Laboratory of Animal Genomics is devoted to analysis of genomes and gene mapping in farm animals with the aim: (1) to understand the organization, action and interaction of genes controlling economically important traits and disease resistance, (2) to disect QTLs to individual Mendelistically inherited traits and enable their use in marker assisted selection, (3) to isolate for study or manipulation important genes by ”reverse genetics”, (4) to study genomic organization and evolutionary relationships of the studied species and other mammals, and (5) to develop animal models (especially porcine) of human disease.
In the nineties broad international collaboration on mapping and genome analyses of main farm animal species has been established, with the perspective to use the knowledge from gene mapping for QTL mapping and MAS. More than 20 laboratories (from Europe, USA, Japan) participated in the construction of the gene (linkage) maps of the pig. The present linkage map encompasses more than 2000 polymorphic loci, mainly microsatelites. Cytogenetic and radiation hybrid (RH) maps of the pig have also been established. Both the linkage map, cytogenetic and RH map are accessible on Internet.
For QTL mapping two approaches have been used – interval mapping and the study of candidate genes. Several studies performed on the porcine three-generation pedigrees revealed QTLs for various economically important traits on chromosomes 1, 2, 3, 4, 6, 7, 8, 13 and X. Of candidate genes with effects on economically important traits, RYR1, FABP3, FABP4, ESR and FUT1 are well known.
For a long time we have been involved in an international endeavour on the porcine linkage and QTL mapping in pigs. In collaboration with the Hohenheim University (Professor Geldermann) we have participated in the construction of the linkage map as well as cytogenetic map. By using RISH, FISH, somatic hybrid pannel and RH panel we have mapped numerous genes. During collaboration on QTL mapping we detected QTL intervals on several chromosomes for some carcass traits as well as traits of meat quality. New results have been obtained during studies of selected candidate genes (identification of new genes, finding polymorphism, linkage cytogenetic and RH mapping, analysis of partial or complete genomic organization and structure, association studies). The greatest attention has been paid to the analyses of genes in QTL regions on chromosomes 4 and X.
Main methodologies used in our laboratory involve various techniques – PCR, PCR-RFLP, DGGE, cloning and subcloning in plasmids, the use of lambda phage porcine genomic and liver cDNA libraries, Southern hybridization, sequencing, analysis of microsatellites, RISH, FISH, etc.
For the detailed study of QTL regions some other approaches will also be used, if needed (analysis of BAC clones and microdisection of chromosomes - in collaboration).
It is expected that in animal genetics, after QTLs are reliably mapped, positional cloning of selected important QTLs will be realized, as well as sequencing of chromosome regions with QTLs (similarly as it is being done with SLA region of the porcine chromosome 7), and finally, sequencing of whole genomes of main farm animal species, followed by functional analysis, will be accomplished.
Studies pertaining to functional genomics are realized as well, namely analysis of ESTs (expressed sequence tags) from cDNA libraries of selected tissues of the studied organism. The study covers gene identification, mapping, cloning and annotation of the cDNA and genomic sequences. It should be realized during EST studies that not only are numerous genes expressed differently in different tissues, but there are also differences between the same tissues of various developmental stages of an organism. Methodologies suitable to study these problems are employed (suppressive subtraction, differential display etc.).
The laboratories are well equipped for the study of molecular-genetics problems (equipment for PCR, electrophoreses in agarose gel and polyacrylamide gel, DGGE, laminar box, orbital shaker, sequencer ALFexpress, vacugene, spectrophotometer, radiobiology laboratory, and in collaboration equipment for RISH, FISH and equipment for microdissection of chromosomes, etc.).