Table 1. Panels of neutral loci and immune-related loci used to screen samples of Atlantic salmon, Salmo salar, from the salmon industry in Chile.
| Locus Type | Motifa | Rangeb | TA c | Labeld | Primerse | Referencef |
| Neutral | ||||||
| SSsp1605 | (GATA)11 | 214–252 | 58 | Fam | F: CGCAATGGAAGTCAGTGGACTGGR: CTGATTTAGCTTTTTAGTGCCCAATGC | [50] |
| SSsp2201 | (GATA)34 | 251–335 | 58 | Fam | F: TTTAGATGGTGGGATACTGGGAGGCR: CGGGAGCCCCATAACCCTACTAATAAC | [50] |
| SSsp2210 | (GTTA)11 | 112–168 | 58 | Fam | F: AAGTATTCATGCACACACATTCACTGCR: CAAGACCCTTTTTCCAATGGGATTC | [50] |
| SSsp2213 | (GTTA)22 | 151–215 | 58 | Hex | F: ATGTGGAGGTCAACTAACCAGCGTGR: CATCAATCACAGAGTGAGGCACTCG | [50] |
| SSsp2215 | (GTTA)14 | 107–175 | 58 | Ned | F: ACTAGCCAGGTGTCCTGCCGGTCR: AGGGTCAGTCAGTCACACCATGCAC | [50] |
| SSsp2216 | (GTTA)25 | 201–257 | 58 | Ned | F: GGCCCAGACAGATAAACAAACACGCR: GCCAACAGCAGCATCTACACCCAG | [50] |
| SSspG7 | (GTTA)18 | 121–215 | 58 | Hex | F: CTTGGTCCCGTTCTTACGACAACCR: TGCACGCTGCTTGGTCCTTG | [50] |
| SSa85 | (GT)14 | 106–186 | 58 | Ned | F: AGGTGGGTCCTCCAAGCTACR: ACCCGCTCCTCACTTAATC | [51] |
| SSa197 | (GT)5C(TG)4TC(TG)3A(GTGA)15 | 162–260 | 58 | Fam | F: GGGTTGAGTAGGGAGGCTTGR: TGGCAGGGATTTGACATAAC | [51] |
| SSa171 | (TGTA)14(TG)7 | 198–252 | 58 | Fam | F: TTATTATCCAAAGGGGTCAAAAR: GAGGTCGCTGGGGTTTACTAT | [51] |
| SSa202 | (CA)3(CTCA)17 | 237–371 | 58 | Ned | F: CTTGGAATATCTAGAATATGGCR: TTCATGTGTTAATGTTGCGTG | [51] |
| SSa14 | (TC)10N15(TC)3N2(AC)12(TC)3N5(CA)4 | 161–165 | NA | Tail | F: CCTTTTGACAGATTTAGGATTTCR: CAAACCAAACATACCTAAAGCC | [52] |
| SSOSL85 | (GT)22 | 201–241 | NA | Tail | F: TGTGGATTTTTGTATTATGTTAR: ATACATTTCCTCCTCATTCAGT | [53] |
| SSOSL311 | (TG)38 | 139–190 | NA | Tail | F: TAGATAATGGAGGAACTGCATTCTR: CATGCTTCATAAGAAAAAGATTGT | [53] |
| SSOSL438 | (AC)26AT(AC)8 | 132–174 | NA | Tail | F: GACAACACACAACCAAGGCACR: TTATGCTAGGTCTTTATGCATTGT | [53] |
| Locus Type | Motif a | Range b | TA c | Label d | Primers e | Reference f |
| Immune-related | ||||||
| SsaIR001TKU | (AG)12 | 113–115 | NA | Tail | F: AAGAGCGAGAGAGAAGGATGGR: GTTTCACAGAATCAACAGTCAGCAA | [47] |
| SsaIR002TKU | (AG)10 | 241–249 | NA | Tail | F: GGGTACAAGCAGGGGTCTTAR: GTTTAAGAGTGGACCGACAACAAT | [47] |
| SsaIR003TKU | (GT)13 | 146–163 | NA | Tail | F: TGTTCTGCAGGTCAGAAGTGAR: GTTTGAGTGGGAGGAAGGGGAGTA | [47] |
| SsaIR004TKU | (AG)10 | 313–321 | NA | Tail | F: AGCTATTTCCAAGGCGTTCAR: GTTTCACCACTCAGGAGAGCATGA | [47] |
| SsaIR005TKU | (CTT)7 | 371–379 | NA | Tail | F: CGACGACTTTTTCATCTGTCTTR: GTTTGGACAACACATCTCATTCCAA | [47] |
| SsaIR007TKU | (AG)9 | 183–191 | NA | Tail | F: GCAATGCTGCCATCTAGTGAR: GTTTCAAGGAAAGCCTACAAAAAGC | [47] |
| SsaIR010TKU | (AG)10 | 192–198 | NA | Tail | F: CAACGACACCATACCAACCAR: GTTTAACCCCTTCCAAGTTCCATC | [47] |
| SsaIR011TKU | (ATC)8 | 364–376 | NA | Tail | F: CCAGCCAACTACGACAACTGR: GTTTGTGGTTATTTTTGGGGTGA | [47] |
| SsaIR012TKU | (AATC)14 | 162–222 | NA | Tail | F: GAGTCCCCTTTGGCCTCTCR: GTTTAAACACAGTAAGCCCATCTATTG | [47] |
| SsaIR014TKU | (ATC)6 | 395–407 | NA | Tail | F: CTGAGGTGGTGGCACAGCR: GTTTATTGTTTGGTTCTTACAGCAGGA | [47] |
| SsaIR016TKU | (AT)9 | 317–327 | NA | Tail | F: CCAAAAATGTCCCATTCACCR: GTTTGTGTGCCACTCAGAATTG | [47] |
| BG934281 | (TCTG)14 | 215–277 | NA | Tail | F: ACTGCTTCTCCCCTGCTACAR: GTTTGCGAACCACACATATACCAC | [46] |
| CA769358 | (AC)22 | 133–173 | NA | Tail | F: TGACGCCATATGCAAAGAGAR: GTTTCCTTTGTCTGCAAAACGTGA | [46] |
| UBA | (CA)17 | 330–364± | NA | Tail | F: GGAGAGCTGCCCAGATGACTTR: CAATTACCACAAGCCCGCTC | [44] |
| MHC_II | GTTATTAAAT | 232–292 | NA | Tail | F: GATGGCAAAGAGGAAAGTGAGR: TTGTTATGCTCTACCTCTGAA | [45] |
a
Motif indicates repeat motif.
b
Range refers to alleles thus far uncovered (may include the 21 bp 50-tail-sequence).
c
TA is optimized annealing temperature. For loci amplified with the tail protocol, a step-down protocol was used so annealing temperature is not applicable (NA).
d
Label refers to dye (6-Fam, Ned, or Hex) used to label forward primer. Tail refers to loci that were amplified using the tail protocol.
e
Primer sequences are forward (F and reverse (R).
f
Citations describing putative function.