Abstract
Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, FST, is a useful index for evaluation of genetic differentiation between populations. The aim of this study was to detect selective signatures between different chicken groups based on SNP-wise FST calculation. A total of 96 individuals of three commercial layer breeds and 14 non-commercial fancy breeds were genotyped with three different 600K SNP-chips. After filtering a total of 1 million SNPs were available for FST calculation. Averages of FST values were calculated for overlapping windows. Comparisons of these were then conducted between commercial egg layers and non-commercial fancy breeds, as well as between white egg layers and brown egg layers. Comparing non-commercial and commercial breeds resulted in the detection of 630 selective signatures, while 656 selective signatures were detected in the comparison between the commercial egg-layer breeds. Annotation of selection signature regions revealed various genes corresponding to productions traits, for which layer breeds were selected. Among them were NCOA1, SREBF2 and RALGAPA1 associated with reproductive traits, broodiness and egg production. Furthermore, several of the detected genes were associated with growth and carcass traits, including POMC, PRKAB2, SPP1, IGF2, CAPN1, TGFb2 and IGFBP2. Our approach demonstrates that including different populations with a specific breeding history can provide a unique opportunity for a better understanding of farm animal selection.
Highlights
Charles Darwin suggested that the domestic chicken is descended from a single original species, the Red Jungle fowl (Gallus gallus), and that this happened in Southeast Asia nearly 10,000 years ago [1]
The commercial individuals from Lohmann Tierzucht GmbH originated from three breeds: One commercial white egg layer breed based on White Leghorn (WL) with three separate lines and two brown egg layer breeds based on White Rock (WR) and Rhode Island Red (RIR), respectively, with two separate lines per breed
The commercial white egg-layer breeds were separated by component 1 from brown egg-layers
Summary
Charles Darwin suggested that the domestic chicken is descended from a single original species, the Red Jungle fowl (Gallus gallus), and that this happened in Southeast Asia nearly 10,000 years ago [1]. Reduction or loss of nucleotide diversity at and near the selected locus caused by strong selection on desirable alleles is often referred to as genetic hitch-hiking or as a selective sweep [7]. Studying such signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selective pressure and can help in understanding important genotype-phenotype relationships. The discovery of a massive number of single nucleotide polymorphisms (SNPs) in the genomes of several species has enabled exploration of genome-wide signatures of selection via an assessment of variation in marker allele frequencies among populations [8]. Genes responsible for phenotypic differences between populations are expected to show large allele frequency differences [11]
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