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Evidence for and localization of proposed causative variants in cattle and pig genomes

Johnsson, Martin and Jungnickel, Melissa K. (2021). Evidence for and localization of proposed causative variants in cattle and pig genomes. Genetics Selection Evolution. 53 , 67
[Article Review/Survey]

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Abstract

Background This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. Results For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome. Conclusions Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.

Authors/Creators:Johnsson, Martin and Jungnickel, Melissa K.
Title:Evidence for and localization of proposed causative variants in cattle and pig genomes
Series Name/Journal:Genetics Selection Evolution
Year of publishing :2021
Volume:53
Article number:67
Number of Pages:18
Publisher:BMC
ISSN:0999-193X
Language:English
Publication Type:Article Review/Survey
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 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
URN:NBN:urn:nbn:se:slu:epsilon-p-113622
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113622
Additional ID:
Type of IDID
DOI10.1186/s12711-021-00662-x
Web of Science (WoS)000692787300001
ID Code:25373
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:17 Sep 2021 10:11
Metadata Last Modified:17 Sep 2021 10:21

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