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

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.

Keywords: SNP chips; beagle dogs; genetic diversity; genetic structure; selection signals.

Figure 1

The number of SNPs per chromosome before and after quality control. The x-axis represents the chromosome number, while the y-axis indicates the number of SNPs. The white bars show the number of SNPs before quality control, while the black bars represent the SNPs retained after quality control.

Figure 2

The population structure of the Beagle dogs.

Figure 3

(A) Genetic relationship visualization based on the IBS distance matrix; (B) genetic relationship visualization based on the G matrix.

Figure 4

(A) The distribution of ROH quantity on each chromosome in Beagle dogs. (B) The distribution of ROH length in Beagle dogs. (C) The distribution of ROH sample numbers in Beagle dogs. The abscissa represents the length interval of ROH, and the ordinate represents the number of individuals. (D) The distribution of the inbreeding coefficient (F_ROH) based on ROH in Beagle dogs. The violin plot visualizes the data distribution, with the central white dot representing the median. The white box’s edges indicate the upper and lower quartiles.

Figure 5

Cluster analysis results for the stud Beagle dogs. The colors in the evolutionary tree are the male samples, and each color represents a family. The numbers in the colors represent the individual ear numbers of the Beagle dogs.

Figure 6

The distribution of positively selected regions on chromosomes in the Beagle population.

Figure 7

Gene ontology enrichment analysis of candidate genes in Beagle dogs (p < 0.01).

Figure 8

KEGG pathway enrichment analysis of candidate genes in Beagle dogs (p < 0.01).