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Dissecting selective signatures and candidate genes in grandparent lines subject to high selection pressure for broiler production and in a local Russian chicken breed of Ushanka

Romanov, Michael N., Shakhin, Alexey V., Abdelmanova, Alexandra S., Volkova, Natalia A., Efimov, Dmitry N., Fisinin, Vladimir I., Korshunova, Liudmila G., Anshakov, Dmitry V., Dotsev, Arsen V., Griffin, Darren K., and others. (2024) Dissecting selective signatures and candidate genes in grandparent lines subject to high selection pressure for broiler production and in a local Russian chicken breed of Ushanka. Genes, 15 (4). Article Number 524. E-ISSN 2073-4425. (doi:10.3390/genes15040524) (KAR id:105714)

Abstract

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

Item Type: Article
DOI/Identification number: 10.3390/genes15040524
Uncontrolled keywords: selection signatures; genomic regions; candidate genes; chicken; SNPs; White Cornish breed; Plymouth Rock White breed; Ushanka breed; genetic diversity; broiler production
Subjects: Q Science > QH Natural history > QH426 Genetics
S Agriculture > SF Animal culture
Divisions: Divisions > Division of Natural Sciences > Centre for Interdisciplinary Studies of Reproduction
Divisions > Division of Natural Sciences > Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Mike Romanov
Date Deposited: 23 Apr 2024 08:36 UTC
Last Modified: 09 May 2024 10:13 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/105714 (The current URI for this page, for reference purposes)

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