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Black line below loci: PCR amplicons.
Underlined locus identifiers were downregulated in response to ranalexin, none of the below loci were upregulated.
After the first round of scoring and map assembly (details below), loci that appeared to contain double crossovers for individual plants that could not be fixed by reordering loci, as well as those that could not be mapped, were reexamined for scoring errors, and allele calls were manually adjusted as appropriate.
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As these deviations are very likely to be the result of the significant spatial genetic structure detected in the subsequent analyses (see sections below), all loci were assumed to be statistically independent and were retained for further analyses.
As will become relevant below, this locus encompassed Slit2, Kcnip4 and Fbxw7, associated with the Lbx-free Nkx3.2 locus in tetrapods.
However, some of these changes are, indeed, due to sequence assembly errors in the database, which we document below for locus 17 in strains Rahman and MS96-3382.
Drosophila pseudoobscura bogotana carrying a white eye mutation were used in the crosses described below, as the white locus is linked to an inversion that distinguishes between D. p. bogotana and D. persimilis.
One example discussed further below is the CSF1R/PDGFRB locus, part of which is duplicated in the current pig genome assembly.
Childhood GWAS have uncovered novel loci below the detection range in adult studies, suggesting that obesity genes may be more easily uncovered in the pediatric setting.
No loci below 1% copy number frequency were reported in this study.
Because the estimate in the JRT is markedly below 0.70, other loci may be exerting an effect on any major locus responsible for deafness in the JRT.
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