Cargando…

Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions

Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal’s immune function. Animal...

Descripción completa

Detalles Bibliográficos
Autores principales: Walugembe, Muhammed, Bertolini, Francesca, Dematawewa, Chandraratne Mahinda B., Reis, Matheus P., Elbeltagy, Ahmed R., Schmidt, Carl J., Lamont, Susan J., Rothschild, Max F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339939/
https://www.ncbi.nlm.nih.gov/pubmed/30693019
http://dx.doi.org/10.3389/fgene.2018.00737
_version_ 1783388715263983616
author Walugembe, Muhammed
Bertolini, Francesca
Dematawewa, Chandraratne Mahinda B.
Reis, Matheus P.
Elbeltagy, Ahmed R.
Schmidt, Carl J.
Lamont, Susan J.
Rothschild, Max F.
author_facet Walugembe, Muhammed
Bertolini, Francesca
Dematawewa, Chandraratne Mahinda B.
Reis, Matheus P.
Elbeltagy, Ahmed R.
Schmidt, Carl J.
Lamont, Susan J.
Rothschild, Max F.
author_sort Walugembe, Muhammed
collection PubMed
description Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal’s immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of São Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix Axiom(®)600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments.
format Online
Article
Text
id pubmed-6339939
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-63399392019-01-28 Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions Walugembe, Muhammed Bertolini, Francesca Dematawewa, Chandraratne Mahinda B. Reis, Matheus P. Elbeltagy, Ahmed R. Schmidt, Carl J. Lamont, Susan J. Rothschild, Max F. Front Genet Genetics Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal’s immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of São Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix Axiom(®)600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments. Frontiers Media S.A. 2019-01-14 /pmc/articles/PMC6339939/ /pubmed/30693019 http://dx.doi.org/10.3389/fgene.2018.00737 Text en Copyright © 2019 Walugembe, Bertolini, Dematawewa, Reis, Elbeltagy, Schmidt, Lamont and Rothschild. http://creativecommons.org/licenses/by/4.0/ 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.
spellingShingle Genetics
Walugembe, Muhammed
Bertolini, Francesca
Dematawewa, Chandraratne Mahinda B.
Reis, Matheus P.
Elbeltagy, Ahmed R.
Schmidt, Carl J.
Lamont, Susan J.
Rothschild, Max F.
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions
title Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions
title_full Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions
title_fullStr Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions
title_full_unstemmed Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions
title_short Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions
title_sort detection of selection signatures among brazilian, sri lankan, and egyptian chicken populations under different environmental conditions
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339939/
https://www.ncbi.nlm.nih.gov/pubmed/30693019
http://dx.doi.org/10.3389/fgene.2018.00737
work_keys_str_mv AT walugembemuhammed detectionofselectionsignaturesamongbraziliansrilankanandegyptianchickenpopulationsunderdifferentenvironmentalconditions
AT bertolinifrancesca detectionofselectionsignaturesamongbraziliansrilankanandegyptianchickenpopulationsunderdifferentenvironmentalconditions
AT dematawewachandraratnemahindab detectionofselectionsignaturesamongbraziliansrilankanandegyptianchickenpopulationsunderdifferentenvironmentalconditions
AT reismatheusp detectionofselectionsignaturesamongbraziliansrilankanandegyptianchickenpopulationsunderdifferentenvironmentalconditions
AT elbeltagyahmedr detectionofselectionsignaturesamongbraziliansrilankanandegyptianchickenpopulationsunderdifferentenvironmentalconditions
AT schmidtcarlj detectionofselectionsignaturesamongbraziliansrilankanandegyptianchickenpopulationsunderdifferentenvironmentalconditions
AT lamontsusanj detectionofselectionsignaturesamongbraziliansrilankanandegyptianchickenpopulationsunderdifferentenvironmentalconditions
AT rothschildmaxf detectionofselectionsignaturesamongbraziliansrilankanandegyptianchickenpopulationsunderdifferentenvironmentalconditions