Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds
International audience AbstractBackgroundThousands 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 b...
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ftunivnantes:oai:HAL:hal-02931480v1 2023-05-15T18:28:35+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 2020-12 https://hal.archives-ouvertes.fr/hal-02931480 https://hal.archives-ouvertes.fr/hal-02931480/document https://hal.archives-ouvertes.fr/hal-02931480/file/12711_2020_Article_571.pdf https://doi.org/10.1186/s12711-020-00571-5 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-020-00571-5 hal-02931480 https://hal.archives-ouvertes.fr/hal-02931480 https://hal.archives-ouvertes.fr/hal-02931480/document https://hal.archives-ouvertes.fr/hal-02931480/file/12711_2020_Article_571.pdf doi:10.1186/s12711-020-00571-5 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 0999-193X EISSN: 1297-9686 Genetics Selection Evolution https://hal.archives-ouvertes.fr/hal-02931480 Genetics Selection Evolution, BioMed Central, 2020, 52 (1), pp.52. ⟨10.1186/s12711-020-00571-5⟩ [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2020 ftunivnantes https://doi.org/10.1186/s12711-020-00571-5 2022-06-29T03:42:21Z International audience AbstractBackgroundThousands 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.ResultsFive 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).ConclusionsWe 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 ... Article in Journal/Newspaper Subarctic Université de Nantes: HAL-UNIV-NANTES Genetics Selection Evolution 52 1 |
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Open Polar |
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Université de Nantes: HAL-UNIV-NANTES |
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ftunivnantes |
language |
English |
topic |
[SDV]Life Sciences [q-bio] |
spellingShingle |
[SDV]Life Sciences [q-bio] 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 |
topic_facet |
[SDV]Life Sciences [q-bio] |
description |
International audience AbstractBackgroundThousands 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.ResultsFive 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).ConclusionsWe 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 ... |
format |
Article in Journal/Newspaper |
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 |
HAL CCSD |
publishDate |
2020 |
url |
https://hal.archives-ouvertes.fr/hal-02931480 https://hal.archives-ouvertes.fr/hal-02931480/document https://hal.archives-ouvertes.fr/hal-02931480/file/12711_2020_Article_571.pdf https://doi.org/10.1186/s12711-020-00571-5 |
genre |
Subarctic |
genre_facet |
Subarctic |
op_source |
ISSN: 0999-193X EISSN: 1297-9686 Genetics Selection Evolution https://hal.archives-ouvertes.fr/hal-02931480 Genetics Selection Evolution, BioMed Central, 2020, 52 (1), pp.52. ⟨10.1186/s12711-020-00571-5⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-020-00571-5 hal-02931480 https://hal.archives-ouvertes.fr/hal-02931480 https://hal.archives-ouvertes.fr/hal-02931480/document https://hal.archives-ouvertes.fr/hal-02931480/file/12711_2020_Article_571.pdf doi:10.1186/s12711-020-00571-5 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1186/s12711-020-00571-5 |
container_title |
Genetics Selection Evolution |
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52 |
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1 |
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1766211111261044736 |