An Analysis of the Genetic Diversity, Genetic Structure, and Selection Signal of Beagle Dogs Using SNP Chips

TL;DR

This study analyzes the genetic diversity and structure of Beagle dogs to support breeding strategies and conservation efforts.

Contribution

The study provides new insights into Beagle genetic diversity and identifies genes under selection using SNP chip data.

Findings

Beagle dogs show high genetic diversity with an average minor allele frequency of 0.224.

Selection signals were identified for genes related to muscle function and immune regulation.

Phylogenetic analysis grouped 106 stud dogs into 13 distinct lineages.

Abstract

Background: Beagle dogs are widely used in biomedical research, but their genetic diversity and population structure require further investigation. This study aimed to assess genetic diversity, population structure, and selection signals in a foundational Beagle breeding population using genome-wide SNP genotyping. Methods: A total of 459 Beagle dogs (108 males, 351 females) were genotyped using the Canine 50K SNP chip. After quality control, 456 individuals and 31,198 SNPs were retained. Genetic diversity indices, principal component analysis (PCA), identity-by-state (IBS) distance, a genomic relationship matrix (G-matrix), runs of homozygosity (ROH), and Tajima’s D selection scans were analyzed. Results: The average minor allele frequency was 0.224, observed heterozygosity was 0.303, and expected heterozygosity was 0.305. A total of 2990 ROH segments were detected, with a mean inbreeding coefficient of 0.031. Phylogenetic analysis classified 106 stud dogs into 13 lineages. Selection signal analysis identified TTN (muscle function) and DLA-DRA, DLA-DOA, DLA-DMA (immune regulation) under selection. Conclusions: The Beagle population exhibits high genetic diversity and low inbreeding. To maintain genetic stability and ensure the long-term conservation of genetic resources, structured breeding strategies should be implemented based on lineage classifications.

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