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 p...
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ftslunivuppsala:oai:pub.epsilon.slu.se:17762 2023-05-15T18:28:38+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 Khansefid, Majid Moghaddaszadeh-Ahrabi, Sima Parna, Nahid Davoudi, Pourya Javanmard, Arash 2020 application/pdf https://pub.epsilon.slu.se/17762/ https://pub.epsilon.slu.se/17762/1/ghoreishifar_sm_et_al_201008.pdf en eng eng https://pub.epsilon.slu.se/17762/1/ghoreishifar_sm_et_al_201008.pdf Ghoreishifar, Seyed Mohammad and Eriksson, Susanne and Johansson, Anna and Khansefid, Majid and Moghaddaszadeh-Ahrabi, Sima and Parna, Nahid and Davoudi, Pourya and Javanmard, Arash (2020). Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genetics Selection Evolution. 52 , 52 , 1-15 [Research article] Animal and Dairy Science Research article NonPeerReviewed info:eu-repo/semantics/article 2020 ftslunivuppsala 2022-01-09T19:15:26Z 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 statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses. Article in Journal/Newspaper Subarctic Swedish University of Agricultural Sciences (SLU): Epsilon Open Archive |
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Swedish University of Agricultural Sciences (SLU): Epsilon Open Archive |
op_collection_id |
ftslunivuppsala |
language |
English |
topic |
Animal and Dairy Science |
spellingShingle |
Animal and Dairy Science Ghoreishifar, Seyed Mohammad Eriksson, Susanne Johansson, Anna 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 |
Animal and Dairy Science |
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 statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses. |
format |
Article in Journal/Newspaper |
author |
Ghoreishifar, Seyed Mohammad Eriksson, Susanne Johansson, Anna Khansefid, Majid Moghaddaszadeh-Ahrabi, Sima Parna, Nahid Davoudi, Pourya Javanmard, Arash |
author_facet |
Ghoreishifar, Seyed Mohammad Eriksson, Susanne Johansson, Anna 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 |
publishDate |
2020 |
url |
https://pub.epsilon.slu.se/17762/ https://pub.epsilon.slu.se/17762/1/ghoreishifar_sm_et_al_201008.pdf |
genre |
Subarctic |
genre_facet |
Subarctic |
op_relation |
https://pub.epsilon.slu.se/17762/1/ghoreishifar_sm_et_al_201008.pdf Ghoreishifar, Seyed Mohammad and Eriksson, Susanne and Johansson, Anna and Khansefid, Majid and Moghaddaszadeh-Ahrabi, Sima and Parna, Nahid and Davoudi, Pourya and Javanmard, Arash (2020). Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genetics Selection Evolution. 52 , 52 , 1-15 [Research article] |
_version_ |
1766211172089987072 |