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Identification of selection signatures involved in performance traits in a paternal broiler line

BACKGROUND: Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting conti...

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Autores principales: Almeida, Octávio Augusto Costa, Moreira, Gabriel Costa Monteiro, Rezende, Fernanda Marcondes, Boschiero, Clarissa, de Oliveira Peixoto, Jane, Ibelli, Adriana Mercia Guaratini, Ledur, Mônica Corrêa, de Novais, Francisco José, Coutinho, Luiz Lehmann
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547531/
https://www.ncbi.nlm.nih.gov/pubmed/31159736
http://dx.doi.org/10.1186/s12864-019-5811-1
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author Almeida, Octávio Augusto Costa
Moreira, Gabriel Costa Monteiro
Rezende, Fernanda Marcondes
Boschiero, Clarissa
de Oliveira Peixoto, Jane
Ibelli, Adriana Mercia Guaratini
Ledur, Mônica Corrêa
de Novais, Francisco José
Coutinho, Luiz Lehmann
author_facet Almeida, Octávio Augusto Costa
Moreira, Gabriel Costa Monteiro
Rezende, Fernanda Marcondes
Boschiero, Clarissa
de Oliveira Peixoto, Jane
Ibelli, Adriana Mercia Guaratini
Ledur, Mônica Corrêa
de Novais, Francisco José
Coutinho, Luiz Lehmann
author_sort Almeida, Octávio Augusto Costa
collection PubMed
description BACKGROUND: Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (F(ST)) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and F(ST)-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. RESULTS: ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. F(ST)-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and F(ST) windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. CONCLUSIONS: Identification of ROH and F(ST)-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5811-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-65475312019-06-06 Identification of selection signatures involved in performance traits in a paternal broiler line Almeida, Octávio Augusto Costa Moreira, Gabriel Costa Monteiro Rezende, Fernanda Marcondes Boschiero, Clarissa de Oliveira Peixoto, Jane Ibelli, Adriana Mercia Guaratini Ledur, Mônica Corrêa de Novais, Francisco José Coutinho, Luiz Lehmann BMC Genomics Research Article BACKGROUND: Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (F(ST)) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and F(ST)-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. RESULTS: ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. F(ST)-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and F(ST) windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. CONCLUSIONS: Identification of ROH and F(ST)-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5811-1) contains supplementary material, which is available to authorized users. BioMed Central 2019-06-03 /pmc/articles/PMC6547531/ /pubmed/31159736 http://dx.doi.org/10.1186/s12864-019-5811-1 Text en © The Author(s). 2019 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
Almeida, Octávio Augusto Costa
Moreira, Gabriel Costa Monteiro
Rezende, Fernanda Marcondes
Boschiero, Clarissa
de Oliveira Peixoto, Jane
Ibelli, Adriana Mercia Guaratini
Ledur, Mônica Corrêa
de Novais, Francisco José
Coutinho, Luiz Lehmann
Identification of selection signatures involved in performance traits in a paternal broiler line
title Identification of selection signatures involved in performance traits in a paternal broiler line
title_full Identification of selection signatures involved in performance traits in a paternal broiler line
title_fullStr Identification of selection signatures involved in performance traits in a paternal broiler line
title_full_unstemmed Identification of selection signatures involved in performance traits in a paternal broiler line
title_short Identification of selection signatures involved in performance traits in a paternal broiler line
title_sort identification of selection signatures involved in performance traits in a paternal broiler line
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547531/
https://www.ncbi.nlm.nih.gov/pubmed/31159736
http://dx.doi.org/10.1186/s12864-019-5811-1
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