Making sense of DNA sequencing puts researcher at forefront of new science

Animal biologist specializes in bioinformatics

Helen Metella - 19 April 2018

Information overload is a growing problem in animal science, so researchers are inventing tools to manage it-and a significant portion of that problem solving in Canada is happening in the Department of Agricultural, Food and Nutritional Science (AFNS).

Thanks to recent advances in chemistry and molecular biology, scientists can now characterize the entire genome of an animal (its total DNA) in mere hours, instead of years. Obtaining this sequence information is a key step toward understanding the hereditary instructions that control what cells do and contribute to differences between individuals.

However, when the genomes of many animals are sequenced-for example, a thousand head of cattle-the amount of data generated is overwhelming.

To organize and digest it, a relatively new science called bioinformatics has become hugely important in the past decade.

"We use computers and software to make genomic comparisons, to tell us where the differences exist, so we can relate that to other characteristics, such as milk production and feed efficiency," said Paul Stothard, a biologist specializing in bioinformatics and genomics in AFNS.

Knowing the connections between genomic traits and animal characteristics then allows scientists to develop specific DNA tests that allow producers to breed efficiently and inexpensively, he said.

"Before the use of DNA testing, selective breeding was done on the basis of the observable characteristics of an animal or its close relatives," said Stothard.

"But sometimes the physical characteristics of an animal can't tell you everything you want to know, or it's a trait that's difficult to observe, such as milk production-dairy bulls carry those genes but they are only expressed in their daughters."

The development of a DNA test begins with tracking down DNA samples from enough animals with information on the trait of interest recorded. Genome sequencing is then performed, and the resulting data analyzed to first find the differences in the DNA sequences, and then to correlate those differences with the trait. Additional work can then be done to verify the influence of specific DNA sites on phenotype (observable characteristics).

Livestock production creates tremendous opportunities for identifying the genes and DNA differences that affect traits because a great deal of information on animal phenotypes has been collected, said Stothard.

"A lot of other researchers in AFNS have embarked on large-scale projects involving the use of DNA sequencing. Bioinformatics is an important part of all of these studies, and we contribute in any way we can."

Already, in collaboration with Stothard, the department's researchers have created genetic tests to increase hybrid vigour in cattle, and have identified new genes that govern immune response and feed processing.

Stothard's skills in bioinformatics are also in demand elsewhere. Collaborating with a UAlberta researcher in biological sciences, he is characterizing the genomes of bacteriophages (viruses that infect bacteria). With researchers in the School of Public Health, he is identifying microorganisms present in treated waste water, to understand the risks associated with waste water reuse.

The software tools he and his team create are also shared with the world's research community.

"They are used by hundreds of people daily and have been cited in thousands of studies. So that's another impact of our work. DNA is the common thread across all these studies and it applies to everything, from viruses to bacteria, invertebrates to mammals to plants."