Abstract
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.
Highlights
Goats (Capra hircus) are one of the first ruminant animals to be domesticated around 10,000 to 9900 years ago (Zeder and Hesse, 2000) at the dawn of the Neolithic period in the Fertile Crescent
Among the five goat populations, we identified 13,061,914 unique single-nucleotide polymorphisms (SNPs) based on these stringent thresholds and used for detection of positive selection signature analysis
The largest number 12,229,657 of SNPs was detected in CH goat followed by the AB goat (11,137,576), which likely reflects a larger number of samples size
Summary
Goats (Capra hircus) are one of the first ruminant animals to be domesticated around 10,000 to 9900 years ago (Zeder and Hesse, 2000) at the dawn of the Neolithic period in the Fertile Crescent They were subsequently dispersed across the continents, adapting themselves to diverse biophysical and production environments. The country is home for 30.2 million goats (CSA, 2017), with seven genetically characterized groups and 14 local phenotypically classified populations (Getinet, 2016) which are characterized by their unique adaptive ability, and different physical characteristics in terms of morphology, body size, coat colors, and other production traits (Hassen et al, 2012), this implies that natural selection has most probably played a key role in the adaptation of these populations under the diverse range of environments. Ethiopian indigenous goats are primarily used as a source of income, milk, meat, manure and many other sociocultural functions (Abegaz et al, 2013)
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