Comprehensive linkage maps are presented by vertical bars on the left, and the corresponding RH maps are shown on the right. The 217 markers positioned on both maps are indicated in red and their positions on the two maps are joined by dotted lines. Gene-based markers are indicated in italics and highlighted yellow, markers corresponding to TOASTs (Jiang et al. 1998) are indicated by the suffix (T). Chromosome-specific markers are designated by a blue highlighted asterisk. Framework markers ordered with statistical support higher than 1000:1 are underlined. When two or more RH groups were associated with a single chromosome, the orientation of the RH groups with respect to each other and to the chromosome was established by comparison with markers mapped by linkage analysis and by analysis of two-point breakage probability between markers in the different RH groups.
CFA nomenclature is used for linkage groups and their associated RH groups that have been assigned to specific chromosomes; anonymous groups are termed Syntenic group 1 (S1), Syntenic Group 2 (S2) etc., in order of decreasing size. Distances between markers on the linkage map and the RH map are measured in centiMorgans (cM) and centiRays5000 (cR5000), respectively, and were calculated using the Kosambi and the RH Haldane mapping functions. Known chromosomal locations are reported for human orthologous genes.
A comprehensive radiation hybrid map (Figure 1) consisting of 600 markers typed on 126 radiation hybrids was constructed. Two hundred and eighteen markers are gene-based and 382 are canine-specific microsatellites. An initial pairwise analysis identified 77 distinct RH groups. Each marker was linked to at least one other marker in the same group with a Lod score of ³ 8.0. Initially, a framework map was constructed for each group by multipoint analysis, using a threshold lod score of 3.0 to support the order of markers within the group. Subsequently, all remaining markers were positioned on the map, relative to the framework markers, to produce a comprehensive RH map. Five hundred and twenty three markers (87%) were linked to at least one other marker with an average inter-marker distance of 24.3 cR5000 and 77 markers (13%) were unlinked to any other marker on the map. Three hundred and eight framework markers were identified that could be ordered with odds higher than 1000:1 (log likelihood ratio of 3.0). Markers comprising the framework map are underlined in the map figures.
Markers were assigned to linkage groups using a Lod score of 5.0. Markers are ordered within linkage groups using a Lod of 2.0 for the framework map (underlined on the map figures) and 0.01 for the comprehensive map. The single linkage group for which no RH group was assigned is called linkage group 1. A total of 247 animals were genotyped to build this map, with a total of 163 F2 individuals. The majority of pedigrees are from the Cornell Canine Reference Families.
