Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya; School of Life Sciences, University of Nottingham, University Park, Nottingham, UK; Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia; LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia; Animal and Veterinary Sciences, SRUC, The Roslin Institute Building, Midlothian, Edinburgh, UK.
Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan.
Genomics. 2022 Sep;114(5):110448. doi: 10.1016/j.ygeno.2022.110448. Epub 2022 Aug 12.
African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.
非洲绵羊表现出多样化但明显不同的生理解剖特征，这些特征是自然和人为选择的结果。在这里，我们从 150 只原产于东北非的绵羊基因组中生成了 3480 万个变体，这些基因组在 130 个样本（埃塞俄比亚、利比亚）中平均测序深度约为 54×，在 20 个样本（苏丹）中平均测序深度约为 20×。这些样本代表了来自不同环境、尾部形态和新石器时代后引入非洲的绵羊。系统发育和基于模型的混合分析提供了证据，证明有四个遗传群体对应于海拔地理位置、尾巴形态类型以及该物种可能的历史引入和在非洲大陆内部和之间的扩散。在更高水平的 K（6≤K≤25）上运行混合分析，揭示了基因组混合的隐蔽水平，以及一些群体中明显不同的遗传背景。比较基因组分析确定了选择的目标，这些目标跨越了重叠基因和基因家族簇的保守单倍型结构。这些与缺氧反应、耳朵形态、尾骨和尾巴骨骼长度以及尾巴脂肪储存结构有关。我们的研究结果为非洲本土绵羊的形态变异和对人为选择以及环境适应的反应提供了新的见解。
