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Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium

Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium
Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium
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,
DRYAD
Pengelly, Reuben
af97c0c1-b568-415c-9f59-1823b65be76d
Gheyas, Almas A
a8e916b5-922c-4f61-ba2d-244d6759cc14
Kuo, Richard
dcebaf27-ae8e-442b-a4af-34a5e175c50f
Mossotto, Enrico
96f778af-f51a-464e-8e73-dfa24b4132de
Seaby, Eleanor G
f9011f96-bbc5-4364-970a-0f510489c539
Burt, David W
25cc154a-ea27-4540-b188-3c6943b6f905
Ennis, Sarah
7b57f188-9d91-4beb-b217-09856146f1e9
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Pengelly, Reuben
af97c0c1-b568-415c-9f59-1823b65be76d
Gheyas, Almas A
a8e916b5-922c-4f61-ba2d-244d6759cc14
Kuo, Richard
dcebaf27-ae8e-442b-a4af-34a5e175c50f
Mossotto, Enrico
96f778af-f51a-464e-8e73-dfa24b4132de
Seaby, Eleanor G
f9011f96-bbc5-4364-970a-0f510489c539
Burt, David W
25cc154a-ea27-4540-b188-3c6943b6f905
Ennis, Sarah
7b57f188-9d91-4beb-b217-09856146f1e9
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64

Gheyas, Almas A, Kuo, Richard and Burt, David W (2016) Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium. DRYAD doi:10.5061/dryad.48gp0 [Dataset]

Record type: Dataset

Abstract

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,

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More information

Published date: 1 January 2016

Identifiers

Local EPrints ID: 448417
URI: http://eprints.soton.ac.uk/id/eprint/448417
PURE UUID: f50d88a2-bc2f-4704-946c-0c6ab559b8a6
ORCID for Reuben Pengelly: ORCID iD orcid.org/0000-0001-7022-645X
ORCID for Enrico Mossotto: ORCID iD orcid.org/0000-0003-3996-3931
ORCID for Sarah Ennis: ORCID iD orcid.org/0000-0003-2648-0869
ORCID for Andrew Collins: ORCID iD orcid.org/0000-0001-7108-0771

Catalogue record

Date deposited: 22 Apr 2021 16:30
Last modified: 23 Apr 2021 01:43

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Contributors

Contributor: Reuben Pengelly ORCID iD
Creator: Almas A Gheyas
Creator: Richard Kuo
Contributor: Enrico Mossotto ORCID iD
Contributor: Eleanor G Seaby
Creator: David W Burt
Contributor: Sarah Ennis ORCID iD
Contributor: Andrew Collins ORCID iD

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