Whole-genome resequencing reveals loci under selection during chicken domestication

By C. Rubin, M. Zody, J. Eriksson, J. Meadows, Ellen Sherwood, M. Webster, Lin Jiang, Max Ingman, Ted Sharpe, Sojeong Ka and 9 more. Nature, 2010

1,044 citations recorded by the source corpus.

Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.

Subfields: Animal Science and Zoology, Genetics

View Paper: https://www.semanticscholar.org/paper/c42c1891cd7e0283f7c5f061e50bb85c7dc2aa6e

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Citations in the corpus

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies (2014, background): “Recent studies searching for genes potentially under selection among populations relied on identifying the most common allele at polymorphic sites as well as alleles fixed within populations [38], which can be accomplished through consensus generation.”
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes (2011, background): “…Weiming He2,8, Guojie Zhang1,2,4, Xiaoming Zheng3,4, Fumin Zhang3, Yingrui Li2, Chang Yu2, Karsten Kristiansen2,9, Xiuqing Zhang2, Jian Wang2, Mark Wright10, Susan McCouch10, Rasmus Nielsen1,9,11, Jun Wang2,9 & Wen Wang1 Rice is a staple crop that has undergone substantial phenotypic and…”
Development and Application of High-density SNP Arrays in Genomic Studies of Domestic Animals (2010, neutral): “However, Rubin et al. (2010) using massively parallel sequencing identified a possible selective sweep resulting from domestication and specialization of broiler and layer birds and found one putative region including TSHR that was associated with metabolic regulation and photoperiod control of…”
A reference genome for common bean and genome-wide analysis of dual domestications (2014, neutral): “2012) or reduced heterozygosity (Rubin et al. 2010) among populations.”
The Evolution of Animal Domestication (2014, background): “…were homozygous for the sweep allele, the authors concluded that the TSHR locus may have played a crucial role during chicken domestication (Rubin et al. 2010) and may be a domestication gene. www.annualreviews.org • Evolution of Animal Domestication 129 A more recent study tested this…”