Tarekegn, Getinet Mekuriaw and Khayatzadeh, Negar and Liu, Bin and Osama, Sarah and Haile, Aynalem and Rischkowsky, Barbara and Zhang, Wenguang and Tesfaye, Kassahun and Dessie, Tadelle and Mwai, Okeyo A. and Djikeng, Appolinaire and Mwacharo, Joram M.
(2021).
Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats.
Evolutionary applications. 14
, 1716-1731
[Research article]
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Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
Authors/Creators: | Tarekegn, Getinet Mekuriaw and Khayatzadeh, Negar and Liu, Bin and Osama, Sarah and Haile, Aynalem and Rischkowsky, Barbara and Zhang, Wenguang and Tesfaye, Kassahun and Dessie, Tadelle and Mwai, Okeyo A. and Djikeng, Appolinaire and Mwacharo, Joram M. | ||||||
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Title: | Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats | ||||||
Series Name/Journal: | Evolutionary applications | ||||||
Year of publishing : | 2021 | ||||||
Volume: | 14 | ||||||
Page range: | 1716-1731 | ||||||
Number of Pages: | 16 | ||||||
Publisher: | WILEY | ||||||
ISSN: | 1752-4571 | ||||||
Language: | English | ||||||
Publication Type: | Research article | ||||||
Article category: | Scientific peer reviewed | ||||||
Version: | Published version | ||||||
Copyright: | Creative Commons: Attribution 4.0 | ||||||
Full Text Status: | Public | ||||||
Subjects: | (A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Evolutionary Biology | ||||||
Keywords: | autozygosity, diversity, effective population size, genome dynamics, LD decay, runs of homozygosity, selection signatures | ||||||
URN:NBN: | urn:nbn:se:slu:epsilon-p-112578 | ||||||
Permanent URL: | http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112578 | ||||||
Additional ID: |
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ID Code: | 25003 | ||||||
Faculty: | VH - Faculty of Veterinary Medicine and Animal Science | ||||||
Department: | (VH) > Dept. of Animal Breeding and Genetics | ||||||
Deposited By: | SLUpub Connector | ||||||
Deposited On: | 24 Aug 2021 10:25 | ||||||
Metadata Last Modified: | 24 Aug 2021 10:31 |
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