Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds
Abstract 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 ada...
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ftdoajarticles:oai:doaj.org/article:24e04c3fb8cc44a1a88a36ba7628b992 2023-05-15T18:28:37+02:00 Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds Seyed Mohammad Ghoreishifar Susanne Eriksson Anna M. Johansson Majid Khansefid Sima Moghaddaszadeh-Ahrabi Nahid Parna Pourya Davoudi Arash Javanmard 2020-09-01T00:00:00Z https://doi.org/10.1186/s12711-020-00571-5 https://doaj.org/article/24e04c3fb8cc44a1a88a36ba7628b992 DE EN FR ger eng fre BMC http://link.springer.com/article/10.1186/s12711-020-00571-5 https://doaj.org/toc/1297-9686 doi:10.1186/s12711-020-00571-5 1297-9686 https://doaj.org/article/24e04c3fb8cc44a1a88a36ba7628b992 Genetics Selection Evolution, Vol 52, Iss 1, Pp 1-15 (2020) Animal culture SF1-1100 Genetics QH426-470 article 2020 ftdoajarticles https://doi.org/10.1186/s12711-020-00571-5 2022-12-31T09:21:31Z Abstract 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, XKR 4, 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 ... Article in Journal/Newspaper Subarctic Directory of Open Access Journals: DOAJ Articles Genetics Selection Evolution 52 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
German English French |
topic |
Animal culture SF1-1100 Genetics QH426-470 |
spellingShingle |
Animal culture SF1-1100 Genetics QH426-470 Seyed Mohammad Ghoreishifar Susanne Eriksson Anna M. Johansson Majid Khansefid Sima Moghaddaszadeh-Ahrabi Nahid Parna Pourya Davoudi Arash Javanmard Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds |
topic_facet |
Animal culture SF1-1100 Genetics QH426-470 |
description |
Abstract 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, XKR 4, 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 ... |
format |
Article in Journal/Newspaper |
author |
Seyed Mohammad Ghoreishifar Susanne Eriksson Anna M. Johansson Majid Khansefid Sima Moghaddaszadeh-Ahrabi Nahid Parna Pourya Davoudi Arash Javanmard |
author_facet |
Seyed Mohammad Ghoreishifar Susanne Eriksson Anna M. Johansson Majid Khansefid Sima Moghaddaszadeh-Ahrabi Nahid Parna Pourya Davoudi Arash Javanmard |
author_sort |
Seyed Mohammad Ghoreishifar |
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 |
BMC |
publishDate |
2020 |
url |
https://doi.org/10.1186/s12711-020-00571-5 https://doaj.org/article/24e04c3fb8cc44a1a88a36ba7628b992 |
genre |
Subarctic |
genre_facet |
Subarctic |
op_source |
Genetics Selection Evolution, Vol 52, Iss 1, Pp 1-15 (2020) |
op_relation |
http://link.springer.com/article/10.1186/s12711-020-00571-5 https://doaj.org/toc/1297-9686 doi:10.1186/s12711-020-00571-5 1297-9686 https://doaj.org/article/24e04c3fb8cc44a1a88a36ba7628b992 |
op_doi |
https://doi.org/10.1186/s12711-020-00571-5 |
container_title |
Genetics Selection Evolution |
container_volume |
52 |
container_issue |
1 |
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1766211151916433408 |