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Semen was subsequently used to inseminate females according to the genetic management programme aiming at equalizing the founders' contribution and avoiding inbreeding.
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On the other hand, founder contribution varied significantly along the autosomes.
In contrast, the loci associated with Tb.N and Conn.D (Trl3 and Trl5, respectively) had a more varied founder contribution.
The median founder contribution ranged from 10.6% (PWK/PhJ) to 13.2% (C57BL/6J consistent with an expectation of 12.5%.
The tool also automatically generates stacked histograms that show the distribution of subspecific origin and founder contribution for a user-selected subset of lines.
Although the genome of each CC line receives a balanced contribution from each founder strain, the founder contribution is not uniformly distributed along the genome because of the small number of recombination events undergone by each CC line.
We simulated 20,000 independent sets of 350 lines and tabulated the founder contribution over all haplotype segments within each set (a haplotype segment is the region from one recombination breakpoint to the next in any of the 350 lines).
Expectations for the founder contribution for chr X (and estimation of the TRD significance) would be best achieved by simulations based on the actual funnel codes of the 350 independent CC lines.
Permutations of the founders are used to randomize the genomes and balance the founder contributions to the resulting CC lines.
When founder contributions are equal, this increases Ne; thus reducing inbreeding and loss of genetic variation (Woodworth et al. 2002).
Individual DO animals displayed a wide range of founder contributions with a minimum of 3.4% and a maximum of 25.1%.
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