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Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

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
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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, 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.

Authors/Creators: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
Title:Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds
Year of publishing :2020
Volume:52
Article number:52
Number of Pages:15
Publisher:BMC
ISSN:0999-193X
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 402 Animal and Dairy Science > Animal and Dairy Science.
URN:NBN:urn:nbn:se:slu:epsilon-p-107938
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-107938
Additional ID:
Type of IDID
DOI10.1186/s12711-020-00571-5
ID Code:17762
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:08 Oct 2020 15:47
Metadata Last Modified:09 Oct 2020 11:52

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