Background: 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. Therefore, the exploration of selection signals on sex chromosomes has important biological significance.
Results: In this study, we used the Cross Population Extend Haplotype Homozygosity Test (XPEHH), F-statistics (Fst) and EigenGWAS to assess selection footprints on the Z chromosome in 474 broiler chickens via Illumina chicken 60K SNP chips. SNP genotype data were downloaded from publicly available resources. We identified 35 selection regions, amongst which 1, 9 and 27 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 219 candidate genes were located in 35 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, 198 candidate genes were expressed with 11 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.
Conclusions: We 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 signals.