<OL> <LI> Creation of sequence-ready bacterial artificial chromosome (BAC) contigs of the cattle and swine genomes.<LI> Creation of comparatively anchored whole-genome physical maps of the cattle and swine genomes. <LI> Targeted sequencing of chromosomal regions containing genes of economic importance to the livestock industry.
NON-TECHNICAL SUMMARY: In the new millennium, the demands of a rapidly growing world population will continue to put pressure on the U.S. animal agriculture industry. The industry must develop new products that create value within the agricultural system, and as a result, increase the profitability of agriculture and revitalize rural America. These challenges come at a time when many current agricultural technologies are being questioned, when key productivity enhancers (such as medicated feeds) are in jeopardy, and when waste management constrains the formation of economically viable units. At the same time, the safety of the food supply is in question because of the incidence of BSE (Mad Cow Disease) and foot and mouth disease in Europe as well as frequents outbreaks of food-borne pathogens here in the U.S. The Livestock Genome Sequencing Initiative directly addresses these major challenges. Results of this project to date have provided producers and the breeding industry with genetic tests to reduce the incidence of genetic and infectious diseases, to trace the origin of meat and dairy products, and to increase productivity and swine and cattle. These genomically-based tools thus provide for the sustainable and secure production of meat and dairy products for American consumers and world markets. A major challenge is to identify additional genes and the accompanying genetic mechanisms that are responsible for the economically important traits of food animal species. Only a few of the "low hanging fruit" have been harvested for direct application by the livestock industry. By using the complete DNA sequences of the human, mouse, cattle, and pig genomes, and by applying comparative genomics and other advanced technologies developed at Illinois, will be able to identify many more genes affecting economically important traits, probably faster than any other group in the world. To date, scientists at Illinois have been directly involved in the discovery and characterization of a significant share of the genes for production and disease traits. With the new tools and technologies for rapid, high throughput genotyping and sequencing, scientists at Illinois are uniquely positioned to move their discovery pipeline to the next level, and to deliver new technologies to producers and the private sector. Thus, the timing is right to continue down our productive path and to set the stage for the next wave of gene discovery. Our gene discovery pipeline will enable advanced DNA breeding strategies, phenotypic modifications through transgenesis, and development of novel pharmaceuticals for the animal agriculture sector. <P>APPROACH: Two bovine chromosomal regions have been selected for targeted resequencing. The first selected region is a 3.0 Mbp region on BTA3 that contains a QTL affecting milk yield and composition. Two known QTL heterozygous bulls will be resequenced in this region using the sequence capture method by NimbleGen. All newly identified SNPs will be converted to SNP assays (Sequenom) and used to genotype the offspring of the two QTL-heterozygous bulls and panel of dairy and beef animals. This information will be used to generate a multisite haplotype analysis that can be used directly for marker assisted selection. The second chromosomal region on BTA24 harbors a locus responsible for a condition referred to as Idiopathic Epilepsy (IE), a genetic defect recently described in the Hereford cattle. The cattle-human comparative map indicates that this region includes two homologous synteny blocks (HSBs) both on HSA18. Within these comparative segments, a total of 47 genes have been annotated in the human genome, most of which have complete or contiguous sequences in the current bovine genome assembly. Due to the extensive LD within the region surrounding the causative mutation, two approaches are plausible. First, we have identified 11 individuals within the resource population that in theory are only heterozygous for the molecular variation causing IE. Therefore, it would be feasible to capture and resequence all potential coding and regulatory sequences within this region for one or more of these selected individuals. Alternatively, resequencing of selected positional candidate genes within the region may be more economically efficient. Thus, we have prioritized each of these genes based on their putative function and/or tissue expression profiles (i.e., those with neuromuscular function or expressed in the CNS or skeletal muscle). This is expected to result in identification of the causative mutation and the development of a diagnostic assay for industry use. Targeted resequencing of the pig genome will be conducted for two regions, one contains a QTL responsible for lean muscle accretion on SSC6 and the second region on SSC2 encompasses two putative QTLs influencing pork tenderness. Continued refinement of these QTL positions will be accomplished by developing region-specific high density SNP panels for LD analysis within the Illinois Meat Quality Pedigree and other populations. This will be achieved by utilizing SNP information generated from a parallel genome-wide SNP discovery project. The completed genomic sequence will be used to identify all SNPs within these regions. Assays using the Illumina Golden Gate platform will be developed for all high quality SNPs within each region. Genotypes will be used to further refine the postion of each QTL. Once completed, two approaches may be used to identify the putative QTN. Capture and resequencing of these more highy refined regions within known QTL-heterozgous animals can be accomplished using the NimbleGen capture technology coupled with high-throughput sequencing. Alternatively, positional candidate genes within these regions may be selected for resequencing.