PDF(Pubmed)
Abstract：
The wide distribution and diverse varieties of chickens make them important models for studying genetic adaptation. The aim of this study was to identify genes that alter heat adaptation in commercial chicken breeds by comparing genetic differences between tropical and cold-resistant chickens. We analyzed whole-genome resequencing data of 186 chickens across various regions in Asia, including the following breeds: Bian chickens (B), Dagu chickens (DG), Beijing-You chickens (BY), and Gallus gallus jabouillei from China; Gallus gallus murghi from India; Vietnam native chickens (VN); Thailand native chickens (TN) and Gallus gallus spadiceus from Thailand; and Indonesia native chickens (IN), Gallus gallus gallus, and Gallus gallus bankiva from Indonesia. In total, 5,454,765 SNPs were identified for further analyses. Population genetic structure analysis revealed that each local chicken breed had undergone independent evolution. Additionally, when K = 5, B, BY, and DG chickens shared a common ancestor and exhibited high levels of inbreeding, suggesting that northern cold-resistant chickens are likely the result of artificial selection. In contrast, the runs of homozygosity (ROH) and the ROH-based genomic inbreeding coefficient (FROH) results for IN, TN, and VN chickens showed low levels of inbreeding. Low population differentiation index values indicated low differentiation levels, suggesting low genetic diversity in tropical chickens, implying increased vulnerability to environmental changes, decreased adaptability, and disease resistance. Whole-genome selection sweep analysis revealed 69 candidate genes, including LGR4, G6PC, and NBR1, between tropical and cold-resistant chickens. The genes were further subjected to GO and KEGG enrichment analyses, revealing that most of the genes were primarily enriched in biological synthesis processes, metabolic processes, central nervous system development, ion transmembrane transport, and the Wnt signaling pathway. Our study identified heat adaptation genes and their functions in chickens that primarily affect chickens in high-temperature environments through metabolic pathways. These heat-resistance genes provide a theoretical basis for improving the heat-adaptation capacity of commercial chicken breeds.
摘要：
鸡的广泛分布和多样化的品种使其成为研究遗传适应的重要模型。这项研究的目的是通过比较热带和耐寒鸡之间的遗传差异来鉴定改变商业鸡品种热适应性的基因。我们分析了亚洲不同地区186只鸡的全基因组重测序数据，包括以下品种:边鸡(B)，大骨鸡(DG),北京优鸡(BY),来自中国的Gallusgallusjabouillei；来自印度的Gallusgallusmurghi；越南本地鸡（VN）；泰国本地鸡（TN）和泰国的Gallusgallusspadiceus；和印度尼西亚本地鸡（IN），Gallusgallusgallus,和来自印度尼西亚的GallusGallusBankiva.总的来说,5,454,765个SNP被鉴定用于进一步分析。种群遗传结构分析表明，每个地方鸡品种都经历了独立的进化。此外,当K=5,B,BY,和DG鸡有着共同的祖先，表现出高水平的近亲繁殖，这表明北方耐寒鸡很可能是人工选择的结果。相比之下,纯合性(ROH)和基于ROH的基因组近交系数(FROH)结果为IN，TN,VN鸡的近亲繁殖水平较低。低群体分化指数值表明低分化水平，表明热带鸡的遗传多样性低，意味着对环境变化的脆弱性增加，适应性下降，和抗病性。全基因组选择扫描分析揭示了69个候选基因，包括LGR4、G6PC、和NBR1，介于热带和耐寒鸡之间。这些基因进一步进行了GO和KEGG富集分析，揭示大多数基因主要富集在生物合成过程中，代谢过程，中枢神经系统发育，离子跨膜运输，和Wnt信号通路。我们的研究确定了鸡的热适应基因及其功能，这些基因主要通过代谢途径影响高温环境中的鸡。这些耐热性基因为提高商品化鸡种的热适应能力提供了理论依据。
