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Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data

BACKGROUND: The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing...

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Autores principales: Peripolli, Elisa, Reimer, Christian, Ha, Ngoc-Thuy, Geibel, Johannes, Machado, Marco Antonio, Panetto, João Cláudio do Carmo, do Egito, Andréa Alves, Baldi, Fernando, Simianer, Henner, da Silva, Marcos Vinícius Gualberto Barbosa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488563/
https://www.ncbi.nlm.nih.gov/pubmed/32917133
http://dx.doi.org/10.1186/s12864-020-07035-6
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author Peripolli, Elisa
Reimer, Christian
Ha, Ngoc-Thuy
Geibel, Johannes
Machado, Marco Antonio
Panetto, João Cláudio do Carmo
do Egito, Andréa Alves
Baldi, Fernando
Simianer, Henner
da Silva, Marcos Vinícius Gualberto Barbosa
author_facet Peripolli, Elisa
Reimer, Christian
Ha, Ngoc-Thuy
Geibel, Johannes
Machado, Marco Antonio
Panetto, João Cláudio do Carmo
do Egito, Andréa Alves
Baldi, Fernando
Simianer, Henner
da Silva, Marcos Vinícius Gualberto Barbosa
author_sort Peripolli, Elisa
collection PubMed
description BACKGROUND: The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. RESULTS: A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations’ historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. CONCLUSION: The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
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spelling pubmed-74885632020-09-16 Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data Peripolli, Elisa Reimer, Christian Ha, Ngoc-Thuy Geibel, Johannes Machado, Marco Antonio Panetto, João Cláudio do Carmo do Egito, Andréa Alves Baldi, Fernando Simianer, Henner da Silva, Marcos Vinícius Gualberto Barbosa BMC Genomics Research Article BACKGROUND: The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. RESULTS: A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations’ historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. CONCLUSION: The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions. BioMed Central 2020-09-11 /pmc/articles/PMC7488563/ /pubmed/32917133 http://dx.doi.org/10.1186/s12864-020-07035-6 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.
spellingShingle Research Article
Peripolli, Elisa
Reimer, Christian
Ha, Ngoc-Thuy
Geibel, Johannes
Machado, Marco Antonio
Panetto, João Cláudio do Carmo
do Egito, Andréa Alves
Baldi, Fernando
Simianer, Henner
da Silva, Marcos Vinícius Gualberto Barbosa
Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_full Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_fullStr Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_full_unstemmed Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_short Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
title_sort genome-wide detection of signatures of selection in indicine and brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488563/
https://www.ncbi.nlm.nih.gov/pubmed/32917133
http://dx.doi.org/10.1186/s12864-020-07035-6
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