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Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds
BACKGROUND: The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left se...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9951459/ https://www.ncbi.nlm.nih.gov/pubmed/36829208 http://dx.doi.org/10.1186/s40104-022-00813-0 |
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author | Romanov, Michael N. Abdelmanova, Alexandra S. Fisinin, Vladimir I. Gladyr, Elena A. Volkova, Natalia A. Koshkina, Olga A. Rodionov, Andrey N. Vetokh, Anastasia N. Gusev, Igor V. Anshakov, Dmitry V. Stanishevskaya, Olga I. Dotsev, Arsen V. Griffin, Darren K. Zinovieva, Natalia A. |
author_facet | Romanov, Michael N. Abdelmanova, Alexandra S. Fisinin, Vladimir I. Gladyr, Elena A. Volkova, Natalia A. Koshkina, Olga A. Rodionov, Andrey N. Vetokh, Anastasia N. Gusev, Igor V. Anshakov, Dmitry V. Stanishevskaya, Olga I. Dotsev, Arsen V. Griffin, Darren K. Zinovieva, Natalia A. |
author_sort | Romanov, Michael N. |
collection | PubMed |
description | BACKGROUND: The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. RESULTS: Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) F(ST) based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). CONCLUSION: Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40104-022-00813-0. |
format | Online Article Text |
id | pubmed-9951459 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-99514592023-02-25 Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds Romanov, Michael N. Abdelmanova, Alexandra S. Fisinin, Vladimir I. Gladyr, Elena A. Volkova, Natalia A. Koshkina, Olga A. Rodionov, Andrey N. Vetokh, Anastasia N. Gusev, Igor V. Anshakov, Dmitry V. Stanishevskaya, Olga I. Dotsev, Arsen V. Griffin, Darren K. Zinovieva, Natalia A. J Anim Sci Biotechnol Research BACKGROUND: The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. RESULTS: Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) F(ST) based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). CONCLUSION: Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40104-022-00813-0. BioMed Central 2023-02-24 /pmc/articles/PMC9951459/ /pubmed/36829208 http://dx.doi.org/10.1186/s40104-022-00813-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://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 Romanov, Michael N. Abdelmanova, Alexandra S. Fisinin, Vladimir I. Gladyr, Elena A. Volkova, Natalia A. Koshkina, Olga A. Rodionov, Andrey N. Vetokh, Anastasia N. Gusev, Igor V. Anshakov, Dmitry V. Stanishevskaya, Olga I. Dotsev, Arsen V. Griffin, Darren K. Zinovieva, Natalia A. Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds |
title | Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds |
title_full | Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds |
title_fullStr | Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds |
title_full_unstemmed | Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds |
title_short | Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds |
title_sort | selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9951459/ https://www.ncbi.nlm.nih.gov/pubmed/36829208 http://dx.doi.org/10.1186/s40104-022-00813-0 |
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