We also wondered if estimates of s based on analysis of certain marker densities could be extrapolated to other marker densities for analysis of the same phenotypes.
However, in practice this can be computationally burdensome and an appealing alternative is to estimate γ and s ~ based on the observed marker genotypes only.
Compared with dominant markers, selection markers based on complementation do not require supplements in the cultivation medium.
We also determined that it may be reasonable to consider specifying values for s for one marker density based on a previous estimate from another marker density by taking into account the inverse relationship between s and marker density.
An ITS2 sequence was considered as paralogous if it was assigned to a clade (or clades) that conflicted with the species assignment based on chloroplast marker(s) and morphology.
To verify root infection by 15 dpi, 10 plants from each of the inoculated R and S groups (based on marker detection) were kept in pots until 21 dpi for examination of root symptoms.
For faster computing, an alternative to using the full log-likelihood is to determine parameters γ and s ~ based on observed marker genotypes only, i.e. by maximising ℓ ~ mark (γ, s ~ ), and to estimate the remaining parameter based on ℓ ~ y ∣ m o (σ a 2, σ e 2, ω, γ, s ~ ) for a grid of values for ω, with estimates of γ and s ~ plugged in.
The reproducibilities S of pathway markers (based on the GPF method, i.e., proportions of top pathways in common among different data sets) are 0.40, 0.33, and 0.18 in the stage, survival, and metastasis data sets, respectively.
The Gn1a-17 SNP marker and GS5-03 SNP marker were developed based on this method.
We filtered marker pairs based on linkage.
