Directed integration of the physical and genetic linkage maps of swine chromosome 7 reveals that the SLA spans the centromere

The first integrated physical and genetic linkage map encompassing the entire swine chromosome 7 (SSC7) reveals that the porcine MHC (SLA) spans the centromere. A SLA class II antigen gene lies on the q arm, whereas class I and III genes lie on the p arm, suggesting that the presence of a centromere within the SLA does not preclude a functional complex. The SLA appears smaller than other mammalian MHC, as the genetic distance across two class I, three class II, and three class III SLA gene markers is only 1.1 cM. There are significant variations in recombination rates as a function of position along the chromosome, and the SLA lies in the region with the lowest rate. Furthermore, the directed integration approach used in this study was more efficient than previous efforts that emphasized the screening of large insert libraries for random microsatellites.