基于全基因组测序的藏鸡基因组选择信号分析。

Analysis of the Selection Signal of the Tibetan Black Chicken Genome Based on Whole-Genome Sequencing.

机构信息

Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China.

Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850009, China.

出版信息

Genes (Basel). 2023 Aug 24;14(9):1672. doi: 10.3390/genes14091672.

DOI:10.3390/genes14091672

PMID:37761812

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10531317/

Abstract

BACKGROUND

The Tibetan chicken has adapted well to high altitudes genetically after its long-term habitation in the plateau. In this study, we analyzed the selection signal of Tibetan black chickens (TBCs) and discovered genes associated with the characteristics of germplasm.

METHODS

Whole-genome sequencing (WGS) was used to identify the single-nucleotide polymorphism (SNP) markers and genetic structures in the genome of Tibetan black chickens. Further, we performed a comparative population genomics analysis between the genomic data obtained in this present study and the genomic data for five wild red jungle fowls (RJFs) accessed from the NCBI database (GenBank accession number PRJNA241474). Thereafter, the Fst and selections were used to identify genes under positive selection in the Tibetan black chicken genome.

RESULTS

A total of 9,490,690 SNPs were identified in the Tibetan black chickens. In addition, the results from the gene ontology (GO) analysis showed that 732 genes of TBCs were enriched in a total of 210 GO terms with specific molecular functions such as regulation of cellular catabolic process, the MAPK signaling pathway, regulation of ion transport, growth, morphogenesis and lung alveolus development which may provide a better mechanism to facilitate oxygen transport and utilization in TBCs. Moreover, the results from the KEGG analysis showed that 732 genes of the TBCs were significantly enriched in the calcium signaling pathway, circadian entrainment (, and ), oxytocin signaling pathway and pathways of multiple neurodegeneration diseases. In addition, the CD86 antigen () was identified as a gene associated with the immune response in chickens. It was also revealed that genes such as , , and were discovered under selection in Tibetan black chickens on chromosome 23. These genes may be related to the local adaptive characteristics of Tibetan black chickens, for instance, and may be involved in the high-altitude adaption of oxygen delivery in Tibetan black chickens.

CONCLUSIONS

In summary, we found that selection mainly affects the disease resistance and cold acclimatization of Tibetan black chickens. Hence, these results may provide important genetic information for the evolution and breeding of Tibetan black chickens.

摘要

背景

藏鸡经过长期高原生活，在遗传上已经很好地适应了高海拔环境。本研究分析了藏鸡的选择信号，发现了与种质特征相关的基因。

方法

利用全基因组测序（WGS）技术识别藏鸡基因组中的单核苷酸多态性（SNP）标记和遗传结构。进一步，我们对本研究中获得的基因组数据与从 NCBI 数据库（GenBank 登录号 PRJNA241474）中获取的五个野生红原鸡（RJF）的基因组数据进行了比较种群基因组学分析。然后，使用 Fst 和选择来识别藏鸡基因组中受正选择影响的基因。

结果

在藏鸡中鉴定出了 9490690 个 SNP。此外，GO 分析结果表明，TBCs 的 732 个基因富集在总共 210 个 GO 术语中，具有特定的分子功能，如细胞分解代谢过程的调节、MAPK 信号通路、离子转运的调节、生长、形态发生和肺肺泡发育等，这可能为藏鸡提供更好的氧气运输和利用机制。此外，KEGG 分析结果表明，TBCs 的 732 个基因在钙信号通路、昼夜节律同步（、和）、催产素信号通路和多种神经退行性疾病途径中显著富集。此外，CD86 抗原（）被鉴定为与鸡的免疫反应相关的基因。还发现，藏鸡第 23 号染色体上的基因如、、和等受到选择。这些基因可能与藏鸡的局部适应特征有关，例如和可能参与藏鸡的氧气输送高原适应。