Whole genome re-sequencing of mother and offspring D. magna genotypes

Inbreeding refers to the fusion of related individuals' gametes, with
self-fertilization (selfing) being an extreme form of inbreeding—involving
gametes produced by the same individual. Selfing is expected to reduce
heterozygosity by an average of 50 % in one generation; however, little is
known about the empirical variation on a genome level surrounding this
figure, and the factors that affect variation. We selfed genotypes of the
cyclic parthenogen Daphnia magna and analyzed whole genomes of mothers and
selfed offspring, observing the predicted 50 % heterozygosity reduction on
average. We also saw substantial variation around this value and
significant differences among mother-offspring pairs. Crossover analysis
confirmed the known trend of recombination occurring more often towards
the telomeres. This effect was shown, through simulations, to increase the
variance of heterozygosity reduction compared to when a uniform
distribution of crossovers was used. Similarly, we simulated inbred line
production after several generations of selfing and we observed higher
variance in achieved homozygosity when we consider a higher recombination
rate towards the telomeres. Our empirical and simulation study highlights
that the expected mean values of heterozygosity reduction show remarkable
variation, which can help understand, for example, differences among
inbred individuals.