As Lep-MAP2 requires sex information at least for two parents, does it mean Lep-MAP is not suitable for plant genetic mapping? If not, am I supposed to set them randomly and leave the F1 progeney gender blank? Thanks very much.
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I have a related question:
How do we interprete the results for hermaphroditic organisms ?
For example, recently I have started applying Lep-MAP2 to a family of oil palm (Elaeis guinensis) consisting of:
1 female parent of the Dura variety,
1 male parent of the Pisifera variety,
and their offspring, which are of the Tenera variety (natural result of crossing Dura and Pisifera).
The Tenera oil palms are hermaphroditic.
However, the results of the OrderMarkers step shows both "male position" and "female position" for each marker. (in addition to information about error estimate and phase)
In this case, how to determine which position to use for each marker?
Thank you very much !
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you have 1 male and 1 female as you stated — the male and female in the results is the recombination map for that male and that female, not the male/female in the offspring. The male and female maps differe because of (1) differences in recombination between males and females and (2) stocasticity.
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Thank you for the the information !
I have found out that by setting SexAveraged=1,
the "male position" and "female position" for each marker becomes the same.
Would this result be applicable for the hermaphroditic offspring?
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With SexAveraged=1 you find the average linkage map (average of the two parents). In general, you should use this average map for the QTL mapping; the fact the offspring are hermaphodites is irrelevant.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I have a related question:
How do we interprete the results for hermaphroditic organisms ?
For example, recently I have started applying Lep-MAP2 to a family of oil palm (Elaeis guinensis) consisting of:
1 female parent of the Dura variety,
1 male parent of the Pisifera variety,
and their offspring, which are of the Tenera variety (natural result of crossing Dura and Pisifera).
The Tenera oil palms are hermaphroditic.
However, the results of the OrderMarkers step shows both "male position" and "female position" for each marker. (in addition to information about error estimate and phase)
In this case, how to determine which position to use for each marker?
you have 1 male and 1 female as you stated — the male and female in the results is the recombination map for that male and that female, not the male/female in the offspring. The male and female maps differe because of (1) differences in recombination between males and females and (2) stocasticity.
Dear Pasi Rastas,
As Lep-MAP2 requires sex information at least for two parents, does it mean Lep-MAP is not suitable for plant genetic mapping? If not, am I supposed to set them randomly and leave the F1 progeney gender blank? Thanks very much.
Dear Chenxi Zhou,
Thanks for you question.
I think Lep-MAP can be used for plants. For full-sib crosses it is straight forward.
I think you could format the data to full-sib-like if the crosses involve selfing.
For polyploidy, I don't know.
Cheers,
Pasi
Dear Pasi Rastas,
I have a related question:
How do we interprete the results for hermaphroditic organisms ?
For example, recently I have started applying Lep-MAP2 to a family of oil palm (Elaeis guinensis) consisting of:
1 female parent of the Dura variety,
1 male parent of the Pisifera variety,
and their offspring, which are of the Tenera variety (natural result of crossing Dura and Pisifera).
The Tenera oil palms are hermaphroditic.
However, the results of the OrderMarkers step shows both "male position" and "female position" for each marker. (in addition to information about error estimate and phase)
In this case, how to determine which position to use for each marker?
Thank you very much !
you have 1 male and 1 female as you stated — the male and female in the results is the recombination map for that male and that female, not the male/female in the offspring. The male and female maps differe because of (1) differences in recombination between males and females and (2) stocasticity.
Thank you for the the information !
I have found out that by setting SexAveraged=1,
the "male position" and "female position" for each marker becomes the same.
Would this result be applicable for the hermaphroditic offspring?
With SexAveraged=1 you find the average linkage map (average of the two parents). In general, you should use this average map for the QTL mapping; the fact the offspring are hermaphodites is irrelevant.
you have 1 male and 1 female as you stated — the male and female in the results is the recombination map for that male and that female, not the male/female in the offspring. The male and female maps differe because of (1) differences in recombination between males and females and (2) stocasticity.
BW
F
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Federico Calboli
f.calboli@gmail.com