Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.
BMC Genom Data. 2021 May 31;22(1):18. doi: 10.1186/s12863-021-00971-6.
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 signatures on sex chromosomes has important biological significance.
In this study, we used the Cross Population Extend Haplotype Homozygosity Test (XPEHH), F-statistics (F) 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, F, 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.
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 signatures.
选择信号的发现使人们能够识别受选择压力影响的基因组区域，从而增强了对进化基因型-表型的认识。性染色体在物种形成和进化中起着重要作用。因此，探索性染色体上的选择信号具有重要的生物学意义。
本研究使用交叉群体扩展单倍型纯合性检验（XPEHH）、F 统计量（F）和 EigenGWAS 方法，通过 Illumina 鸡 60K SNP 芯片评估了 474 只肉鸡 Z 染色体上的选择信号。SNP 基因型数据从公开资源下载。我们鉴定出了 17 个选择区域，其中 XPEHH、F 和 EigenGWAS 分别鉴定出 1、11 和 12 个选择区域。Z 染色体的每一端似乎都受到了最高水平的选择压力。17 个选择区域中共定位了 215 个候选基因，其中一些基因参与了脂肪生成、脂肪酸生成、脂肪代谢和脂肪分解，包括 FGF10、ELOVL7 和 IL6ST。使用肉鸡腹部脂肪组织的表达数据，在脂肪与瘦肉系中鉴定出 15 个差异表达基因（DEGs），187 个候选基因在其中表达。在这些 DEGs 中，VCAN 与脂肪代谢有关。进行了 GO 通路富集分析和 QTL 注释，以充分描述鸡腹部脂肪含量的选择机制。
我们在 Z 染色体上发现了一些与脂肪代谢有关的选择区域和候选基因。这些发现增强了我们对性染色体选择信号的理解。
