Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds
BACKGROUND: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation...
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ftpubmed:oai:pubmedcentral.nih.gov:7487911 2023-05-15T18:28:33+02:00 Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds Ghoreishifar, Seyed Mohammad Eriksson, Susanne Johansson, Anna M. Khansefid, Majid Moghaddaszadeh-Ahrabi, Sima Parna, Nahid Davoudi, Pourya Javanmard, Arash 2020-09-04 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487911/ http://www.ncbi.nlm.nih.gov/pubmed/32887549 https://doi.org/10.1186/s12711-020-00571-5 en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487911/ http://www.ncbi.nlm.nih.gov/pubmed/32887549 http://dx.doi.org/10.1186/s12711-020-00571-5 © 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. CC0 PDM CC-BY Genet Sel Evol Research Article Text 2020 ftpubmed https://doi.org/10.1186/s12711-020-00571-5 2020-09-20T00:37:19Z BACKGROUND: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. RESULTS: Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). CONCLUSIONS: We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different ... Text Subarctic PubMed Central (PMC) Genetics Selection Evolution 52 1 |
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Research Article Ghoreishifar, Seyed Mohammad Eriksson, Susanne Johansson, Anna M. Khansefid, Majid Moghaddaszadeh-Ahrabi, Sima Parna, Nahid Davoudi, Pourya Javanmard, Arash Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds |
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Research Article |
description |
BACKGROUND: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. RESULTS: Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). CONCLUSIONS: We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different ... |
format |
Text |
author |
Ghoreishifar, Seyed Mohammad Eriksson, Susanne Johansson, Anna M. Khansefid, Majid Moghaddaszadeh-Ahrabi, Sima Parna, Nahid Davoudi, Pourya Javanmard, Arash |
author_facet |
Ghoreishifar, Seyed Mohammad Eriksson, Susanne Johansson, Anna M. Khansefid, Majid Moghaddaszadeh-Ahrabi, Sima Parna, Nahid Davoudi, Pourya Javanmard, Arash |
author_sort |
Ghoreishifar, Seyed Mohammad |
title |
Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds |
title_short |
Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds |
title_full |
Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds |
title_fullStr |
Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds |
title_full_unstemmed |
Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds |
title_sort |
signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five swedish cattle breeds |
publisher |
BioMed Central |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487911/ http://www.ncbi.nlm.nih.gov/pubmed/32887549 https://doi.org/10.1186/s12711-020-00571-5 |
genre |
Subarctic |
genre_facet |
Subarctic |
op_source |
Genet Sel Evol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487911/ http://www.ncbi.nlm.nih.gov/pubmed/32887549 http://dx.doi.org/10.1186/s12711-020-00571-5 |
op_rights |
© 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. |
op_rightsnorm |
CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s12711-020-00571-5 |
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Genetics Selection Evolution |
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52 |
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