Research at USMARC characterizes genetic differences ranging from DNA sequence differences through breed differences. These genetic differences arise by chance in the DNA sequence, by geographic isolation, by the mating restrictions of breed associations, by crossbreeding, and by natural and human imposed selection. Close cooperation with USMARC scientists from many disciplines results in comprehensive evaluations of genetic differences. Collaborations with researchers at other locations across the United States and internationally are used to advance the research.
Genomic scientists skilled in obtaining DNA sequence, identifying sequence differences, developing DNA markers, and determining genotypes have worked with computational biologists trained in comparison and analysis of very large collections of data to achieve significant successes. Until recent efforts to produce whole genome sequences for cattle and pigs, much of the publicly available DNA sequence for these species was developed at USMARC. Many QTL studies with cattle and pigs conducted worldwide use information from the linkage maps developed by USMARC and collaborators. A genetic marker for beef tenderness has been widely adopted by beef genomics companies and beef cattle breeders. A Gene Atlas was developed to identify what genes are being expressed in different tissues. New insights into genome organization, such as microRNA elements and copy number variants, are gained from whole genome sequence and are being evaluated in livestock. It is now feasible to obtain tens and hundreds of thousands of genotypes on a single animal from marker chips. These chips were used to quickly identify a defective mutation for marble bone disease and the affected breed is using a test based on these results to prevent the disease from propagating. Thousands of cattle and pigs at USMARC have been genotyped with these chips and associations with the genetic markers and prediction equations based on the genotypes have been released. The chips are being used to find associations in additional industry animals using a lower-cost method called pooling.
Geneticists skilled in quantitative genetics, experimental design, and statistics develop populations of animals that are measured for traits such as growth, efficiency of production, carcass, meat quality, reproduction, and indicators of health. Information is analyzed to estimate breed differences, heterosis, and heritabilities. Selected populations verify whether predicted selection responses are obtained and correlated changes in other traits are measured. Genomic scientists work with these populations to evaluate linkage and associations of traits with genetic markers. USMARC continues to be a premier source of information on breed differences and heterosis. In cattle, breed differences have been incorporated into across breed EPD adjustments increasing the impact of the research. Current research is expanding to include more direct connections to prominent industry sires. In sheep, emphasis is on easy-care maternal breeds and disease resistance. Selection experiments in pigs and cattle have emphasized selection for reproduction. Results have demonstrated that genetic change can be made even for traits with low heritabilities or genetic antagonisms. Current selection experiments incorporate genetic markers into breeding decisions to evaluate their potential contributions.