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Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium

Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium
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 that 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 hot spots, are enriched near CpG islands and transcription start sites (P<2.2 × 10?16), consistent with recent evidence described in finches, but concordance in hot spot 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.
0018-067X
375-382
Pengelly, Reuben
af97c0c1-b568-415c-9f59-1823b65be76d
Gheyas, Almas A.
a8e916b5-922c-4f61-ba2d-244d6759cc14
Kuo, Richard
dcebaf27-ae8e-442b-a4af-34a5e175c50f
Mossotto, Enrico
a2a572db-3e95-41c6-94f6-f1b019594372
Seaby, Eleanor G.
a7290ab8-98ea-4093-9aa7-641d319d6064
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
a2a572db-3e95-41c6-94f6-f1b019594372
Seaby, Eleanor G.
a7290ab8-98ea-4093-9aa7-641d319d6064
Burt, David W.
25cc154a-ea27-4540-b188-3c6943b6f905
Ennis, Sarah
7b57f188-9d91-4beb-b217-09856146f1e9
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64

Pengelly, Reuben, Gheyas, Almas A., Kuo, Richard, Mossotto, Enrico, Seaby, Eleanor G., Burt, David W., Ennis, Sarah and Collins, Andrew (2016) Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium. Heredity, 117 (5), 375-382. (doi:10.1038/hdy.2016.47). (PMID:27381324)

Record type: Article

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 that 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 hot spots, are enriched near CpG islands and transcription start sites (P<2.2 × 10?16), consistent with recent evidence described in finches, but concordance in hot spot 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.

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Pengelly et al chicken LD.pdf - Accepted Manuscript
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More information

Accepted/In Press date: 19 May 2016
e-pub ahead of print date: 6 July 2016
Published date: November 2016
Organisations: Human Development & Health

Identifiers

Local EPrints ID: 395382
URI: https://eprints.soton.ac.uk/id/eprint/395382
ISSN: 0018-067X
PURE UUID: b112c73a-8313-4326-9cd8-0ebe77ffa6a5
ORCID for Reuben Pengelly: ORCID iD orcid.org/0000-0001-7022-645X
ORCID for Sarah Ennis: ORCID iD orcid.org/0000-0003-2648-0869
ORCID for Andrew Collins: ORCID iD orcid.org/0000-0001-7108-0771

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Date deposited: 27 May 2016 13:56
Last modified: 19 Nov 2019 06:46

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