10.5061/DRYAD.48GP0
Pengelly, Reuben
University of Southampton
Gheyas, Almas A
Roslin Institute
Kuo, Richard
Mossotto, Enrico
University of Southampton
Seaby, Eleanor G
University of Southampton
Burt, David W
Roslin Institute
Ennis, Sarah
University of Southampton
Collins, Andrew
University of Southampton
Data from: Commercial chicken breeds exhibit highly divergent patterns of
linkage disequilibrium
Dryad
dataset
2016
Recombination Hotspot
Holocene
Gallus gallus
2016-05-23T16:53:55Z
2016-05-23T16:53:55Z
en
https://doi.org/10.1038/hdy.2016.47
88193807 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The analysis of linkage disequilibrium (LD) underpins the development of
effective genotyping technologies, trait mapping and understanding of
biological mechanisms such as those driving recombination and the impact
of selection. We apply the Malécot-Morton model of LD to create additive
LD maps which describe the high-resolution LD landscape of commercial
chickens. We investigated LD in chickens (Gallus gallus) at the highest
resolution to date for broiler, white egg and brown egg layer commercial
lines. There is minimal concordance between breeds of fine scale LD
patterns (correlation coefficient < 0.21), and even between
discrete broiler lines. Regions of LD breakdown, which may align with
recombination hotspots, are enriched near CpG islands and transcription
start sites (p < 2.2x10-16), consistent with recent evidence
described in finches, but concordance in hotspot locations between
commercial breeds is only marginally greater than random. As in other
birds functional elements in the chicken genome are associated with
recombination, but, unlike evidence from other bird species, the LD
landscape is not stable in the populations studied. The development of
optimal genotyping panels for genome-led selection programmes will depend
on careful analysis of the LD structure of each line of interest. Further
study is required to fully elucidate the mechanisms underlying highly
divergent LD patterns found in commercial chickens.
Genotypes from three chicken breedsFiles contain in archive
Gallus_genotypes.zip contain genotype data from Pengelly et al, 2016.
'Commercial chicken breeds exhibit highly divergent patterns of
linkage disequilibrium'. The three breed types are in separate file:
WEL - white egg layers, BEL - brown egg layers, BRO - broilers. Genotypes
have been QCed, providing SNPs with an allele frequency > 5%, HWE p
> 0.001, and having 95% genotyping rate accross the breed. Genotype
data are provided in the PLINK format, see
http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml for further details
including file format specifications.Gallus_genotypes.zip