HESTEFORSK H-21-47-653 Genomic Characterization as a Tool Towards Sustainable Breeding of Nordic Native Horse Breeds

The aim of the project is to characterize genomic diversity and inbreeding, within and between Nordic native horse breeds, with special focus on the Norwegian and Swedish breeds. For this we will use whole genome sequencing of individual and pooled DNA samples. Genomic characterization is an essential first step in describing standing genetic variation within breeds to be preserved, and unique variation between breeds. It can further provide knowledge about genomic regions with unique characteristics and diversity, as well as genomic regions where breeds lack variation and are completely inbred. Plans for necessary administration and collection of samples were developed, with regular online meetings in the project group. An ethical permits for collection of blood samples has been granted. Pedigree information has been used to identify horses for DNA sampling. The sequencing been completed on a of total 190 samples and of these 187 samples gave sequence data of high quality, and 3 of lower quality. In addition, the pooled and individual sequence data from a previous project that were mentioned in the application has been retrieved. Bioinformatics is at present applied to the sequence data to ensure quality and to provide manageable data for further analysis of genetic diversity and relationships. Two different reference genomes will be utilized for this. We have started with the “standard” EquCab3 that was based on a Thoroughbred which is needed in order to be able to compare our data with data from other breeds. For comparison we have access to a new reference genome based on a Finnhorse, through collaboration with Juha Kantanen. The purpose is to see if the latter gives a better result for the Nordic native horse breeds. Collaborations were already last year initiated with Danish (Bernt Guldbrandtsen and Anna Schönherz) and Icelandic (Heidrún Sigurdardottir) researchers to get access to genomic data from other Nordic breeds. Also, a MSc-project with a student from the Faroe Islands (Signa Kallsoy Joensen) has started in University of Copenhagen, in collaboration with us. She has got access to the raw sequence data for 10 Faroese ponies from our project and had performed initial analysis of these together with sequence data for some additional breeds from outside this project.

The aim of the project is to characterize genomic diversity and inbreeding, within and between Nordic native horse breeds, with special focus on the Norwegian and Swedish breeds. For this we will use whole genome sequencing of individual and pooled DNA samples. Genomic characterization is an essential first step in describing standing genetic variation within breeds to be preserved, and unique variation between breeds. It can further provide knowledge about genomic regions with unique characteristics and diversity, as well as genomic regions where breeds lack variation and are completely inbred. Therefore, this information can be utilized by breed associations to make well informed conservation and breeding plans. Our research also lays the foundation for further research leading to increased positive synergy in the horse sector.