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United States Department of Agriculture

Agricultural Research Service

Research Project: Whole Genome Selection Through Genome Wide Imputation in Beef Cattle

Location: Genetics, Breeding, & Animal Health

2013 Annual Report


1a.Objectives (from AD-416):
For the beef cattle industry to become more competitive, it must embrace change and seize new opportunities. This project will deliver new genomic tools to allow cattle to meet new markets and improve production efficiencies with a corresponding improvement in environmental impact, such as a reduction in greenhouse gas production. Genetic improvement is a powerful tool and genomics offers new opportunities for genetic improvement in beef production, most notably the ability to change difficult traits like feed efficiency and beef tenderness, which have previously been almost impossible to change. The Bovine Genome Sequence, published in 2009, resulted in key technological breakthroughs that enable the proposed research. The resulting Bov50SNP Chip has revolutionized dairy breeding but there remain many barriers to the same breakthrough in beef cattle, specifically the need to develop more specific gene tags (causal mutations) correlated to economically important traits or alternatively the development of breed or population specific tools derived from a knowledge of the haplotype structure within and across breeds. The proposed collaborative project will enable implementation of highly accurate Genome Wide Selection at low cost in cattle.


1b.Approach (from AD-416):
Next Generation sequencing and re-sequencing will be used on a key ancestral individuals in several breeds and populations. Additional genotyping will be obtained with decreasing density (800K, 50K and low density or trait specific panels) of genotypes on increasing numbers of animals with desired phenotypic information further down the breeding pyramid. Imputation methods will be developed and used to derive the haplotype structure of the commercial herds at the bottom of each pyramid. This strategy will then be applied with a focus on the targeted areas of efficiency of feed utilization, reproduction, and longevity of cows. Smaller sets of genotypes will be identified and evaluated for efficacy in predicting desired animal traits.


3.Progress Report:

Our collaborators have identified key individuals in eight cattle populations with ties to Canada and North America. We have identified additional sires from seven of the breeds with many progeny in United States herds. Genotyping these animals is well underway. Sequencing the DNA of some of these animals also is progressing. Discussions have resolved data formats and the data is being transferred. The collaborators have developed software for imputing genotypes when animals are genotyped using different genetic marker panels or have missing genotypes.


Last Modified: 7/27/2014
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