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Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats

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.
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:
Type of IDID
DOI10.1111/eva.13118
Web of Science (WoS)000661497000001
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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