Signatures of Selection in the Genomes of Commercial and Non-Commercial Chicken Breeds

Abstract

Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

“…The availability of genomic data that has been generated using genome-wide single nucleotide polymorphism (SNP) analyses and the comparison of genomic patterns of SNP variation between divergent breeds has successfully identified putative genomic regions and genes associated with differences in selection pressure in various livestock species including sheep (Kijas et al, 2012;Lv et al, 2014), Yak (Qiu et al, 2012), cattle (Xu et al, 2015) and chicken (Elferink et al, 2012).…”

Systematic differences in the response of genetic variation to pedigree and genome-based selection methods

“…When genome-wide marker panels are used for selection, it is possible to use these markers to investigate the dynamics of allelic diversity across the genome. Most methods developed for assessing the allelic diversity through genomic analysis are based on calculating population genetics statistics such as allele frequencies (either directly or indirectly) (Elferink et al, 2012) and linkage disequilibrium (LD) (Ennis, 2007). Previous studies have shown that frequencies of the favorable alleles, as well as alleles in neighboring regions, increase over time when a favorable mutation occurs in a population under selection (Smith and Haigh, 1974;Barton, 2000).…”

Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

“…Recently, population genomics studies, which search for genetic signatures of selection in the genome (Akey, 2009), have been conducted using high density SNPs genotyping and whole genome sequencing techniques in the livestock genome (e.g., Rubin et al, 2010;Elferink et al, 2012;Fan et al, 2013;Qanbari et al, 2015). This population genomics approach has allowed gene-level resolution mapping of loci that have been positively selected for, without any phenotypic information (Qanbari et al, 2014).…”