Genomic inbreeding and selection signatures analyses in the Doberman Pinscher breed

The Doberman Pinscher population has undergone strong artificial selection for morphology and behavior, which can reduce genomic diversity and increase autozygosity. Here, we characterized the genome structure and identified selection signatures in Doberman Pinschers using complementary within- and between-population approaches. Genotypes from 3,226 Dobermans Dogs (Illumina CanineHD; 216,184 SNPs) provided by the Doberman Diversity Project were analyzed after purpose-specific quality control. Genomic inbreeding was quantified using four allele-frequency–based metrics and the runs of homozygosity (F ROH ) approach. Selection signatures were detected using intrapopulation (i.e., Runs of Homozygosity—ROH; Integrated Haplotype Score—iHS; and Number of Segregating Sites by Length—nSL) and interpopulation methods (i.e., Fixation Index—FST; Cross-Population Extended Haplotype Homozygosity—XP-EHH; and Cross-Population Number of Segregating Sites by Length—XP-nSL) comparing the Doberman Pinscher breed to Labrador Retriever (n=237). Dobermans showed high overall inbreeding, with a mean F ROH of 0.42 (range 0.22–0.68), whereas the allele-frequency–based inbreeding estimators had similar means (~0.04). The partitioning of the ROH indicated high contributions from medium-to-long ROHs, consistent with recent inbreeding. The ROH scans identified 39,512 SNPs in ROH islands (≥50% frequency across individuals), with notable concentrations on CFA2, CFA3, and CFA31. Haplotype-based scans identified 2,820 candidate iHS SNPs and 2,173 candidate nSL SNPs (|score|>2). A common set of 310 SNPs was shared among ROH, iHS, and nSL, mapping near 279 genes that were mostly enriched for developmental pathways, particularly neurodevelopment and neuron-related cellular components. Between breeds, 349 highly differentiated SNPs were detected by FST, while XP-EHH and XP-nSL highlighted more than 1,000 haplotype-based signals differentiating Doberman Pinschers from the Labrador Retriever reference population. A total of nine SNPs overlapped across FST, XP-EHH, and XP-nSL, which were located mainly on CFA8 (~59.48–60.61 Mb) near the KCNK10 , SPATA7 , PTPN21, NEGR1, and BTG1 genes. Functional annotations for some candidate genes, including BTG1 and KCNK10 , suggest possible links to cellular regulatory and cardiac-related biological processes; however, direct associations with Doberman disease phenotypes remain to be validated. Overall, the Doberman Pinscher breed exhibits high genome-wide autozygosity and levels of inbreeding. In addition, our results showed consistent, multi-method evidence of selection at loci associated with neurodevelopmental and regulatory pathways. These findings provide prioritized candidate regions for follow-up studies that integrate phenotypes relevant to breed health and performance.