全基因组分析揭示了中国家猪对不同环境的独特适应特征。

IF 6.3 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Zhen Wang, Bangmin Song, Jianyu Yao, Xingzheng Li, Yan Zhang, Zhonglin Tang, Guoqiang Yi
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引用次数: 0

摘要

背景:长期的自然选择和人工选择在不同农业生态区域的猪种基因组中留下了许多遗传足迹。然而,这些特征有助于表型多样性和环境适应的机制仍不清楚:在这里,我们利用了来自热带、高海拔和寒带地区 6 个家猪品种 82 个个体的全基因组测序数据。种群遗传分析表明,栖息地隔离极大地影响了遗传多样性,并导致了中国地方猪种的种群分层。对选择信号的分析表明,在热带地区(55.5 Mb)、高海拔地区(43.6 Mb)和寒带地区(17.72 Mb)存在着适应性选择区域。选择扫描区域的潜在功能与某些可能在不同地理环境中发挥关键作用的复杂性状有关,包括寒冷环境中的脂肪覆盖率以及热带和高海拔环境中的血液指标。受选择的候选基因在涉及环境适应的生物通路中明显富集。这些途径包括适应热带环境的血液循环、蛋白质降解和炎症;适应高海拔环境的心肺发育、缺氧反应和DNA损伤修复;以及适应寒冷环境的产热、冷诱导血管舒张(CIVD)和细胞周期。通过研究选择特征的染色质状态,我们发现肺和回肠是环境适应的两个候选功能组织。最后,我们确定了ABCA1顺式调控区的一个突变(chr1: G246,175,129A)是适应热带环境的一个看似有希望的变异:本研究在全基因组范围内探讨了中国地方猪种对热带、高海拔和寒冷环境适应性的遗传机制。我们的研究结果揭示了顺式调控因子在猪环境适应中的突出作用,可作为人类高原相关疾病和心血管疾病的重要生物学模型。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs.

Background: Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.

Results: Here, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.

Conclusions: In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.

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CiteScore
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