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

• Published in: Genes Vol. 15; no. 4; p. 524
• Main Authors: 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., Zinovieva, Natalia A.
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 22.04.2024
• Subjects: Animals; artificial selection; Body weight; Breeding; chickens; Chickens - genetics; computer software; Fat metabolism; Females; Genes; Genetic diversity; Genetic engineering; Genetic markers; genome; Genomes; Genomics; Grandparents; humans; International economic relations; lipid metabolism; marker-assisted selection; Meat production; Muscles; phenotype; Plymouth Rock; Polymorphism, Single Nucleotide; Poultry; Poultry industry; poultry production; Quality control; Quantitative genetics; Quantitative Trait Loci; quantitative traits; Russia; selection pressure; Selection, Genetic; Single-nucleotide polymorphism; Software; Whole Genome Sequencing - methods; Russia; United Kingdom; Germany; Ukraine; United States > US; genetic diversity; chicken; Ushanka breed; genomic regions; Plymouth Rock White breed; White Cornish breed; candidate genes; broiler production; selection signatures; SNPs
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes15040524

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.