Jasieniuk:Notebook/Apomixis in hybrid Rubus/2010/07/19

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Apomixis in hybrid Rubus
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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List of mother plants

 * Two genotypes of R. ursinus x armeniacus: are these apomictic or sexual?
 * One genotype of R. ursinus x pensilvanicus: is this 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.

Some References

 * Ellstrand & Scierenbeck: Hybridization as a stimulation for the evolution of invasiveness in plants?
 * Kollmann et al.: Evidence of sexuality in European Rubus species based on AFLP and allozyme analysis.
 * Amsellem et al.: Evidence for a switch in reproductive biology of Rubus alceifolius towards apomixis, between its native range and area of introduction
 * Werlemark & Nybom: Pollen donor impact on the progenies of pseudogamous blackberries.

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


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