Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium

Reuben J. Pengelly, Almas Gheyas, Richard Kuo, Enrico Mossotto, Eleanor G. Seaby, David Burt, Sarah Ennis, Andrew Collins

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Pages (from-to)375-382
Issue number5
Early online date6 Jul 2016
Publication statusE-pub ahead of print - 6 Jul 2016


  • Linkage disequilibrium
  • Gallus gallus
  • recombination hotspots

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