Jasieniuk:Notebook/Apomixis in hybrid Rubus/2010/07/19: Difference between revisions

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===Analysis===
===Analysis===
The simplest thing to do is, for each group of mother plus progeny, calculate a pairwise distance matrix between individuals.  Then we will look at the distributions of within-group distances.  Shorter distances indicate apomixis, while larger distances indicate sexual reproduction.  Mother plants that have a mix of the two reproductive modes should show a bimodal distribution.
A more complex analysis could involve looking at the probabilities of seeing certain genotypes under the hypotheses of sexual and asexual reproduction.  Theoretically we should expect 100% identical genotypes under asexual reproduction, but we should leave some wiggle room for mutations or scoring errors.
===References===
===References===


Revision as of 17:08, 19 July 2010

Apomixis in hybrid Rubus <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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Experimental Design

List of mother plants

  • Two genotypes of R. ursinus x armeniacus: are these apomictic or sexual?
  • One genotype of R. ursinus x pensilvanicus: are these apomictic or sexual?
  • R. ursinus: expect to see sexual recombination (dioecious)
  • R. armeniacus: expect ~90% asexual progeny
  • R. pensilvanicus: expect to see mostly asexual progeny
  • R. ulmifolius: an extra control; should reproduce sexually
  • Another clone that is similar to R. armeniacus: also expect to see ~90% asexual progeny. This clone is included because it was unexpected that we found a second invasive clone on the West Coast, and so characterizing it in general would be a good idea.

Microsatellite markers

These are chosen based on how much heterozygosity they show in our mother plants of interest.

  • CBA15 - only really useful in the R. armeniacus types
  • CBA23
  • CBA28 - should be especially useful
  • CBA14
  • RUB126 - also should be very useful
  • RUB262

Analysis

The simplest thing to do is, for each group of mother plus progeny, calculate a pairwise distance matrix between individuals. Then we will look at the distributions of within-group distances. Shorter distances indicate apomixis, while larger distances indicate sexual reproduction. Mother plants that have a mix of the two reproductive modes should show a bimodal distribution.

A more complex analysis could involve looking at the probabilities of seeing certain genotypes under the hypotheses of sexual and asexual reproduction. Theoretically we should expect 100% identical genotypes under asexual reproduction, but we should leave some wiggle room for mutations or scoring errors.

References

PCR Run today

Stella, you can put whatever notes you like in here about what you are doing.


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