ARS | Publication request: SNPs to Chips: Changing the paradigm of mapping and selection in cattle

Submitted to: Animal Breeding and Animal Genetic Resources Proceedings
Publication Type: Proceedings/Symposium
Publication Acceptance Date: November 27, 2007
Publication Date: December 5, 2007
Citation: Sonstegard, T.S., Liu, G., Matukumalli, L.K., Van Tassell, C.P. 2007. Snps to chips: changing the paradigm of mapping and selection in cattle. [abstracat].Animal Breeding and Animal Genetic Resources Proceedings.

Interpretive Summary: This paper presents an overview of the strategies that have been and currently are being used to develop tools for applied genomics in cattle. The long term goal of this research is to gain an understanding of the genetic component of phenotypic variation to facilitate stable changes in production, fertility and health through selection. This goal aligns completely with the application-based goal for genetic improvement in the U.S. dairy industry, which is to select animals based on DNA marker information in order to account for the substantial variation inherent in quantitative genetic approaches of selection. The economic value of research to the U.S. dairy industry stems from the potential of marker-assisted selection (MAS) to shorten generation intervals and reduce the cost of progeny testing by more accurately distinguishing animals with desired allele combinations for well-defined selection objectives. Further characterization of the genome will enhance research into MAS solutions, and will provide substantial information to other livestock researchers attempting to better understand how genetic variation affects phenotype.

Technical Abstract: The past 25 years of research on the cattle genome has focused on DNA marker based tools that can be applied to genetic improvement in cattle. However, the paradigm of marker assisted selection for complex traits has recently shifted from focusing on genetic variation contained in specific quantitative trait loci (QTL) regions to genome-wide information. This shift is due in part, to the availability of the draft sequence assembly of the bovine genome and corresponding resources for high throughput single nucleotide polymorphism (SNP) based genotyping on a genome-wide basis. Dense marker information applied directly to current industry breeding schemes promises to provide better accuracy of predictions of genetic merit; while enhancing heritability and reliability of these predictions through improved pedigree information. We present an overview of this paradigm shift with an emphasis on the development and use of a bovine 58K SNP chip, and also include discussion on additional genomic tools that will better characterize the structure and function of the bovine genome. Delivery of knowledge and tools like the 58K SNP chip to industry partners will facilitate genome-wide selection for immediate application to progeny test bulls; thus, changing the way the U.S. dairy industry practices selection for genetic improvement. The subsequent genome information generated from these applied efforts will also enhance both the detection of novel QTL for traits of importance to cattle and the development of tools that accelerate gene discovery.