Abstract
We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r2 ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF < 0.1 are highly correlated with SNPs more than 100 kb distant. Although SNPs within regions with polymorphic inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses or discordance between genotype and karyotype. Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines.
Highlights
We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count $5
Linkage disequilibrium (LD) is a challenge to all genome-wide association (GWA) studies, because it confounds the signal from variant sites that cause phenotypic variation with those that are genetically correlated with the causal variant but Manuscript received February 4, 2015; accepted for publication June 8, 2015; published Early Online June 10, 2015
We focused our attention on Linkage (gametic-phase) disequilibrium (LD) at focal sites with minor allele counts (MAC) of five or more, we calculated correlations of these focal sites with those where MAC was three or more
Summary
We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count $5. The analysis by Huang et al (2014) suggests that three of these are fixed in seven or more lines These more common inversion types are substantially differentiated from the Standard karyotypes and cause LD (Corbett-Detig and Hartl 2012; Langley et al 2012; Huang et al 2014). Pool (2015) analyzed whether small genomic regions in the DGRP lines were likely to reflect African rather than European ancestry, following the joint colonization of North America by a mixture of D. melanogaster from these two source populations (Duchen et al 2013). The cytogenetic karyotype assignments by Huang et al (2014) do not always agree with other PCR-based or sequence-based assignments in other works (Corbett-Detig and Hartl 2012; Langley et al 2012), and we use genotypic data to investigate why these assignments differ
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