The main objective of this proposal is to sequence the whole mitochondrial genome (mtWGS) in 500 to 600 bulls or cows (440 to 540 belonging to Istrian cattle, Busha cattle, Slavonian-Syrmian Podolian cattle and Holstein population in Croatia) The goal is to: 1) identify polymorphic sites within the mtWGS in genetically small populations and analyse (confirm) the presence of selection for both the whole mitochondrial genome and for each individual gene (comparing non-synonymous with synonymous mutations); 2) identify potentially deleterious mutations and estimate the deleterious burden in all analysed populations; 3) develop a computational approach (a set of algorithms) to impute the sequenced mtWGS haplotypes for other members of the phylogenetic tree with a given probability, as well as highlight animals that are misassigned to the phylogenetic tree; 4.) identify mutations associated with phenotypic variability in milk production and fertility traits and estimate the magnitude of mtWGS effects (haplotypes) in terms of variance components; and 5.) identify private (specific) mutations that can be used for traceability or genetic barcoding of species and breeds (this is of particular interest for endangered populations). In conducting these comprehensive analyses, we will use newly developed high-throughput sequencing methods and complex computational analyses. We believe that this research will encourage other researchers involved in animal genetics and breeding in other species (dog, horse, pig, rabbit, etc.) to conduct similar research. Moreover, the results of the project will be used commercially in both cattle breeding and conservation management of endangered Croatian breeds. At the same time, we hope that the innovative and technologically advanced component of this research will lead to a good publication record for all scientists involved, which will further increase our competitiveness when applying for EU funded projects.
