I'm using the CloudMap Hawaiian C. elegans mapping workflow and everything seems to have worked well. I got mapping intervals and homozygous mutations in a gene that was expected. My question concerns what I should expect to see at the site of a GFP transgene insertion that was used for screening and selecting F2 recombinants. The transgene is reported to be in LGIII and for one of my mapped strains, I do see a broad 5 Mb region on the chromosome with a high frequency of parental alleles. However, for the second strain from the same screen with the same transgene, I don't see this region with linkage in LGIII. For reference, average coverage is over 40x and the number of pooled F2s was 43-59; also both strains have a 3-4 Mb region of LGIV with a high frequency of parental alleles and they both have homozygous mutations in the same gene within the LGIV region (one that we expected).
A couple things seem odd to me:
1) Why wouldn't the transgene on LGIII be mapped similarly in both strains?
2) Because the transgene was only in my starting strains and not in Hawaiian, shouldn't it be present in only 2/3 copies of LGIII in the pooled F2s (1/4 GFP/GFP and 1/2 GFP/Hawaiian). GFP transgene is dominant so some of my F2s should have been heterozygous for the transgene. Because roughly 1/3 of the pooled LGIII copies should be Hawaiian, I was expecting to see weak linkage in both strains, but I see strong linkage in one and no linkage in the other.
Anyone have experience of insight into what I'm seeing or what I should be seeing?