In tomato, we have shown that GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure.
In order to understand whether introgression for single markers deviated from neutral expectations, we estimated genomic clines for each locus in the admixed population and using the pure populations as reference populations [ 40].
For the causal allele, a risk model [6] with relative risk <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0007928.e111.PNG" class= inline-graphic"/> was used for both the discrete population and the admixed population.
With a sample size of just 10 individuals for the admixed population, perfect classification is achieved using the informative wavelet variance, while the ABS metric correctly classifies only 60% of cases.
Results of simulation studies are shown in Figure 11(a) and Additional file 11, Table S5 for the admixed population from CEU and YRI, where random subsets of 20 AIMs were used, and Figure 11(b) and Additional file 12, Table S6 for the admixed population from CHB and JPT, where random subsets of 50 AIMs were used.
Then, molecular coancestry between individuals of the admixed population and the pure exogenous individuals of this foreign population was calculated and used to remove the exogenous genetic material.
Because of the proximity of the admixed population C′ and the reference A′, the test detects long-range correlated LD and concludes that using A′ as a reference may produce unreliable results.
The noise levels of the fitted dates (estimated by ALDER using the jackknife) are the lowest for the Yoruba–French curve, as expected, followed by the one-reference curve with French, consistent with the admixed population being mostly Yoruba.
We show how data from unadmixed and admixed populations can be combined to estimate these ancestry-specific allele frequencies within the admixed population under study, allowing for variation between allele frequencies in unadmixed and admixed populations.
