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Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel.

Houle D, Márquez EJ - G3 (Bethesda) (2015)

Bottom Line: We make available the list of all highly correlated SNPs for use in association studies.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.Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32308 dhoule@bio.fsu.edu.

No MeSH data available.


Related in: MedlinePlus

Probability that a focal site is correlated at r2 > 0.5 with at least one other site in the genome as a function of location relative to inversions. Inversion sites lie between the breakpoints defined by Corbett-Detig et al. (2012), with the exception of the distal segment of chromosome 3R, which was treated as part of In(3R)Mo (Corbett-Detig and Hartl 2012).
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fig3: Probability that a focal site is correlated at r2 > 0.5 with at least one other site in the genome as a function of location relative to inversions. Inversion sites lie between the breakpoints defined by Corbett-Detig et al. (2012), with the exception of the distal segment of chromosome 3R, which was treated as part of In(3R)Mo (Corbett-Detig and Hartl 2012).

Mentions: Figure 3 shows the probability that a SNP is highly correlated with at least one other SNP. SNPs were classified as inside or outside the breakpoint of the three inversions fixed in more than four DGRP lines [In(2L)t, In(2R)NS, and In(3R)Mo]. For local disequilibrium, it makes little difference whether a SNP is in an inversion or not, but SNPs in inversions are more likely to be in high LD with a SNP that is distant (in the Standard gene order). The inversion karyotypes themselves have frequencies of 0.1 or less (see below), precluding SNPs characteristic of inversions from being highly correlated with high MAF variants. More importantly, simply excluding SNPs within inversions does not appreciably reduce the likelihood that a variant will be highly correlated with at least some other SNPs, nor does it preclude those highly correlated SNPs from being distant.


Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel.

Houle D, Márquez EJ - G3 (Bethesda) (2015)

Probability that a focal site is correlated at r2 > 0.5 with at least one other site in the genome as a function of location relative to inversions. Inversion sites lie between the breakpoints defined by Corbett-Detig et al. (2012), with the exception of the distal segment of chromosome 3R, which was treated as part of In(3R)Mo (Corbett-Detig and Hartl 2012).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528326&req=5

fig3: Probability that a focal site is correlated at r2 > 0.5 with at least one other site in the genome as a function of location relative to inversions. Inversion sites lie between the breakpoints defined by Corbett-Detig et al. (2012), with the exception of the distal segment of chromosome 3R, which was treated as part of In(3R)Mo (Corbett-Detig and Hartl 2012).
Mentions: Figure 3 shows the probability that a SNP is highly correlated with at least one other SNP. SNPs were classified as inside or outside the breakpoint of the three inversions fixed in more than four DGRP lines [In(2L)t, In(2R)NS, and In(3R)Mo]. For local disequilibrium, it makes little difference whether a SNP is in an inversion or not, but SNPs in inversions are more likely to be in high LD with a SNP that is distant (in the Standard gene order). The inversion karyotypes themselves have frequencies of 0.1 or less (see below), precluding SNPs characteristic of inversions from being highly correlated with high MAF variants. More importantly, simply excluding SNPs within inversions does not appreciably reduce the likelihood that a variant will be highly correlated with at least some other SNPs, nor does it preclude those highly correlated SNPs from being distant.

Bottom Line: We make available the list of all highly correlated SNPs for use in association studies.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.Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32308 dhoule@bio.fsu.edu.

No MeSH data available.


Related in: MedlinePlus