Whole-genome resequencing reveals loci under selection during chicken domestication

Abstract

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.

Is evolution of domestication driven by tameness? A selective review with focus on chickens

“…Previously, comprehensive analyses of genetic sweeps (genomic regions associated with selection) have identified a large number of genomic regions that have been under selection during chicken domestication (Rubin et al, 2010). These and other studies strongly indicate that the main selection responses affect regulatory regions (for example, promoters and enhancers) rather than protein-coding sequences.…”

Haplotype-phased synthetic long reads from short-read sequencing

“…Although it may be that GC-rich regions of the genomes are underrepresented in the synthetic reads, we did not detect GC bias in the synthetic reads relative to the overall GC content of the genome (S7 Fig). We further evaluated the accuracy of our method with genomic DNA isolated from higher organisms with well-developed draft genome assemblies. From Gallus gallus (chicken) genomic DNA [24], we collected 103,601,271 paired-end 150-bp reads (S1 Table), from which we assembled 125,203 synthetic reads longer than 1 kb, with an N50 length of 2.0 kb. The length distribution (S8 Fig) and low N50 length relative to the shearing length indicate that this library was under-sequenced, and additional sequencing would yield longer synthetic reads.…”

Regional issues on animal genetic resources: trends, policies and networking in Europe

“…This would provide new possibilities to reveal how domestication and selection have affected the genomes. The approach has been recently used in chicken (Rubin et al, 2010).…”