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)
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.
More information
Identifiers
Catalogue record
Export record
Altmetrics
Contributors
University divisions
- Faculties (pre 2018 reorg) > Faculty of Medicine (pre 2018 reorg) > Human Development & Health (pre 2018 reorg)
Current Faculties > Faculty of Medicine > Human Development and Health > Human Development & Health (pre 2018 reorg)
Human Development and Health > Human Development & Health (pre 2018 reorg) - Current Faculties > Faculty of Medicine > Human Development and Health > Human Genetics
Human Development and Health > Human Genetics - Current Faculties > Faculty of Medicine > Human Development and Health
Human Development and Health
Download statistics
Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.