Leutz [ 35] has described three prototypical models and phases in increasing integration: linkage, co-ordination and full integration.
Specific model improvements would be based on further testing and evaluation of existing models, the development and testing of modular model components and integration, and linkages of model integration platforms to new data management and visualization tools.
In addition, bioinformatic tool such as TEAM (a tool for the integration of expression and linkage and association maps) is designed to integrate linkage, association and expression data, together with functional annotations however currently it is not implemented to handle GWAS data [ 8].
Therefore, the composite maps with 22 linkage groups (LG) were established, of which 17 derived from integration of linkage groups in two or three individual maps.
Although the number of polymorphic SNPs in FL population is insufficient for a dense linkage map construction, these SNPs provide important markers to allow comparison and integration of linkage maps in the future.
Detailed information regarding integration of linkage map and physical map is provided in Supplementary data S2.
Detailed information on the initial integration of linkage group 1 (LG1) is showed in Figure 1 and Additional file 1.
These contigs would be a useful resource for the future integration with linkage map and whole genome sequence assembly.
Therefore, BACs and their end sequences can be effectively used for integration of linkage and physical maps [ 12, 28, 29].
BAC libraries for switchgrass have recently been developed and may be utilized for the integration of linkage and physical maps through BAC-FISH probing.
