The programme is dealing with the application of molecular genetic and immunological methods into basic research in the field of animal genetics. The programme consists of four main modules which allow rational exploitation of technical expertise and infrastructure of the research group. The module dealing with regulation of lactoprotein expression in the mammary gland we analyzed promoter regions of beta and kappa casein genes and tested functionality of putative transcription factor binding sites. The cell system for gene expression experiments was set up and numerous polymorphisms in the non coding region of both casein genes were identified. The most important result of this research module is sequencing of regulatory regions of beta and kappa casein genes in cattle and horse, cDNA sequences for alpha s1, beta and kappa casein in horse and identification of alternative splicing of mRNA for equine beta and kappa casein. We proposed a new model for co-transcriptional mRNA processing involving the qualitative effect of promoter sequence on selection of splicing sites. In the field of regulation of growth the effect of hg locus deletion has been characterized, we demonstrated association between PGC1 polymorphisms and growth and fattening parameters in pig and identified QTL for obesity in mouse. Within the biodiversity module the numerous molecular markers for salmonid species were developed, we elucidated relationships among salmonid populations in the Balkan region and discovered several autochtonous population for which we propose action plan for their preservation as significant evolutionary or management units (ESU, MU). We characterized autochtonous grayling population in the Northern Adria for which we propose working name Adriatic grayling. We also tried to explain the origin of trout, sporadically appearing in the Adriatic see as well as relationship among "archaic" trout species in the Neretva drainage, which occupied numerous researchers of salmonid species in the past. Molecular characterization of Lipizzan horse breed, which was performed in the frame of this programme was among the firs published analyses of pedigreed populations. Research on antigenic variation of avian mycoplasmas revealed complex mechanisms for the generation of antigenic variation, incuding large gene families, recombinations, gene conversion and switching mechanisms involved in the regulation of gene expression with the final goal to escape the host immune response. We described the structure of vlhA gene family in M. synoviae and numerous gene variants within the pMGA gene family in M. gallisepticum. These results explain molecular background of antigenic variation in avian mycoplasmas and open new possibilities for development of new diagnostic reagents and more efficient vaccines.