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)

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