100. Interpopulation Selection Signatures Between Doberman Pinschers and Labrador Retrievers Reveal Candidate Regions Associated with Breed-specific Differentiation.

Abstract Intense selective breeding has shaped the Doberman Pinscher into a genetically distinct breed with unique morphological and behavioral characteristics. Comparing Dobermans with Labrador Retrievers may help identify genomic regions underlying breed-specific differentiation. The objective of this study was to identify genomic regions associated with breed-specific differentiation and recent selection in Doberman Pinschers using Labrador Retrievers as a reference population. Genotypic data from 3,226 Doberman Pinschers were compared with 237 Labrador Retrievers using complementary allele frequency- and haplotype-based methods. After quality control and restriction to SNPs shared between breeds, two datasets were created: one for fixation index (FST) analysis, containing 47,688 SNPs, and another for cross-population haplotype analyses, containing 144,855 SNPs. Interpopulation signatures of selection were evaluated using FST, XP-EHH, and XP-nSL to detect loci showing strong population differentiation or extended haplotype patterns in Dobermans relative to Labradors. The FST analysis identified 349 highly differentiated markers distributed across all autosomes, with the greatest numbers observed on CFA11, CFA16, CFA3, and CFA2. Cross-population haplotype analyses detected 3,101 candidate SNPs with XP-EHH and 2,832 with XP-nSL. XP-EHH signals were detected on nearly all autosomes except CFA26 and CFA28, whereas XP-nSL signals were absent from CFA2, CFA23, CFA26, CFA28, and CFA36. Overlap among methods showed 10 markers shared between FST and XP-EHH, 8 between FST and XP-nSL, and 2,441 between XP-EHH and XP-nSL. Most importantly, 7 markers were consistently identified by all 3 methods, representing the strongest evidence of Doberman-specific selection relative to Labrador Retrievers. These 7 shared markers mapped to genomic regions containing 13 nearby genes, including 9 protein-coding genes and 4 long non-coding RNAs. Most shared signals were concentrated on CFA8, in a region harboring genes such as KCNK10, SPATA7, and PTPN21. Additional candidate regions were identified near ERMP1 on CFA1, NEGR1 on CFA6, and BTG1 on CFA15. These genes are involved in biological functions related to neuronal development, intracellular signaling, and cardiac physiology. In particular, NEGR1 has been associated with neurodevelopment and behavior, whereas KCNK10 is notable because ion-channel genes may be relevant to the known susceptibility of Dobermans to dilated cardiomyopathy. Overall, the comparison between Doberman Pinschers and Labrador Retrievers revealed a focused set of differentiated loci supported by multiple analytical approaches, highlighting candidate genomic regions that may contribute to breed-specific health, behavior, and morphology.