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Series of USDA grants to propel genomic studies

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USDA awards $6.5m to create three functional genomics projects led by Iowa State University (swine), University of California-Davis (cattle) and Western University of Health Sciences (chickens).

Iowa State University will host a national center of excellence devoted to understanding the genomic mechanisms that govern important genetic traits in swine such as growth and disease resistance.

The U.S. Department of Agriculture’s National Institutes of Food & Agriculture recently announced its decision to fund the center of excellence with a $2.5 million grant over four years as part of a larger effort that also will include similar genomics work with cattle and chickens at other universities.

The grant is a portion of $6.5 million USDA recently awarded to create three functional genomics projects. In addition to the Iowa State-led center of excellence for swine genomics, USDA awarded grants to create programs for cattle genomics at the University of California-Davis and chicken genomics at Western University of Health Sciences in Pomona, Cal.

Western University said the funding for the three projects falls within the Functional Annotation of Animal Genomes (FAANG) consortium.

The swine genomics center will include personnel at Iowa State, Michigan State University, the University of California-Davis and the USDA Agriculture Research Service. The research effort aims to allow pork producers to use genetics more efficiently to predict the traits their herds possess, Iowa State said.

Christopher Tuggle, a professor of animal science and USDA national swine genome co-coordinator who will lead the center, said the effort will focus on functional genomics of pigs, or building a better understanding of how the genome functions to influence performance in pigs.

“We’ve sequenced the pig’s genome, but we don’t necessarily have all the information we need to make the best use of that data,” Tuggle said. “We’re going to find out exactly what many of those genes are doing and what controls them.”

The researchers will test a range of tissues from pigs at various stages of development, with a major focus on chromatin, the complex in cells where DNA is packaged. The scientists will analyze the functions of various genetic structures and mechanisms, Tuggle said. The group will focus on exploring the genetics of disease immunity, he said.

The project also will share the data it produces with the public and other scientists. Tuggle said the project’s findings likely will have implications for a wide range of swine management practices, from how producers handle herd nutrition to treating disease.

Much of the data storage and analysis will occur at Iowa State as well. James Koltes, an assistant professor of animal science, and Jim Reecy, associate vice president for research, will lead the computational aspects of the project.

“The data generated in this project will provide unprecedented opportunities to learn how genes are regulated and controlled over different growth phases and during disease in the pig,” Koltes said. “The ability to combine different types of genetic data will allow us to predict genetic regulation in ways that have not been performed previously.”

“This will create a more precise way of predicting traits. If we gather enough information, we can predict in the future what a genotype will mean for a particular phenotype or trait,” Tuggle said. “This could allow pork producers to breed for better disease resistance, for example, or for better muscle growth or a range of other desirable traits.”

Chicken genome

Western University of Health Sciences College of Veterinary Medicine associate professor Dr. Yvonne Drechsler has received a $1 million USDA grant to functionally annotate the chicken genome, which she said has wide-ranging implications for better understanding of genetic factors influencing growth, reproduction and disease resistance in production.

Drechsler is the project director, and University of Washington associate professor Dr. R. David Hawkins and Western University College of Veterinary Medicine associate professor Dr. Suzana Tkalcic are co-investigators.

These studies, built on Drechsler’s research conducted with colleagues at Western and Hawkins’ work at the University of Washington, will contribute to national and international efforts to understand the role epigenomics plays in regulating health, disease resistance, growth and reproduction in agriculturally important animals.

This work potentially has far-reaching implications to better understand gene regulation that is important in egg production, growth and disease resistance, Drechsler said. Several tissues, including reproductive tissues as well as different immune cells, will be investigated.

“It’s basically a mapping project, identifying genomic regions that are regulatory elements,” Drechsler said. “One example of these regulatory elements for which we are looking is histone modifications that can affect accessibility of the DNA, affecting how genes get turned on or off.”

Data generated from this project will be shared with other researchers in the agricultural community to further enable research efforts in poultry and other agricultural species, the announcement said.

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