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USDA Awards Researchers $15M to Use Genotyping Arrays to Study Cattle


By Justin Petrone

The US Department of Agriculture has awarded a team of US researchers two grants worth a total of nearly $15 million to discover biomarkers in cattle associated with improved feed efficiency and resistance to bovine respiratory disease.

Scientists at the University of Missouri and Texas A&M University will use high-density genotyping arrays manufactured by Affymetrix or Illumina to develop panels for selecting breeding cattle with desirable traits.

Both grants have "common elements of genotyping a large number of animals with a high-density SNP assay in order to develop models to predict genetic merit for feed efficiency and resistance to pathogens leading to respiratory disease," Jerry Taylor, a professor of animal genomics at the University of Missouri and investigator on both grants, told BioArray News this week. "Some animals will be common to both grants and thus we will be genotyping the animals with the same assay."

The US is the "world's largest producer of beef and milk and has the largest fed-cattle industry in the world," Roger Beachy, director of the USDA's National Institute of Food and Agriculture, said in a statement.

"As the demand for food rises due to a growing global population, it will be critically important to develop methods to produce more food with greater efficiency, while lowering the prevalence of bovine respiratory disease that inflicts significant losses each year," he said.

The University of Missouri's $4.9 million NIFA grant will support a five-year research project led by Taylor to discover methods to improve feed efficiency in beef cattle. USDA defines "feed efficiency" as the "amount of milk, meat, or eggs produced per unit of feed consumed."

Increased feed efficiency leads to "more food produced with fewer resources and less waste, thereby reducing the environmental impact of farms."
Taylor's team will use microarrays to genotype 8,000 individually fed cattle in order to develop DNA models that link genotypes with superior feed efficiency. The project also aims to develop marker-assisted management systems that increase profitability.

Meantime, Texas A&M University's $9.75 million NIFA grant will help researcher James Womack reduce the prevalence of bovine respiratory disease in beef and dairy cattle. UM's Taylor is a co-investigator on this grant.

BRD is the leading natural cause of death in beef and dairy cattle: It kills more than 1 million animals valued at nearly $700 million each year, according to USDA.

Womack and colleagues will use arrays to genotype 4,000 cattle to identify those that are resistant to known disease-causing pathogens and to uncover new BRD-causing organisms.

The data will be used to develop BRD diagnostic tests and genetic-selection tools to identify BRD-resistant animals, and to assess the welfare of cattle afflicted with BRD, according to USDA.

Building Models

Taylor helped develop the Illumina BovineHD and Affymetrix BOS1 genotyping arrays, and said that "one of these" chips will be used to genotype all the animals in the two projects.

Affy debuted the BOS 1 in January. The chip contains 648,000 SNPs selected in collaboration with the Affymetrix Bovine Consortium, a group that includes UM, USDA's Agricultural Research Service, the Roslin Institute and ARK-Genomics, the University of Edinburgh, the Technical University of Munich, and the University of Liverpool (BAN 1/18/2011).

By comparison, Illumina launched its BovineHD Genotyping BeadChip in 2010. It contains more than 777,000 markers covering more than 20 distinct cattle breeds. The firm also offers a Bovine SNP50 genotyping BeadChip, which contains 56,000 markers across the bovine genome; and a GoldenGate Bovine3K Genotyping BeadChip, which contains 2,900 for cattle selection (BAN 1/12/2010).

After genotyping the selected cattle, Taylor, Womack, and fellow researchers will "jointly estimate" how the SNPs affect feed efficiency or risk of BRD, and "develop models that predict additive genetic merit for that phenotype."

They will then validate the models in animal populations not used in developing the prediction models, and use them to help improve genotype selections, Taylor said.

He and other researchers are using high-density arrays because linkage disequilibrium "does not extend very far across breeds, and the objective is to build prediction models that work well in any breed."

The objective is to "identify superior animals, not breeds," he stressed.

Discussing the selection tools that result from the discovery work, Taylor suggested that anything that may be commercialized "may not be based on the high-density assays used for model discovery."

Rather, he said, SNPs identified may be "designed onto smaller custom arrays that are used in commercialization." However, "such assays must be predictive of numerous phenotypes," not only FE and pathogens resistant to BRD.

Commercialization "will by necessity be accomplished using the least-expensive approaches that can genotype several thousands of SNPs," Taylor noted without elaborating. "At the moment custom assays and commercial products are used for this purpose."

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.

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