Add'l QTL Effects

[Joshua Havill]

Hi Karl and r/qtl community,

Just to clarify the process for additional QTL identification and effect estimation, in the presence of multiple QTL.

An outcrossing F1 population was generated and multiple QTL were associated with a trait. Those QTL were made into a qtl object and effects were estimated.

However, additional QTL identification was warranted and a subsequent peak was determined to have a high LOD. It's unclear whether a new permutation threshold should be established, however following the addition to the previous QTL model to estimate effects of the newly-identified QTL, the model is unable to estimate effects.

The data was previously parsed from a larger dataset to include only individuals with a phenotype were used for QTL analyses.

Cheers,

Josh

[Karl Broman]

It's pretty common to use the same permutation thresholds for subsequent QTL.

karl

[Joshua Havill]

Hi Karl,

That doesn’t address the inability for estimates to be modeled from the data however. Any clue as to what could be happening?

Cheers,

Josh

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Joshua Havill

612-836-7834

On Nov 13, 2025, at 12:42 PM, Karl Broman <kbr...@gmail.com> wrote:



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[Karl Broman]

I don't understand the question.

karl

[Joshua Havill]

Hi Karl,

After identifying an additional QTL, the QTL was added to the model to estimate genotypic effects. However, the model was unable to estimate genotypic effects with the added QTL.

Why might this be?

Cheers,

Josh

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Joshua Havill, Ph. D.
C: (612)-836-7834

O: (612)-625-5274

USDA-NIFA Postdoctoral Fellow

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