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This page was translated automatically using artificial intelligence (DeepL). The German version is binding. More information about automatic translation
Dogs have been by our side for thousands of years as hunting companions, herding and guard dogs, or members of the family. Thanks to intensive breeding, there are now hundreds of breeds with countless different characteristics. This makes it all the more fascinating that, in the case of some dog breeds, we do not know where or how they originated. The Old German Sheep Poodle, which is now increasingly bred as a family and therapy dog, is an excellent example of this. It is thought to originate from the East German lowlands [1], where it was primarily used as a herding dog. However, the exact origin of the Sheep Poodle remains unclear.
The aim of this study is to determine the genotype of a male Old German Sheepdog Poodle on the basis of DNA sequencing data, in order to subsequently compare it with the genotypes of other dogs and thus be able to place the Old German Sheepdog Poodle within the phylogenetic tree. The genotyping of organisms is often carried out using DNA microarrays, which determine the individual alleles of many different single nucleotide polymorphisms (SNPs) in an organism. In this method, the DNA of the individual under investigation is normally heavily fragmented and amplified. These fragments then bind to specifically designed probes, enabling the single-nucleotide polymorphisms to be analysed. One such array is the CanineHD BeadChip from Illumina, which has already been used to determine the genotypes of a wide variety of breeds, and these genotypes are available online. The BeadChip analyses over 170,000 single nucleotide polymorphisms, which are evenly distributed across the canine genome. To obtain a comparable genotype for the male sheep poodle under investigation based solely on sequencing data, these probe sequences were used to search for matches in the sequencing reads via a global alignment. The respective bases located at the sites of the single-nucleotide polymorphisms were then recorded in order to ultimately determine the genotype.
The resulting genotype was used for comparison with 730 other canine genotypes from 130 different breeds. An identity-by-state (IBS) distance matrix was then calculated using PLINK [2] to construct a cladogram using PHYLIP [3]. The quality of the cladogram was validated using bootstrap analysis. Bootstrap analysis is a method in which the various variants of the genotype are shuffled at random, whereby variants may occur multiple times or not at all. The resulting shuffled genotypes are then used again for the distance matrix calculation and cladogram construction. A total of 100 bootstrap runs were carried out. In the resulting bootstrap cladogram, nodes with bootstrap values above 70 are marked with a yellow circle and those above 95 with a green circle. The bootstrap value indicates the number of times, in the bootstrap test, that the configuration to the right of the node was exactly the same. Values above 70 are considered significant [4]. Initial results show that the Old German Sheep Poodle could be reliably classified into a clade comprising many Italian and German dog breeds, although dogs from other regions are also represented. It has already been demonstrated that genotyping based on sequencing reads works very well and that a comparison with other dogs is possible. The quality of the method developed must now be validated in greater detail; for example, the same dog could be genotyped using the CanineHD BeadChip and sequencing reads, followed by a comparison of the two resulting genotypes. Furthermore, it is necessary to include further dogs in the analysis in order to be able to draw an accurate conclusion about the origin of the sheep poodle.
Anton Ulbricht began his Bachelor’s degree in ‘Biotechnology’ at Mittweida University of Applied Sciences in 2018. After successfully completing his degree, he continued his scientific training with a Master’s degree in ‘Genomic Biotechnology’. As part of his Master’s thesis, Anton Ulbricht is now investigating the genetics of the sheep poodle in collaboration with Professor Röbbe Wünschiers and Nils Schön. Alongside his studies, he volunteers as a breakdance coach with the ‘BrokenBeatCrew’ in Frankenberg/Sa..
Text: Anton Ulbricht
[1] M. Jennissen-Tibbe, ‘schafpudel.net’. schafpudel.de (accessed 15 February 2023).
[2] C. C. Chang, C. C. Chow, L. C. Tellier, S. Vattikuti, S. M. Purcell, and J. J. Lee, “Second-generation PLINK: rising to the challenge of larger and richer datasets”, GigaSci, vol. 4, no. 1, p. 7, Dec. 2015, doi: 10.1186/s13742-015-0047-8.
[3] J. Felsenstein, ‘PHYLIP: Phylogeny Inference Package. Version 3.2’, Cladistics, No. 5, pp. 164–166, Dec. 1989, doi: 10.1086/416571.
[4] D. M. Hillis and J. J. Bull, ‘An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis’, Systematic Biology, Vol. 42, No. 2, p. 182, June 1993, doi: 10.2307/2992540.