Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes

Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse...

Full description

Bibliographic Details
Main Authors: Ahmed R. Elbeltagy, Francesca Bertolini, Damarius S. Fleming, Angelica Van Goor, Chris M. Ashwell, Carl J. Schmidt, Donald R. Kugonza, Susan J. Lamont, Max. F. Rothschild
Format: Article
Language:English
Published: Frontiers Media S.A. 2019-05-01
Series:Frontiers in Genetics
Subjects:
Online Access:https://www.frontiersin.org/article/10.3389/fgene.2019.00376/full
_version_ 1828466394981728256
author Ahmed R. Elbeltagy
Ahmed R. Elbeltagy
Francesca Bertolini
Damarius S. Fleming
Damarius S. Fleming
Angelica Van Goor
Angelica Van Goor
Chris M. Ashwell
Carl J. Schmidt
Donald R. Kugonza
Susan J. Lamont
Max. F. Rothschild
author_facet Ahmed R. Elbeltagy
Ahmed R. Elbeltagy
Francesca Bertolini
Damarius S. Fleming
Damarius S. Fleming
Angelica Van Goor
Angelica Van Goor
Chris M. Ashwell
Carl J. Schmidt
Donald R. Kugonza
Susan J. Lamont
Max. F. Rothschild
author_sort Ahmed R. Elbeltagy
collection DOAJ
description Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations’ ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda–Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda–Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions.
first_indexed 2024-12-11T03:49:45Z
format Article
id doaj.art-8d9e3389af1b44e1a60b6341414aff7a
institution Directory Open Access Journal
issn 1664-8021
language English
last_indexed 2024-12-11T03:49:45Z
publishDate 2019-05-01
publisher Frontiers Media S.A.
record_format Article
series Frontiers in Genetics
spelling doaj.art-8d9e3389af1b44e1a60b6341414aff7a2022-12-22T01:21:55ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-05-011010.3389/fgene.2019.00376398644Natural Selection Footprints Among African Chicken Breeds and Village EcotypesAhmed R. Elbeltagy0Ahmed R. Elbeltagy1Francesca Bertolini2Damarius S. Fleming3Damarius S. Fleming4Angelica Van Goor5Angelica Van Goor6Chris M. Ashwell7Carl J. Schmidt8Donald R. Kugonza9Susan J. Lamont10Max. F. Rothschild11Department of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Biotechnology, Animal Production Research Institute, Giza, EgyptDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesVirus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesInstitute of Food Production and Sustainability, National Institute of Food and Agriculture, United States Department of Agriculture, Washington, DC, United StatesDepartment of Poultry Science, North Carolina State University, Raleigh, NC, United StatesDepartment of Animal and Food Sciences, University of Delaware, Newark, DE, United StatesDepartment of Agricultural Production, Makerere University, Kampala, UgandaDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesNatural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations’ ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda–Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda–Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions.https://www.frontiersin.org/article/10.3389/fgene.2019.00376/fullselection signaturesenvironmental stressesAfrican chickenFSTruns of homozygosity
spellingShingle Ahmed R. Elbeltagy
Ahmed R. Elbeltagy
Francesca Bertolini
Damarius S. Fleming
Damarius S. Fleming
Angelica Van Goor
Angelica Van Goor
Chris M. Ashwell
Carl J. Schmidt
Donald R. Kugonza
Susan J. Lamont
Max. F. Rothschild
Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes
Frontiers in Genetics
selection signatures
environmental stresses
African chicken
FST
runs of homozygosity
title Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes
title_full Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes
title_fullStr Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes
title_full_unstemmed Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes
title_short Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes
title_sort natural selection footprints among african chicken breeds and village ecotypes
topic selection signatures
environmental stresses
African chicken
FST
runs of homozygosity
url https://www.frontiersin.org/article/10.3389/fgene.2019.00376/full
work_keys_str_mv AT ahmedrelbeltagy naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT ahmedrelbeltagy naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT francescabertolini naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT damariussfleming naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT damariussfleming naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT angelicavangoor naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT angelicavangoor naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT chrismashwell naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT carljschmidt naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT donaldrkugonza naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT susanjlamont naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes
AT maxfrothschild naturalselectionfootprintsamongafricanchickenbreedsandvillageecotypes