Reindeer Population genomics
Juha Kantanen from the Natural Resources Institute of Finland studies population genomics and works towards the conservation of rare and endangered animal breeds in agriculture. His recent work involved studying the genetic background of reindeer in the Arctic regions and Siberia. Together with his colleagues, they collected blood and tissue samples of wild and domesticated reindeer and then subcontracted the sequencing work to an international bioinformatics service provider. Juha’s team would normally perform the vast majority of analyses themselves but in this particular project they realised that they could benefit from an extra set of hands.
We simply provided the data and a description of the analyses required and received the results in virtually no time. I especially appreciated the quality and the level of detail in the final report. It has made it much easier to write the manuscript with the complete set of information needed.
At Genevia, the dedicated team of bioinformaticians identified genetic relationships between reindeer subspecies and ecotypes by using SNP information. We first derived a set of variants for all the animals and studied the genetic relationships between the animals sequenced. PCA analysis allowed to identify separate populations of reindeer. To define evolutionary relationships between the populations, we built a phylogenetic tree and derived the population diversity statistics. Additionally, a demographic history analysis was run on selected individuals. As a result of this work, the research team received the complete set of the data generated, publication-grade result figures, and the final report with a detailed description of the work.
The comprehensive analyses allowed Juha’s team to make an unexpected finding. Namely, they identified that domesticated and wild forest reindeer in Finland, despite being closely related, can be genetically distinguished. Even though the manuscript with the findings has yet to be completed, the data has already resulted in real-world implications. The SNP information is now used to ensure that any forest reindeer released into nature represents a wild genotype. In the future, Juha’s team and their Canadian collaborators plan to standardize identifications and facilitate reindeer research. Furthermore, with the SNP data in hand, they are currently in the process of developing a first-in-class commercial reindeer SNP microarray.
Read Juha's experiences with supplying his own bioinformatics team with external support here.