London Swine Conference – Today’s Challenges… Tomorrow’s Opportunities 3-4 April 2007 53 NEW TOOLS TO MAKE GENETIC PROGRESS Jack Dekkers and Max Rothschild Department of Animal Science, Center of Integrated Animal Genomics Iowa State University 239 Kildee Hall, Ames, Iowa 50011 E-mail: jdekkers@iastate.edu or mfrothsc@iastate.edu ABSTRACT Advances in molecular genetics have opened opportunities to enhance strategies for genetic improvement of pigs by directly selecting on genes or chromosomal regions that harbor genes that affect traits of interest. In this paper, we review molecular technologies that have become available, the current state of the use of gene- or marker tests in pig breeding programs, and future prospects. The main conclusion is that, while current applications of molecular technology in selection are limited, recent developments in molecular genotyping technology will greatly accelerate the rate of implementation of molecular methods for pig breeding in the fore-seeable future. These developments include ongoing efforts to sequence the pig genome, availability of high-density genetic marker maps, and cost-effective high-throughput genotyping of large number of markers across the genome. These opportunities open great opportunities for more effective selection to enhance performance under commercial conditions. INTRODUCTION To date, most genetic progress for quantitative traits in pigs has been made by selection on phenotype or on estimates of breeding values (EBV) derived from phenotype, without knowledge of the number of genes that affect the trait or the effects of each gene. In this quantitative genetic approach to genetic improvement, the underlying genetic basis of traits has essentially been treated as a ‘black box’ (Figure 1a). Despite this, the substantial rates of genetic improvement that have been and continue to be achieved are clear evidence of the power of quantitative genetic approaches to selection. This success does, however, not mean that genetic progress could not be enhanced if we could gain insight into the black box of quantitative traits, in particular for traits that are currently difficult to improve. The latter include traits with low heritability (litter size, disease resistance), traits that are difficult to measure (disease resistance), traits that can only be measured on one sex (litter size), traits that are measured late in life (longevity), or traits that require the animal to be slaughtered (meat quality). By being able to study and assess the genetic make-up of individuals at the DNA level through genetic tests, molecular genetics has given us the tools to make those opportunities a reality (Figure 1b). Molecular data is of interest for use in genetic selection because gene tests have heritability equal to 1 (assuming no genotyping errors), can be done on both sexes and on all animals, can be done early in life, and may require the recording of less phenotypic data. The purpose of this paper is to review the current status and future prospects for the use of molecular genetic tools for genetic improvement. Although molecular