Meiotic driver locus on Chr. 2 untrustworthy?

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CJ Harbort

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Jul 2, 2025, 4:34:03 AMJul 2

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Hi Karl and Dan,

Thanks again for all your efforts in this group! It's a fantastic resource.

I have a question regarding the region on Chr 2 where the gene driver (WSB) allele was removed from the DO population: https://pmc.ncbi.nlm.nih.gov/articles/PMC5144960/#s12

Is there any reason the breeding out of one of the founder genomes in this region would lead to spurious unreliable peaks in this region?

We, and another group we know of, have both gotten peaks very close to this region on Chr. 2. We find a peak just before this region with a few somewhat correlated phenotypes, and a peak just after this region with a different set of correlated phenotypes. Some of these peaks are quite over a permutation threshold even with 5000 permutations.

Importantly, the phenotype giving us and the other group a peak in this region are somewhat related and it's reasonable we'd both end up with the same QTL region. However, they have decided to disregard this region due to the decreased diversity and unbalanced allele representation.

Have you ever run into 'spurious' peaks in this region? Is this really a problem in the analysis pipeline, or would it still be robust to the changes in this region?

Thanks a lot for any feedback you have!

Karl Broman

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Jul 9, 2025, 9:39:43 AMJul 9

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I think there could be artifacts or real effects, or even both. You can't say without looking at the details.