Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations
Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations
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全基因组重测序揭示了与埃塞俄比亚本土山羊种群重要性状相关的选择特征
DOI：
10.3389/fgene.2019.01190
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发表时间：
2019-11-28
影响因子：
3.7
通讯作者：
Ma, Yuehui
中科院分区：
文献类型：
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作者：
Berihulay, Haile;Li, Yefang;Ma, Yuehui
埃塞俄比亚被认为是向非洲大陆引进包括山羊在内的牲畜品种的主要门户。埃塞俄比亚山羊具有独特的适应能力，在形态、体型、毛色等重要性状方面具有不同的物理特征。比较群体基因组分析提供了与重要性状相关的有用的基因组信息。对 44 只埃塞俄比亚本土山羊进行的全基因组重测序产生了 1600 万个单核苷酸多态性 (SNP) 以及 123,577 个插入和缺失。具体而言，在 Abergelle、Afar、Begait、Central Highland 和 Meafure 山羊群体中分别检测到 11,137,576、10,760,581、10,833,847、12,229,657 和 10,749,996 个推定 SNP。在这项研究中，我们使用了基于群体分化（FST）和混合杂合性（HP）C 的方法。从 FST 分析中，我们确定了 480 个异常值窗口。 HP 方法分别检测到 Abergelle 和 Begait 的 108 个异常值窗口和 205 个异常值窗口。对于与重要性状相关的两种方法来说，选择性信号下大约有 11 个和 5 个基因是常见的。经过基因组注释，我们发现了 41 个基因本体 (GO) 术语（12 个生物过程术语、8 个细胞成分术语和 11 个分子功能术语）和 10 个京都基因和基因组通路百科全书。一些候选基因与繁殖、体重、脂肪酸和疾病相关性状有关。我们的研究有助于提供有价值的遗传信息，并为设计保护策略、品种管理、遗传改良和利用计划铺平道路。研究中产生的基因组资源将为进一步研究提供机会。
Ethiopia is considered as the main gateway for the introduction of livestock species, including goat, to the African continent. Ethiopian goats are characterized by their unique adaptive ability, and different physical characteristics in terms of morphology, body size, coat colors, and other important traits. The comparative population genomic analysis provides useful genomic information associated with important traits. Whole-genome resequencing of 44 Ethiopian indigenous goats produced 16 million single-nucleotide polymorphisms (SNPs) as well as 123,577 insertions and deletions. Specifically, 11,137,576, 10,760,581, 10,833,847, 12,229,657 and 10,749,996 putative SNPs were detected in Abergelle, Afar, Begait, Central Highland and Meafure goat populations, respectively. In this study, we used population differentiation (FST) and pooled heterozygosity (HP) Cbased approaches. From the FST analysis, we identified 480 outlier windows. The HP approach detected 108 and 205 outlier windows for Abergelle, and Begait, respectively. About 11 and 5 genes under selective signals were common for both approaches that were associated with important traits. After genome annotation, we found 41 Gene ontology (GO) terms (12 in biological processes, 8 in cellular components and 11 in the molecular function) and 10 Kyoto Encyclopedia of Genes and Genomes pathways. Several of the candidate genes are involved in the reproduction, body weight, fatty acids, and disease related traits. Our investigation contributes to deliver valuable genetic information and paves the way to design conservation strategy, breed management, genetic improvement, and utilization programs. The genomic resources generated in the study will offer an opportunity for further investigations.