Trans-regulation of large number of transcripts by Qrr1 is a strong feature of crosses between B6 and D2—both the BXD RI set and B6D2F2 intercrosses—and in the B6 and C3H intercrosses. The feature is much weaker in the large LXS RI set and in the small CXB panel. The effect specificity demonstrates that a major source of the Qrr1 signal is generated by variations between B and D, and B and C3H alleles (H) but not by variations between the ILS and ISS alleles (L and S, respectively), and B and BALB alleles (C). This contrast can be exploited to identify sub-regions that underlie the trans-QTLs [67].
