Genetic base of baroque and working horse breeds

During the long period of human-horse co-habitation a wide variety of horse breeds has been developed in order to serve different needs of the human society. Today, more than 350 horse breeds represent a very valuable, very well sorted genetic pool, representing a blue print for a wide range of phenotypes within this species. In our project proposal we will focus on two baroque breeds, Lipizzan and Old Kladruber horse, and two working horse breeds from the mountain areas, Noriker and Bosnian mountain horse. The origin of both baroque breeds dates back to the 16th century and during the history of both breeds, there were some cases of exchanging genetic material among them. The working horse type will be represented in our study by two old breeds of different origin, both adapted to poor environmental conditions and hard work load. For the preservation of genetic diversity within endangered populations and for the detection of admixture between related breeds, reliable pedigree data is a very important tool. The reliability and completeness of pedigree data in different horse breeds varies significantly and comparison of population parameters based on pedigree and molecular data offers a powerful tool for assessing the quality of pedigrees. However, the application of molecular tools in horse population studies offers the possibility to reveal the population structure, genetic distances among populations, traces of inbreeding, selection signatures and functional characteristics of animal genome including structural variation and epigenetics. Different horse populations show significant genetic and phenotypic differences, including body size and type, working ability, gait, coat colour, and genetic diseases. The horse model differs significantly from other mammalian species in some characteristics. One example is the small number of major genes affecting body size, with four major genes which can explain about 80% of the phenotypic variance in this trait. However, differences in some phenotypic traits could not be explained only by mutations in coding regions of the genome. Therefore, we included in our project proposal two types of analysis which are still deficient in horse: estimation of phenotypic effects of the global methylation pattern and effects of copy number variation (CNV) in different genomic regions. Application of variety of bioinformatic approaches will allow us to identify specific methylation patterns and CNV regions with potential effects on phenotypic traits in selected four horse breeds.     The use of genetic material from four selected breeds will allow us to identify differences in population structure, signatures of selection and structural variation in these breeds. The fact that we have available archived biological material and phenotypic data from two breeding populations (Lipizzans and Kladruber) dating back to 1995 is a very special aspect of our project, that will allow us to analyze the differences that have occurred at the genetic as well as phenotypic level in these two horse breeds over the last 30 years. This unique genetic material and novel methodological approach including epigenetics and structural variation of the genome represent a significant added value to the project which will, for the first time, address also time component in the assessment of population parameters in Lipizzan and Old Kladruber horse.