The cloning of genes for complex traits in polyploid plants that possess la
rge genomes, such as hexaploid wheat, requires an efficient strategy. We pr
esent here one such strategy focusing on the homeologous pairing suppressor
(Ph1) locus of wheat. This locus has been shown to affect both premeiotic
and meiotic processes, possibly suggesting a complex control. The strategy
combined the identification of lines carrying specific deletions using mult
iplex PCR screening of fast-neutron irradiated wheat populations with the a
pproach of physically mapping the region in the rice genome equivalent to t
he deletion to reveal its gene content. As a result, we have located the Ph
l factor controlling the euploid-like level of homologous chromosome pairin
g to the region between two loci (Xrgc846 and Xpsr150A). These loci are loc
ated within 400 kb of each other in the rice genome. By sequencing this reg
ion of the rice genome, it should now be possible to define the nature of t
his factor.