PDF(Pubmed)
Abstract：
Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.
摘要：
埃塞俄比亚大约有5200万只具有明显表型变异性的本地山羊，这是自然和人为选择的结果。这里,我们获得了三个埃塞俄比亚土著山羊种群的全基因组序列数据(阿拉伯，费拉塔,和Oromo）来自埃塞俄比亚西北部，并分析了它们的全基因组遗传多样性，人口结构,和选择的签名。我们纳入了其他四个埃塞俄比亚山羊种群的基因型数据(Abergelle，Keffa,Gumuz,和Woyto-Guji）和来自亚洲的山羊；欧洲；和东部，南方,西方,和北非调查三个埃塞俄比亚种群的遗传易感性，并进行比较基因组分析。遗传多样性分析表明，Fellata山羊表现出最低的杂合值（Ho=0.288±0.005，He=0.334±0.0001）。在阿拉伯山羊中观察到最高值（Ho=0.310±0.010，He=0.347±4.35e-05）。Fellata山羊的近交系数（FROH=0.137±0.016）高于阿拉伯人的0.105±0.030和奥罗莫山羊的0.112±0.034。这表明在未来的保护活动中应优先考虑Fellata山羊种群。Thethreegompopulationsshowedthemajority(jo63%)ofrunsof纯合性intheshort(100-150Kb)lengthcategory,说明古代近亲繁殖和/或小创始人的影响。种群关系和结构分析将埃塞俄比亚土著山羊分为两个缺乏系统地理结构的不同遗传簇。Arab,费拉塔,奥罗莫,Abergelle,Keffa代表了一个基因簇.Gumuz和Woyto-Guji形成了一个单独的簇，并与肯尼亚博兰山羊具有共同的遗传背景。全基因组选择特征分析确定了影响适应干旱和半干旱环境的163个基因的9个最强区域（HOXC12，HOXC13，HOXC4，HOXC6和HOXC9，MAPK8IP2）。免疫应答（IL18，TYK2，ICAM3，ADGRG1和ADGRG3），以及生产和繁殖（RARG和DNMT1）。我们的研究结果为深入了解半干旱热带环境中埃塞俄比亚土著山羊的遗传结构基础选择特征提供了见解，并为山羊遗传改良提供了有价值的信息。保护战略，全基因组关联研究，和标记辅助育种。
