Thanks for developing Lep-MAP and Lep-Anchor. We've had great success using it for linkage mapping in corals and recently submitted a manuscript for a linkage map comparison.
In the maps where we've had success, the species were hermaphrodites but crosses were performed such that we knew which parent was the egg donor and which was the sperm donor. We are now moving on to a set of crosses where we don't have this information. In these crosses, sperm and eggs from each parent were all mixed together, meaning that we can end up with Parent 1 X Parent 2 and Parent 2 X Parent 1 offspring in the same cohort with no way of telling which parent was the sperm or egg donor for each offspring. We have genotype data from both the parents and the offspring and this species has a very very low rate of selfing so selfing should not be something we have to worry about here.
I was hoping to try and figure out maternity using mitochondrial data but it looks like all the parents used in this cross shared identical mitogenomes so this is not possible. How would one set up a pedigree file for this niche case where we have parentage but don't know which was egg or sperm donor? Or would we need to have egg/sperm donor information to run this data successfully in Lep-MAP3? The hope here is to just get an idea of the sex-averaged map. I apologize if this is a duplicate "issue" and this has already been addressed. I found similar issues in the general discussion forum but they weren't exactly the same.
Thank you!
Nick
Last edit: Nicolas 2024-07-02
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Thank you for your question and sorry for taking some time to answer as I was on holiday.
I think you can construct the map as if there were no parental data. This has been in the discussion earlier. I will add the information to the wiki soon. If you are in a hurry, please check the wiki and the old discussion threads.
Cheers,
Pasi
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There should be documentation in the wiki now about linkage mapping without parents. Please ask if it is not clear.
However, it might be possible that your data can be analysed without any of these tricks. Just analyse the data as known parents, the sex averaged map will work anyway...
Cheers,
Pasi
👍
1
Last edit: Pasi Rastas 2024-08-05
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No worries at all on the delay - I really appreciate you taking the time to respond over the summer and thank you for updating the wiki. Hope you had a great holiday. I will give this a go later this week. Fingers crossed it all works smoothly!
Best,
Nick
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Pasi,
Thanks for developing Lep-MAP and Lep-Anchor. We've had great success using it for linkage mapping in corals and recently submitted a manuscript for a linkage map comparison.
In the maps where we've had success, the species were hermaphrodites but crosses were performed such that we knew which parent was the egg donor and which was the sperm donor. We are now moving on to a set of crosses where we don't have this information. In these crosses, sperm and eggs from each parent were all mixed together, meaning that we can end up with Parent 1 X Parent 2 and Parent 2 X Parent 1 offspring in the same cohort with no way of telling which parent was the sperm or egg donor for each offspring. We have genotype data from both the parents and the offspring and this species has a very very low rate of selfing so selfing should not be something we have to worry about here.
I was hoping to try and figure out maternity using mitochondrial data but it looks like all the parents used in this cross shared identical mitogenomes so this is not possible. How would one set up a pedigree file for this niche case where we have parentage but don't know which was egg or sperm donor? Or would we need to have egg/sperm donor information to run this data successfully in Lep-MAP3? The hope here is to just get an idea of the sex-averaged map. I apologize if this is a duplicate "issue" and this has already been addressed. I found similar issues in the general discussion forum but they weren't exactly the same.
Thank you!
Nick
Last edit: Nicolas 2024-07-02
Dear Nick,
Thank you for your question and sorry for taking some time to answer as I was on holiday.
I think you can construct the map as if there were no parental data. This has been in the discussion earlier. I will add the information to the wiki soon. If you are in a hurry, please check the wiki and the old discussion threads.
Cheers,
Pasi
Dear Nick,
There should be documentation in the wiki now about linkage mapping without parents. Please ask if it is not clear.
However, it might be possible that your data can be analysed without any of these tricks. Just analyse the data as known parents, the sex averaged map will work anyway...
Cheers,
Pasi
Last edit: Pasi Rastas 2024-08-05
Dear Pasi,
No worries at all on the delay - I really appreciate you taking the time to respond over the summer and thank you for updating the wiki. Hope you had a great holiday. I will give this a go later this week. Fingers crossed it all works smoothly!
Best,
Nick