National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.
Genes (Basel). 2020 Jul 20;11(7):823. doi: 10.3390/genes11070823.
The Tibet chicken () lives on the Qinghai-Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.
藏鸡（）生活在青藏高原上，能很好地适应缺氧环境。本研究旨在获得与藏鸡胚胎缺氧适应相关的候选基因。在本研究中，我们使用固定指数（Fst）和跨群体扩展单倍型纯合度（XPEHH）统计方法来检测藏鸡的正选择信号，并分析了来自胚胎肝脏和心脏的 RNA 测序数据，使用 HISAT、StringTie 和 Ballgown 分析在低氧条件下孵化的藏鸡和白来航鸡（一种低地鸡）胚胎之间的差异表达基因。通过选择信号分析和 RNA 测序分析筛选出的基因可以被视为鸡胚胎缺氧适应的候选基因。我们通过 XPEHH 筛选出 1772 个基因，通过 Fst 筛选出 601 个基因，在胚胎肝脏和心脏中分别获得 384 个和 353 个差异表达基因。在这些基因中，有 89 个被认为是鸡胚胎缺氧适应的候选基因。ARNT、AHR、GSTK1 和 FGFR1 可以被认为是最重要的候选基因。我们的研究结果为阐明藏鸡胚胎缺氧适应的分子机制提供了参考。
