Jasieniuk:Notebook/Apomixis in hybrid Rubus/2010/07/19
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List of mother plants
These are chosen based on how much heterozygosity they show in our mother plants of interest.
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.
PCR Run today
Stella, you can put whatever notes you like in here about what you are doing.