Abstract
BackgroundThe discovery of selection signatures has enabled the identification of genomics regions under selective pressure, enhancing knowledge of evolutionary genotype-phenotypes. Sex chromosomes play an important role in species formation and evolution. Therefore, the exploration of selection signatures on sex chromosomes has important biological significance.ResultsIn this study, we used the Cross Population Extend Haplotype Homozygosity Test (XPEHH), F-statistics (FST) and EigenGWAS to assess selection signatures on the Z chromosome in 474 broiler chickens via Illumina chicken 60 K SNP chips. SNP genotype data were downloaded from publicly available resources. We identified 17 selection regions, amongst which 1, 11 and 12 were identified by XPEHH, FST, and EigenGWAS, respectively. Each end of the Z chromosome appeared to undergo the highest levels of selection pressure. A total of 215 candidate genes were located in 17 selection regions, some of which mediated lipogenesis, fatty acid production, fat metabolism, and fat decomposition, including FGF10, ELOVL7, and IL6ST. Using abdominal adipose tissue expression data of the chickens, 187 candidate genes were expressed with 15 differentially expressed genes (DEGs) in fat vs. lean lines identified. Amongst the DEGs, VCAN was related to fat metabolism. GO pathway enrichment analysis and QTL annotations were performed to fully characterize the selection mechanism(s) of chicken abdominal fat content.ConclusionsWe have found some selection regions and candidate genes involving in fat metabolism on the Z chromosome. These findings enhance our understanding of sex chromosome selection signatures.
Highlights
The discovery of selection signatures has enabled the identification of genomics regions under selective pressure, enhancing knowledge of evolutionary genotype-phenotypes
Through the integration of gene microarrays in the adipose tissue of NEAUHLF populations, we investigated the expression profiles of the candidate genes on selection regions at 7 weeks of age
The majority of the identified selection regions were present on both ends of the Z chromosome, accounting for about 53%
Summary
The discovery of selection signatures has enabled the identification of genomics regions under selective pressure, enhancing knowledge of evolutionary genotype-phenotypes. Sex chromosomes play an important role in species formation and evolution. The exploration of selection signatures on sex chromosomes has important biological significance. With the availability of high-quality draft sequences of the chicken genome, high-density single nucleotide polymorphism (SNP) genotyping chips, and whole-genome re-sequencing technologies, the detection of selection signatures on the chicken genome have been reported. Rubin et al [4] identified the TSHR gene (thyroid stimulating hormone receptor) as a prominent selection signature in all domestic chickens. Boschiero et al [6] revealed more than 300 regions of selection with many important genes, including AKAP6, IGFBP2 and IGF1R, associated with fat deposition and muscle development
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