Genetics of adaptation in modern chicken.

Saber Qanbari,I Lehr Brisbin,Ruedi Fries,Henner Simianer,Carl-Johan Rubin,Andrew Townsend Peterson,Annett Weigend,Johannes Geibel,Khurram Maqbool,Leif Andersson,Susanne Kerje,Ruedi Preisinger,Christine Wurmser,Steffen Weigend

doi:10.1371/journal.pgen.1007989

Abstract

We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5×10−6). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding.

Highlights

The modern chicken (Gallus gallus domesticus) was domesticated from the red jungle fowl (RJF) [1], but with some contributions from at least one other closely related species, the grey jungle fowl [2]
Chickens were primarily domesticated from the red jungle fowl (Gallus gallus gallus), a bird that still runs wild in most of Southeast Asia
We performed whole genome sequencing of 127 chicken including the red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken

Summary

Introduction

The modern chicken (Gallus gallus domesticus) was domesticated from the red jungle fowl (RJF) [1], but with some contributions from at least one other closely related species, the grey jungle fowl [2]. Domestic chicken segregate into several hundreds of distinct breeds distributed across the world. Most modern commercial layers produce ~300 eggs in a year while the RJF usually lay a single clutch of 5–9 eggs per year. The commercial broiler and layer suppliers produce more than 70 billion birds annually to meet current worldwide consumer demands of more than 120 million tons of meat and over 1.2 trillion eggs [4]

Methods

Results

Conclusion