**4. BACs and marsupial linkage maps**

Linkage (genetic) maps are a useful resource as they provide information not only on the order of genetic markers on a chromosome but on the location and frequencies of crossover events. Such maps are even more valuable if the maps are anchored to chromosomes and integrated with available genome assembly and/or cytogenetic mapping data. Linkage maps have been constructed for two marsupial species, opossum (Samollow et al., 2007) and the wallaby (Wang et al., 2011b). BACs containing markers at the ends of linkage groups have been used to cytogenetically assign these groups to chromosomes and determine the genome coverage of the linkage maps (Samollow et al., 2007; Wang et al., 2011b). The opossum linkage map was integrated with the genome assembly and cytogenetic map by FISH-mapping 34 BAC clones from the ends of linkage groups (Duke et al., 2007; Samollow et al., 2007). A sophisticated approach was used in the marker selection for construction of the wallaby linkage map to facilitate the integration of cytogenetic and linkage map data. Three strategies were developed to fill gaps in the 1st generation linkage map (Zenger et al., 2002) using information from BACs. The first strategy involved identifying microsatellites in BACs that had been previously assigned to chromosomes by FISH. The second strategy identified microsatellites within BAC end sequences and the third used the wallaby genome sequence to identify microsatellite markers near BACs that had been mapped by FISH. This resulted in a linkage map that could easily be incorporated with the physical map data to generate an integrated map (Wang et al., 2011a, 2011b). Information from the integrated map has been used to improve and anchor the tammar wallaby genome assembly (Renfree et al., 2011).
