ARS | Publication request: Overview of genomic selection in small populations of beef cattle

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: February 27, 2011
Publication Date: July 1, 2011
Citation: Bennett, G.L., Snelling, W.M., Thallman, R.M., Keele, J.W., Kuehn, L.A. 2011. Overview of genomic selection in small populations of beef cattle [abstract]. Journal of Animal Science Supplement. 89(E-Supplement 1):665. Abstract # 598.

Technical Abstract: Efficiency and reproduction are important to beef production and are enhanced by using breeds adapted to specific management strategies and environments and by crossbreeding. Thus, dozens of breeds are currently used in the U.S. Genomic prediction of breeding value (MBV) needs large trait and genotypic data sets which favors breeds with many cattle. Breeds with small effective population sizes have longer blocks of linkage disequilibrium which they should exploit. Using equations for MBV trained in one population and applied in another has had limited success. New sources of data and analyses are needed to improve MBV. New genotyping assays with more than ten times the genetic markers on current assays are expected to yield more robust associations across breeds but this is not proven yet. Using multi-breed data to train MBV predictions identifies markers with consistent associations across breeds but limits the proportion of variation that can be predicted within populations because population specific associations are often not detected. Analyses that utilize both general and breed specific marker associations need to be developed. Identifying the breed origin of an allele is a prerequisite for these analyses and haplotypes may have stronger associations across breeds than genetic marker alleles. Phenotypic data, especially for expensive or difficult traits, is particularly limiting in less numerous breeds. Breeds that are genetically less diverse (e.g., European Continental) are more likely to have consistent marker associations and might benefit from combining genetic marker data and expensive phenotypes. Some traits are difficult because they are measured on commercial animals that are not usually genotyped. A strategy of genotyping pools of cattle from the tails of a trait distribution and using genomic relationships to these pools may be useful for some traits, particularly disease and reproduction, measured in unpedigreed progeny. Basic research to develop and use MBV has been done and is being used in the beef cattle industry, but there is a strong need for innovations that will make this progress accessible to more of the industry.