Human chromosome specific libraries (CSLs) were individually applied t
o equine metaphase chromosomes using the fluorescence in situ hybridiz
ation (FISH) technique. All CSLs, except Y, showed painting signals on
one or several horse chromosomes. In total 43 conserved chromosomal s
egments were painted. Homoeology could not, however, be detected for s
ome segments of tire equine genome. This is most likely related to the
very weak signals displayed by some libraries, rather than to the abs
ence of similarity with the human genome. In spite of divergence from
the human genome, dated 70-80 million years ago, a fairly high degree
of synteny conservation was observed. in seven cases, whole chromosome
synteny was detected between the two species. The comparative paintin
g results agreed completely with the limited gene mapping data availab
le in horses, and also enabled us provisionally to assign one linkage
group (U2) and one syntenic group (NP, MPI, IDH2) to specific equine c
hromosomes. Chromosomal assignments of three other syntenic groups are
also proposed. The findings of this study will be of significant use
in the expansion of the hitherto poorly developed equine gene map.