There are different ways to define the order in which the maps are listed in the map selection interfaces. For the sequence maps, chromosomes are displayed on top of the list, ordered by their OrderNo assigned during loading. The rest of the maps are sorted by their length, showing longer maps first. The order of the chromosomes can be managed by using the command 'edit chromosome'. 

To reorder genetic maps use the command 'edit map_order':

PS> edit map_order 55
Map set /Solanum lycopersicum/TraitGenetics EXPEN2012

┌──────────────────────┐
│ ORDER_NO  MAP_NAME   │
│ -------------------- │
│ 0         1          │
│ 1         10         │
│ 2         11         │
│ 3         12         │
│ 4         2          │
│ 5         3          │
│ 6         4          │
│ 7         5          │
│ 8         6          │
│ 9         7          │
│ 10        8          │
│ 11        9          │
│                      │
└──────────────────────┘

N - reorder maps Naturally; A - reorder Alphabetically; F - use records from file; ESC - cancel: N
┌──────────────────────┐
│ ORDER_NO  MAP_NAME   │
│ -------------------- │
│ 0         1          │
│ 1         2          │
│ 2         3          │
│ 3         4          │
│ 4         5          │
│ 5         6          │
│ 6         7          │
│ 7         8          │
│ 8         9          │
│ 9         10         │
│ 10        11         │
│ 11        12         │
│                      │
└──────────────────────┘
Do you want to save the new map order? (Y/N) Y
Assigned new orderNo to 11 maps
DATA_VERSION updated

An alternative method to provide the new map order is using a tab-delimited file. The format of such file is very simple: MapName<tab>OrderNo repeated for each map on a separate line:

Chr1        1
Chr2        2
Chr3        3