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Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array

BACKGROUND: Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the res...

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Autores principales: Fleming, D. S., Koltes, J. E., Markey, A. D., Schmidt, C. J., Ashwell, C. M., Rothschild, M. F., Persia, M. E., Reecy, J. M., Lamont, S. J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882793/
https://www.ncbi.nlm.nih.gov/pubmed/27230772
http://dx.doi.org/10.1186/s12864-016-2711-5
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author Fleming, D. S.
Koltes, J. E.
Markey, A. D.
Schmidt, C. J.
Ashwell, C. M.
Rothschild, M. F.
Persia, M. E.
Reecy, J. M.
Lamont, S. J.
author_facet Fleming, D. S.
Koltes, J. E.
Markey, A. D.
Schmidt, C. J.
Ashwell, C. M.
Rothschild, M. F.
Persia, M. E.
Reecy, J. M.
Lamont, S. J.
author_sort Fleming, D. S.
collection PubMed
description BACKGROUND: Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study’s goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments. RESULTS: Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0.15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions. CONCLUSIONS: The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2711-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-48827932016-05-28 Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array Fleming, D. S. Koltes, J. E. Markey, A. D. Schmidt, C. J. Ashwell, C. M. Rothschild, M. F. Persia, M. E. Reecy, J. M. Lamont, S. J. BMC Genomics Research Article BACKGROUND: Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study’s goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments. RESULTS: Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0.15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions. CONCLUSIONS: The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2711-5) contains supplementary material, which is available to authorized users. BioMed Central 2016-05-26 /pmc/articles/PMC4882793/ /pubmed/27230772 http://dx.doi.org/10.1186/s12864-016-2711-5 Text en © Fleming et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Fleming, D. S.
Koltes, J. E.
Markey, A. D.
Schmidt, C. J.
Ashwell, C. M.
Rothschild, M. F.
Persia, M. E.
Reecy, J. M.
Lamont, S. J.
Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array
title Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array
title_full Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array
title_fullStr Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array
title_full_unstemmed Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array
title_short Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array
title_sort genomic analysis of ugandan and rwandan chicken ecotypes using a 600 k genotyping array
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882793/
https://www.ncbi.nlm.nih.gov/pubmed/27230772
http://dx.doi.org/10.1186/s12864-016-2711-5
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