Premeiotic and meiotic chromosome distribution was studied in rat testes su
spensions by a triple-color fluorescent staining protocol which allows simu
ltaneous visual inspection of two chromosomal targets highlighted by FISH t
ogether with immunostained SCP3 synaptonemal complex (SC) proteins which ar
e marked by a third, composite color. Triple labeling with rat chromosome (
RNO) 4q and 19p specific probes and SCP3 staining disclosed that homologs a
re separated in premeiotic and leptotene nuclei. Pairing of homologous chro
mosome regions commenced during early zygotene, with pairing of the small m
etacentric chromosomes 19 preceding that of the distal region of the long a
rm of RNO4. Our results show that homolog association occurs during zygoten
e of rat spermatogenesis, with small and large chromosomes showing a consid
erable asynchrony. Comparison with pairing progression in meiosis of other
mammals suggests that asynchronous chromosome pairing reflects size differe
nces within a complement.