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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01190

Whole genome re-sequencing reveals selection signatures associated with important traits in Ethiopian indigenous goat populations

 Haile B. Gebreselasse1, 2*,  Li Yefang1, Berihu Gebrekidan3, Gebremedhin Gebreselassie1, Xuexue Liu1,  Lin Jiang1 and Ma Yuehui1
  • 1Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, China
  • 2Chinese Academy of Agricultural Sciences, China
  • 3College of Veterinary Medicine, Mekelle University, Ethiopia

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, 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 re-sequencing of 44 Ethiopian indigenous goats produced 16 million single-nucleotide polymorphisms (SNPs) as well as 123,577 insertions and deletions. Specially, 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) based 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 and 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.

Keywords: candidate genes, Capra Hircus, pooled heterozygosity, population differentiation, Positive selection signature

Received: 01 Mar 2019; Accepted: 28 Oct 2019.

Copyright: © 2019 Gebreselasse, Yefang, Gebrekidan, Gebreselassie, Liu, Jiang and Yuehui. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Haile B. Gebreselasse, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China, haile.berihulay@yahoo.com