Recombination and allelic association in the Xq/Yq homology region

The ends of the long arms of the human X and Y chromosomes contain a homologous region that can undergo sequence exchange. We have developed new polymorphic markers to analyze the genetic behavior of this region in the three-generation CEPH reference families. These Xq/Yq markers undergo crossovers in approximately 2% of male meioses in a pattern consistent with reciprocal recombination rather than gene conversion. Although the rate of recombination in males is significantly higher than in females or in autosomal sequences, it is more than an order of magnitude lower than in the short arm pseudoautosomal region at Xp/Yp. The Xq/Yq markers exhibit allelic association with one another, but not with markers in the X-specific or Y-specific regions of the sex chromosomes. Hence the Xq/Yq homology region displays behavior that is intermediate between sex-linked and true pseudoautosomal, and is unlikely to be essential for proper chromosome segregation.