AMES, Iowa – Iowa State University animal scientists are leading a new study to look ways to measure and predict different traits in pigs – especially disease resilience.

“Many of the traits pork producers want to improve by genetic selection are difficult to measure and predict,” said Christopher Tuggle, Iowa State University professor of animal science.

“Growth rate is easy to measure, and as a result, we’ve made significant improvements in this area,” he said, adding he and his team will be working with USDA researchers. “Disease resilience, on the other hand, is much more challenging, and an area where we haven’t made enough progress.”

Tuggle will serve as the lead investigator on a new $650,000 grant from the USDA National Institute of Food and Agriculture.

He said he and his team will be focusing on transcriptomics, which is the study of the transcriptome – the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell. (RNA is a nucleic acid present in all living cells that has structural similarities to DNA.)

He said he is interested in using transcriptomics transcripts to study “pig gene expression in blood to make a practical disease predictor, but my close collaborators had a lot of input and will perform a lot of the work as well.”

Jack Dekkers, an Iowa State University quantitative geneticist and distinguished professor of animal science, is a co-investigator on the USDA National Institute of Food and Agriculture grant.

Other collaborators are Crystal Loving, a specialist in swine immunology at the USDA-Agricultural Research Service National Animal Disease Center in Ames, Iowa, and Joan Lunney, a swine immunologist and geneticist at the USDA-Agricultural Research Service Animal Parasitic Diseases Laboratory in Beltsville, Md.

Luke Kramer, an Iowa State University post-doctoral fellow and computational scientist in animal science, will also assist and mentor two graduate students involved with the study.

For the first phase of the grant, primarily managed by Loving, blood samples will be collected from young pigs under a variety of healthy and infected conditions that mimic conditions found on farms. Tuggle and Loving will work together to analyze all cell types across these samples.

Tuggle said blood samples are often used as a practical way to search for markers of disease or immunity.

“Blood is easily collected and can tell a lot, but blood is a very complex mixture of cells doing a lot of things,” he said. “To make blood useful as a test for disease resistance, we need to better understand the composition of the cells and their numbers, as well as learn what they are actually doing.”

For example, he said, a neutrophil is a frontline soldier in the immune system that attacks invading disease threats immediately and has a different expression pattern of its genes than lymphocytes, like B cells (white blood cells), which make antibodies that enhance disease resistance over time.

“One of our primary purposes is to very accurately measure the nature of all these different types of cells under different conditions,” he said. “This will improve our ability to link the phenotypes of blood cells (traits we can measure) with an animal’s health status, such as what is a B cell doing, and how is it changing when an animal is healthy versus when it is sick?”

He said one of the team’s tools for its blood detective work is single-cell analysis, a new technique that can measure the expression of genes in each individual cell in a sample, rather than taking an average of cells.

“This gives us the vision to look more precisely at all the cell types in a complex sample to untangle the knots,” he said.

Loving said the basic immunological data connected to these blood samples will be made publicly available.

“This could have a very broad impact on improving understanding of the swine immune system, and on improving animal genetic selection,” she said.

Tuggle said, “Dr. Loving will perform much of the animal work and I will help her collect blood samples from pigs under different conditions. Her group will also process the blood to component parts.”

Once the molecular nature of all the cell types is known, Tuggle and Dekkers will apply that information to improve the use of blood data to predict the most resilient pigs.

“On all samples, one graduate student in my group will collect the gene expression data at the Iowa State University sequencing facility, and analyze the data to get gene expression patterns,” Tuggle said.

He added Dekkers and the second graduate student will use statistical and computational methods with this data to determine the cellular composition of whole blood gene expression data to standardize it for broader use.

This step will use data from over 1,800 pigs that have been followed from weaning (about five weeks of age) to market, provided by a project funded through the PigGen Canada research consortium, which Dekkers will direct in the United States.

In the final phase, Tuggle said, he will collaborate with Lunney to create “a practical method to quickly measure such predictive patterns in industry populations, providing a new tool to improve pig health.”

“We have been trying for eight years to get this funding from different study sections at the Agriculture and Food Research Initiative, succeeding on the third try, after we had sufficient preliminary data using single-cell technology that had caught up with our ideas,” he said.

“We applied in 2021 and were awarded funding in early 2022,” he added. “We have hired the students and staff and are just getting started with the project, although we will be using a large data set of blood gene expression data that were collected through previous USDA National Institute of Food and Agriculture funding to Dr. Dekkers and myself, with additional funding from (PigGen) Canada and other groups.”