In RI strains, non-syntenic associations can lead to LD between distant loci [89],[106]. In the BXDs, we detected such non-syntenic associations between markers in Qrr1 and markers on distal Chr 2 and proximal Chr 15. As a result of these associations, some transcripts that have strong cis- or trans-QTLs in Qrr1 tend to have weak LOD peaks, usually below the suggestive threshold, on distal Chr 2 and proximal Ch15. However, there is no bias for genes located in these intervals in LD with Qrr1 to have trans-QTLs in Qrr1.
