Table 1.
Comparison of putative linkage groups in Arctic charr and brook charr based upon comparative alignments of homologous marker segments to the rainbow trout genome (see Additional File 9 for these arm assignments)
| Arctic charr linkage group | Chromosome Type* | Brook charr linkage group | Chromosome Type* | No. of BC arms detected |
|---|---|---|---|---|
| AC-1 | M | BC-1 | M | 2 |
| AC-3 | M | BC-3 | M | 2 |
| AC-4 | M | BC-4** | M | 2 |
| AC-5 | A | BC-5 | A | 1 |
| AC-6 | A? | BC-6 | A? | 1 |
| AC-7 | A | BC-7 | A | 1 |
| AC-8 | M | BC-8 | A? | 1 |
| AC-9 | A | BC-9 | A | 1 |
| AC-10 | A | BC-10 | M1 | 2 |
| AC-11 | A | BC-11 | A | 1 |
| AC-12 | A | BC-12 | A | 1 |
| AC-13 | M | BC-13a | A | 1 |
| BC-13b | A | 1 | ||
| AC-14 | A | BC-14 | A | 1 |
| AC-15 | M? | BC-15 | M? | 2 |
| AC-16 | A | BC-16** | M2 | 2 |
| AC-17 | A | BC-17 | M3? | 2 |
| AC-18 | M | BC-18 | M | 2 |
| AC-19 | M? | BC-19a | A | 1 |
| arm b in BC-17 | see3 | |||
| AC-20 | M | BC-20a | A | 1 |
| BC-20b | A | 1 | ||
| AC-21 | A | BC-21 | A | 1 |
| AC-22 | A | BC-22 | A | 1 |
| AC-23 | M? | BC-23b | A | 1 |
| arm a in BC-35 | see5 | |||
| AC-24 | A | BC-24 | A | 1 |
| AC-25 | M | BC-25 | M? | 2 |
| AC-26 | A | arm in BC-30 | see4 | |
| AC-27 | A? | BC-27 | A | 1 |
| AC-28 | M | BC-28a | A | 1 |
| arm b in BC-16** | see2 | |||
| AC-30 | A | BC-30 | M4 | 2 |
| AC-31 | A | ? | ||
| AC-32 | A | BC-32 | A | 1 |
| AC-33 | A | ? | ||
| AC-34 | A | BC-34 | A | 1 |
| AC-35 | A | BC-35 | M5 | 2 |
| AC-36 | A | BC-36 | A | 1 |
| AC-37 | A | BC-37 | A | 1 |
| AC-39 | A | arm in BC-10 | see1 | |
| AC-43 | A | BC-43 | A | 1 |
| Total No. Arms | 49 | total arms | 46 | |
* Chromosome is defined as either metacentric (M) or acrocentric (A).
** Polymorphisms were detected with both BC-4 and BC-16 linkage groups. BC-4 appears to form a metacentric linkage group in females, but a singleton position was detected with SSOSL32 in HL7 male, suggesting the formation of two acrocentrics. BC-16 markers appear to form a larger linkage group in the HL7 female (= metacentric structure), but only form two smaller linkage group clusters in the HL3 female (= 2 acrocentric linkage groups?).
Superscripts 1, 2, 3, 4, 5 indicates that two Arctic charr chromosome arms are part of a single brook charr metacentric chromosome. see1-5 designates which Arctic charr chromosome arm appears to be part of the brook charr metacentric having the same superscript numeral.