | 248 | – | TD61/2mM | CFA 5 | q11-q12prox. | CFA 5 |
| AHT H248 | GGCCACCCCCCAACAC | TGTAGAGTGGAGCTCAAGAATTTG | 139 | (CA)19 | PCR55/3mM | CFA 5 | q12 | CFA 5 |
| AHT K315 | GCCAAAATCGCTCTCCCA | TTGGAGTGGGCACCAAAA | 260 | (TG)19 | TD46/2mM | CFA 5 | q33distal-q34.1 | CFA 5 |
| AHT H201Ren | CCTCACAGGTTCCCTATATCAGCTT | ATGGAAGGTGGATTAGACAGAGAGG | 248 | – | TD61/2mM | CFA 5 | q35-q36 | CFA 5 |
| AHT H171 | CTCACCAGGCATAGACACTCAG | CTCATTTGTTCACGCACCC | 131 | (GT)19 | TD53/1mM | CFA 6 | q11distal-q12prox. | CFA 6 |
| LEI 2A11 | CATAGCGACATCACATAAGT | GGGCTGATAATTCAGTGAGA | 184 | (AC)17 | TD72/2mM | CFA 6 | q21.3 | CFA 6 |
| AHT H228Ren | GCCTTATTTTTGTCTCTGCTCCAGT | GGGAGGTTCACAGACTTACAGGAAT | 234 | – | TD61/2mM | CFA 6 | q21.3distal-q22 | CFA 6 |
| AHT H289 | GGGACCTGGTAGGCTGAACT | ATGAGCATGATGGTGTTCCA | 153 | – | TD63/4.5mM | CFA 7 | q11 | CFA 7 |
| LEI 1B10 | TTGTCTTTAGACTCAATAGTAGC | CCCAACGATCCGTTCTTTGAC | 119 | (GT)18 | TD63/4.5mM | CFA 7 | q15-q16.2 | CFA 7 |
| AHT H71Ren | CAGGGCAGTGTCCCTAGAAG | GGGTGGTGGACAAAGTCATT | 159 | – | TD69/2mM | CFA 7 | q25distal-q26prox. | CFA 7 |
| AHT H240 | GTCCATGACTGGCTCAGGTTT | TTGAGGCCTAGAACTCTG | 163 | (GT)27 | PCR55/4mM | CFA 8 | q11 | CFA 8 |
| AHT H240Ren | CCCCACTTCCTCTGGTCAGT | GCTCCAATCACCACCATTCT | 141 | – | TD65/2mM | CFA 8 | q11 | CFA 8 |
| LEI 2D2 | CGAGACCACATTGGGCTCC | CCAGACGCTCTCCATGCCTC | 390 | (GAAA)9 | TD63/4.5mM | CFA 9 | q25prox. | CFA 9 |
| AHT H183Ren | TTATCAGGTGAGTCCAGTGTCATCA | TTTCTGATCCTTCAAGCCATAAGGT | 252 | – | TD61/2mM | CFA 9 | q26.1-q26.2prox. | CFA 9 |
| AHT H181Ren | CTAGCATGTTGTAGCCCCCTAAACT | TGAGGTTCAGAGTTTCACACATCTTC | 252 | – | TD61/2mM | CFA 10 | q11prox. | CFA 10 |
| AHT H51 | CTGGGTCTGCGCCTAGCTT | CACAGATTTAACTTTCCAGAACTGC | 407 | (AC)22 | PCT45/3mM | CFA 10 | q14distal-q21prox. | CFA 10 |
| AHT H203Ren | CTTTACCTGCTTATGCTCACTCTCG | TCTTCCTGTGGGAGTTGAGAACAT | 157 | – | TD61/2mM | CFA 10 | q23.2-q24prox. | CFA 10 |
| AHT H279 | GCACATGCTCCATTAACCCC | CACTATCTCCTGGCCTCTTCC | 184 | (GT)19 | PCR55/3mM | CFA 11 | q11distal | Synt. 4 |
| AHT H155Ren | CTGCACACCTACCCCAGAAT | CACGCACGTGCTTAAACATT | 123 | – | TD65/2mM | CFA 11 | q22.3-q23 | Synt. 4 |
| AHT H127 | ATCGACTTGTTCTTTGTCTCAGC | TTTGGATATGATGGGGAATTTA | 178 | – | TD55/2mM | CFA 12 | q22-q24 | CFA 12 |
| AHT H1.47 | GGCAGTGAATCTGTTGTGAGTT | GAGAAATGAGGATAAAACGACACC | 258 | (CA)21 | PCR55/2mM | CFA 12 | q23distal-q24 | CFA 12 |
| AHT H239 | TGTTTCATTGGTCTGCGTGT | TAGGAGGCCGATTCTCTTGA | 263 | – | TD67/2mM | CFA 13 | q21.2 | Synt. 8 |
| AHT H310 | CTTTGCCTGCAGGAGTTTTC | ACGTCAGGCATCCATGCATG | 180 | (GA)12 | PCR55/1.5mM | CFA 13 | q22.2 | Synt. 8 |
| AHT H262Ren | CTCATCCATGCACGTCCTTT | TTAGGGAACAGGAAGCCTGA | 146 | – | TD69/2mM | CFA 14 | q11 | Synt. 9 |
| AHT K207 | CAATCTTCCAACAACCTTGT | GTCCTTGAGGGGTTAATAAT | 94 | (GT)18 | TD56/1.5mM | CFA 14 | q23 | Synt. 9 |
| AHT H257 | CCCACACCTTTGCTGGAC | TGGGAGATCCAAGAGGAGG | 126 | (TG)8C(GT)10 | PCR50/3mM | CFA 15 | q13 | Synt. 6 |
| AHT H17Ren | TAGAGTAAGGGGCTCAAACATCACA | ATGGAACCAGAGAACACTTTGGAA | 237 | – | TD61/2mM | CFA 15 | q24 | Synt. 6 |
| AHT H260 | CGCTATACCCACACCAGGAC | CCACAGAGGAAGGGATGC | 245 | – | TD69/2mM | CFA 16 | q14 | Synt. 12 |
| AHT H282Ren | TCCATTAACAAGTGCGTGTCAGATA | CTCAGAGATTCGCTCGACTTAAAGA | 262 | – | TD61/2mM | CFA 17 | q11 | CFA 15 + Synt 16 |
| AHT H265 | GGACCCCTAATACCCAGTAACATT | GTGCAGGCTATAAACCAAAAACTT | 238 | (AC)15 | TD53/4mM | CFA 17 | q15 | CFA 15 + Synt 16 |
| LEI 1E3 | GAGGAGATCCTAGTAACACC | GCTGGTGTTCCTAAAAAGCC | 220 | (TG)14(GA)14 | TD63/4.5mM | CFA 18 | q23-q24prox. | CFA 18 |
| AHT K32 | TACCAAGACCCAACAGCAAG | GAGCCTGCTTCTCCTTAT | 159 | – | TD59/2mM | CFA 18 | q25.1-q25.2 | CFA 18 |
| AHT K292Ren | TTTGTACTCCTAGGACAAGGATTTG | TCCTCCTGTGACAATTTCAGG | 250 | – | TD61/2mM | CFA 18 | q25.3distal | CFA 18 |
| AHT H67 | CAGGGGCTTGTTTTCCTTGA | AGGATGGTTGGTTAAGTG | 282 | (CA)12 | PCR60/3mM | CFA 19 | q21-q22 | CFA 13/19 |
| AHT H216Ren | CGCCCGATTTTCTTTGTTAG | GGCAAAGGAGGACACAGGT | 143 | – | TD69/2mM | CFA 20 | q11prox. | CFA 20 |
| AHT K20 | GTACAGTGGTCACATAGAGG | CTCAAAGGCGTTCTTTCCAG | 169 | – | TD59/2mM | CFA 20 | q15.3prox. | CFA 20 |
| LEI 1B7 | GCAATCCCACCCCAAAGA | CTGTTGCTATGATCATGGGTG | 198 | (GAAA)4(GA) 18(GAAA)13 | TD63/4.5mM | CFA 20 | q15.3distal | CFA 20 |
| AHT H284Ren | CTCTGAGAACAGGAACAGCAAATTC | CTCAGTGAACTCACCCCAAGACATT | 243 | – | TD61/2mM | CFA 20 | q16-q17 | CFA 20 |
| AHT H298 | CCAGGCATTCGAGGGTG | TCCCAGAACTTGAGGAACCATAG | 103 | (GT)12 | PRC45/3mM | CFA 21 | q13.3distal-q21prox. | Synt. 2 |
| AHT H211 | AGCTTCAGGCACAGGGGT | CCAGGGAGGTGAAAAATGACT | 348 | (GT)19 | TD53/2mM | CFA 22 | q11.2 | Synt. 7 |
| AHT K253 | CTCAAAGGCGTTCTTTCCAG | GCACATGGAGGACAAGCAC | 146 | (TG)20 | TD56/2mM | CFA 23 | q13 | CFA 22 |
| AHT H180 | TCTGTGCTTTGATTAGCAGCAT | GGAGCCTGACAGTGAGTGGA | 250 | – | TD59/2mM | CFA 23 | q23 | CFA 22 |
| AHT H138 | ACTGGGTGTCCTATTGATGTTTT | TATACACAGCGCCCAACACAC | 204 | (GT)19 | TD53/2mM | CFA 24 | q11 | Synt. 5 |
| AHT H9bRen | AGTTCAGTCCAGGGCACCTA | CGTGCAGGATTCCCTCTTTA | 154 | – | TD69/2mM | CFA 24 | q24 | Synt. 5 |
| AHT K120 | GGGTCTCAGACACTGTGTGC | TTGCAGGCTAGGCTTTTCTC | 115 | (CA)17 | TD61/2mM | CFA 25 | q21.3-q22 | Synt. 10 |
| AHT H226 | GGGCAAGCTACCTTTCCACTCT | CTTTTTAATGAGCCCTTCATGGAAT | 210 | – | TD61/2mM | CFA 25 | q24distal | Synt. 10 |
| AHT K211 | TTAGCAGCCGAGAAATACGC | ATTCGCCCGACTTTGGCA | 92 | (CA)13 | TD63/4mM | CFA 26 | q13distal-q21 | CFA 26 |
| AHT K200 | GATTTATCAGTTTGGAGGGTG | TGTAGAAATCCTGAACATTACA | 65 | (GT)14 | TD61/2mM | CFA 26 | q23-q24prox. | CFA 26 |
| AHT K18 | CAGATGAGGAAGTGTGCGTG | CTGCCTCCTCTAGCCTTCTG | 89 | (GT)15 | TD59/2mM | CFA 27 | q11 | CFA 16 |
| AHT H197Ren | CGAGGGGCCTAAAATCTAGC | GGCAGGACCCCAAATTAGAT | 156 | – | TD69/2mM | CFA 28 | q11 | Synt. 14 |
| AHT K135 | GCAGCTCTCAGCACCCACAC | GTGAGTCCACTTGGGGCG | 223 | (GT)12 | TD60/2mM | CFA 28 | q18 | Synt. 14 |
| AHT K40 | TAACGTGCTGGTTTTAGACTGATC | CACATGGAGCCTGCTTCTC | 221 | (CA)18 | TD56/2mM | CFA 29 | q13-q15 | Synt. 3 |
| AHT H235Ren | GCCTGCTTCACAAAATGACA | GGCAAGTTTCCTGAGCTGAC | 172 | – | TD69/2mM | CFA 29 | q22-q23.1 | Synt. 3 |
| AHT H134Ren | CCCGTCCTTAACCACATGAT | AGCTGGTGACCCAGGTAGTG | 167 | – | TD69/2mM | CFA 30 | q13-q14prox. | CFA 30 |
| LEI 1F11 | TTTCAGAGTTCTGATGCTCC | GTCAGTTCAATTAGCCAGAG | 175 | (GT)19 | TD54/4.5mM | CFA 30 | q15.1distal-q15.2 | CFA 30 |
| AHT H246 | ATTTTCATTCCGAGGTTCTAACTG | ATTCACCATCTCGTAGCCTTTATC | 260 | (GT)16 | TD53/3mM | CFA 31 | q15.3 | Synt. 13 |
| AHT H327 | TCAGCTTATGTCCTTACATTTG | TCCCGGTGCATGGAG | 301 | (CA)21 | TD57/4mM | CFA 32 | q11.2distal-q13 | Synt. 15 |
| AHT H327Ren | TGCCAGATTCCTCAACTTCC | CTGCACACAAGAGGTGATAAGC | 139 | – | TD69/2mM | CFA 32 | q11.2distal-q13 | Synt. 15 |
| AHT K336 | GGTGAAGATGGGGTGATTTG | TCTTCAGATTCCACCGGTTT | 200 | – | TD69/2mM | CFA 33 | q15.1distal-q15.2 | CFA 29-35 |
| AHT H131Ren | CCCACCCCAAGTATGTCCTA | CCTCCTGCTCTTGAAGCAAC | 145 | – | TD63/2mM | CFA 34 | q12-q13 | RH1-b |
| AHT H163 | AATATAATGGAAAGGAAGATTAGGC | CAATCCAACAGTACCTTGAAAATG | 223 | (CA)22 | PCR45/1.5mM | CFA 34 | q14 | RH1-b |
| AHT H53b | TGGTGTGTGGAAAAGGGACT | AGCAAGCTGGTCAAGAACTCC | 167 | (AC)10 | PCR55/2mM | CFA 35 | q14 | RH5-b |
| AHT H53Ren | CACTGGACTGTGGGCAGAGAT | TCTGAACTGGGCATGGATC | 309 | – | TD69/2mM | CFA 35 | q14 | RH5-b |
| AHT H1261D | AGCTGCTTCTCCCTCCTTTAGTCTG | AGCTGAAAGGTTTCCGGAGG | 100 | (AC)12 | PVR58/1.5mM | CFA 35 | q14 | RH5-b |
| AHT H31Ren | CAGGTTCCCTCTCCACCTTT | TTTCAGGCAAGCCTCTCATT | 150 | – | TD65/2mM | CFA 36 | q13 | Linkage-gp 1 |
| AHT H130 | GTTTCTCTCCCTTCGGGTTC | GACGTGTGTTCACGCCAG | 130 | (GT)22 | TD59/3mM | CFA 36 | q14 | Linkage-gp 1 |
| AHT H128Ren | AGTCCCAGGCAGGAGAGAAT | TGATCCCCGATTGTGTTGTA | 148 | – | TD67/2mM | CFA 37 | q11-12prox. | Synt. 11 |
| AHT H174 | TCAACGGAGTCTTTGAGGAT | AAGGAGTACATTTTCAAGAA | 121 | (TG)16 | PCR45/3mM | CFA 37 | q16 | Synt. 11 |
| AHT H91 | CCCAGTCTTTGTTCTCCTG | AGGACTCTTTCAGGTACTCGGTC | 206 | (GT)17 | PCR45/3mM | CFA 38 | q15.2 | Synt. 17 |
| AHT H91Ren | GGACCGAGTACCTGAAAGAGTC | TTCTTTAACCAGTCAGCCACAC | 200 | – | TD67/2mM | CFA 38 | q15.2 | Synt. 17 |
-
Loci and corresponding PCR primer sequences used to anchor RH and meiotic linkage groups to their corresponding dog chromosome. Where a microsatellite marker was isolated from the clone, the repeat motif is indicated in Column 5. For the PCR conditions (Column 6) the annealing temperature, as either as a single temperature (PCRxx) or a standard touchdown program (TDxx), is presented followed by the magnesium chloride concentration. The chromosome to which each marker was assigned by FISH is indicated in Column 7. The band assignment for each marker is based on the DAPI banded ideogram reported in Breen et al. (1999b). The nomenclature of the RH groups used by Mellersh et al. (2000) are presented in the final column.
