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Copy Number Variants in Two Northernmost Cattle Breeds Are Related to Their Adaptive Phenotypes

Buggiotti, Laura; Yudin, Nikolay S; Larkin, Denis M; (2022) Copy Number Variants in Two Northernmost Cattle Breeds Are Related to Their Adaptive Phenotypes. Genes , 13 (9) , Article 1595. 10.3390/genes13091595. Green open access

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Abstract

Copy number variations (CNVs) are genomic structural variants with potential functional and evolutionary effects on phenotypes. In this study, we report the identification and characterization of CNVs from the whole-genome resequencing data of two northernmost cattle breeds from Russia: the Yakut and Kholmogory cattle and their phylogenetically most related breeds, Hanwoo and Holstein, respectively. Comparisons of the CNV regions (CNVRs) among the breeds led to the identification of breed-specific CNVRs shared by cold-adapted Kholmogory and Yakut cattle. An investigation of their overlap with genes, regulatory domains, conserved non-coding elements (CNEs), enhancers, and quantitative trait loci (QTLs) was performed to further explore breed-specific biology and adaptations. We found CNVRs enriched for gene ontology terms related to adaptation to environments in both the Kholmogory and Yakut breeds and related to thermoregulation specifically in Yakut cattle. Interestingly, the latter has also been supported when exploring the enrichment of breed-specific CNVRs in the regulatory domains and enhancers, CNEs, and QTLs implying the potential contribution of CNVR to the Yakut and Kholmogory cattle breeds’ adaptation to a harsh environment.

Type: Article
Title: Copy Number Variants in Two Northernmost Cattle Breeds Are Related to Their Adaptive Phenotypes
Open access status: An open access version is available from UCL Discovery
DOI: 10.3390/genes13091595
Publisher version: https://doi.org/10.3390/genes13091595
Language: English
Additional information: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).
Keywords: CNV; cattle; cold adaptation
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/10155960
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