Animal Science Publications Animal Science 1-2019 Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions Muhammed Walugembe Iowa State University, [email protected] Francesca Bertolini Iowa State University Chandraratne Mahinda B. Dematawewa University of Peradeniya Matheus P. Reis São Paulo State University Ahmed R. Elbeltagy AFonilmloawl P thirodsu cationdn Raeddseaitrcionh Inalstit wutorke, Gsiza, at :Eghyttpps://lt ib.dr.iastate.edu/ans_pubs Part of the Agriculture Commons, Climate Commons, Genetics and Genomics Commons, and See next page for additional authors the Poultry or Avian Science Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ ans_pubs/457. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Animal Science at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Science Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions Abstract 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 ah pFLK 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. Keywords chickens, environment, selection signatures, adaptation, immune system Disciplines Agriculture | Animal Sciences | Climate | Genetics and Genomics | Poultry or Avian Science Comments This article is published as Walugembe, Muhammed, Francesca Bertolini, Chandraratne Mahinda Dematawewa, Matheus P. Reis, Ahmed R. Elbeltagy, Carl Joseph Schmidt, Susan J. Lamont, and Max F. Rothschild. "Detection of selection signatures among Brazilian, Sri Lankan, and Egyptian chicken populations under different environmental conditions." Frontiers in Genetics 9 (2018): 737. doi: 10.3389/ fgene.2018.00737. Creative Commons License This work is licensed under a Creative Commons Attribution 4.0 License. This article is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/ans_pubs/457 Authors Muhammed Walugembe, Francesca Bertolini, Chandraratne Mahinda B. Dematawewa, Matheus P. Reis, Ahmed R. Elbeltagy, Carl J. Schmidt, Susan J. Lamont, and Max F. Rothschild This article is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/ans_pubs/457 fgene-09-00737 January 9, 2019 Time: 19:8 # 1 ORIGINAL RESEARCH published: 14 January 2019 doi: 10.3389/fgene.2018.00737 Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions Muhammed Walugembe1*, Francesca Bertolini1, Chandraratne Mahinda B. Dematawewa2, Matheus P. Reis3, Ahmed R. Elbeltagy4, Carl J. Schmidt5, Susan J. Lamont1 and Max F. Rothschild1 1 Department of Animal Science, Iowa State University, Ames, IA, United States, 2 Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Kandy, Sri Lanka, 3 Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, Brazil, 4 Department of Animal Biotechnology, Animal Production Research Institute, Giza, Egypt, 5 Animal and Food Sciences, University of Delaware, Newark, DE, United States Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought Edited by: or excessive humidity, may result in reduced performance and reproduction and Peng Xu, Xiamen University, China could compromise the animal’s immune function. Animal survival within extreme Reviewed by: environmental conditions could be in response to natural selection and to artificial Yu Jiang, selection for production traits that over time together may leave selection signatures Northwest A&F University, China Keliang Wu, in the genome. The aim of this study was to identify selection signatures that may be China Agricultural University, China involved in the adaptation of indigenous chickens from two different climatic regions *Correspondence: (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived Muhammed Walugembe from human migration events to the generally tropical State of São Paulo, Brazil. [email protected] To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Specialty section: Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped This article was submitted to using the Affymetrix Axiom R 600k Chicken Genotyping Array. Pairwise Fst analyses Livestock Genomics, a section of the journal among countries did not detect major regions of divergence between chickens from Frontiers in Genetics Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically Received: 13 April 2018 related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected Accepted: 22 December 2018 Published: 14 January 2019 in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common Citation: regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses Walugembe M, Bertolini F, for the three separate countries suggested unique regions that are potentially under Dematawewa CMB, Reis MP, selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, Elbeltagy AR, Schmidt CJ, Lamont SJ and Rothschild MF (2019) Detection and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified of Selection Signatures Among regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different EOMES, and NFAT5 whose biological functions could provide insights in understanding Environmental Conditions. adaptation mechanisms in response to arid and tropical environments. Front. Genet. 9:737. doi: 10.3389/fgene.2018.00737 Keywords: chickens, environment, selection signatures, adaptation, immune system Frontiers in Genetics| www.frontiersin.org 1 January 2019| Volume 9| Article 737 fgene-09-00737 January 9, 2019 Time: 19:8 # 2 Walugembe et al. Environmental Selection Signatures in Chickens INTRODUCTION Fixation Index, Fst (Elferink et al., 2012; Gholami et al., 2015; Fleming et al., 2017) and hapFLK (Gholami et al., 2015) analyses Extreme environmental conditions are a major challenge to detect selection signatures in both commercial and non- in livestock production. Changes in climate, particularly commercial breeds. Inter-population statistics are reported to those that contribute to weather extremes like drought or have more statistical power to detect selection signatures in extreme temperatures or humidity may result in reduced recently diverged populations (Yi et al., 2010). The major concern performance, reproduction and could compromise the animal’s with Fst is that it assumes the populations have same effective immune function (St-Pierre et al., 2003). In chickens, extreme population size and are derived independently from one ancestral environmental temperatures lead to generation of reactive population (Price et al., 2010). HapFLK is a method that is oxygen species (ROS), causing oxidative stress and lipid based on extension of the FLK statistic and accounts for both peroxidation (Altan et al., 2003). However, chickens particularly the hierarchical structure and haplotype information, and its use the local (indigenous)