On Oct. 6, 2004, it was official: The bovine genome had been sequenced. After years of research and $53 million in funding, an international team of scientists released the genome into public databases.
For Dr. John Cole, that was just one step in connecting the genome with actual traits in cattle. Cole, a Research Geneticist with the USDA Agricultural Research Service, says we are still in the early days of understanding the genome.
“Right now, we’re just poking at it with sticks,” Cole said in an interview with the American Society of Animal Science.
Some researchers have connected specific genes to certain traits, but Cole calls those connections “low hanging fruit.” He is curious about traits affected by multiple, elusive genes.
“Now we are looking for the more subtle things,” said Cole. “There are a lot of genes and each seems to have a small effect.”
One mysterious trait is the tendency for some cows to experience dystocia, or difficult calving. Cole said Holstein cows commonly experience dystocia, but the condition is rare in Jersey cows. Somehow, genetic variations change the birthing process for these two breeds.
If scientists figure out which genes are responsible for dystocia in Holstein cows, they could help dairy farmers breed cows without the trait. Solving the mystery would improve animal health.
Cole said an approach called “systems biology” could help scientists study how multiple genes work together. Cole wants to understand relationships between physical traits and gene transcription, proteins and regulatory networks in the body.
“That’s what we really want to do. We want to understand the biology,” said Cole
Animal scientists trade new ideas
In a new paper for the Journal of Animal Science, Cole describes summarizes the Breeding and Genetics Symposium at the 2012 American Dairy Science Association, Canadian Society of Animal Science and American Society of Animal Science Joint Annual Meeting (JAM).
The theme of the symposium was “Systems biology in animal breeding: Identifying relationships among markers, genes and phenotypes.” The symposium was sponsored partly by Monsanto.
“We had great speakers who were willing to come and share their time and expertise,” said Cole.
One reason to get the leading animal geneticists in one room was to help them share genetics research from different breeds and farm animal species.
The first speaker was Dr. Toni Reverter, a Principal Research Scientist with the Commonwealth Scientific and Industrial Research Organisation in Brisbane, Australia. Reverter explained how scientists could use data from multiple breeds to identify crucial genes.
Dr. Warren Snelling, a Research Geneticist with the U.S. Meat Animal Research Center, gave the second presentation. Snelling said comparing different breeds, like Brown Swiss cattle and Ayrshire cattle, can help researchers gather more data when one cattle population is relatively small.
Next, Dr. Guilherme Rosa explained how he used data from farms to study genes related to animal health. Rosa wanted to know if preexisting animal health records could help determine if certain genes actually cause certain traits. He said it is difficult to figure out whether some diseases have a genetic connection or whether they are more influenced by animal diet, housing or management practices.
Poultry researchers are using systems biology with their breeds too. In the fourth presentation, Dr. David Froman explained how he uses genomic tools to study rooster fertility. Froman, a professor of animal sciences at Oregon State University, said multiple genes seem to lead to poor chicken sperm mobility. If scientists can identify roosters without these genes, they may help farmers breed better birds.
In the last presentation of the day, Dr. James Koltes shared his research into how cattle regulate iron content in their skeletal muscle. Koltes, a postdoctoral researcher at Iowa State University, recommended a closer look at mRNA.
Cole said these speakers represent the future of system biology and genomic research. Several of the teams are currently working toward USDA National Institute of Food and Agriculture (NIFA) competitive grants to support their work.
“The scientific community agrees that those guys are doing important, relevant work,” said Cole.
The future of breeding and genetics
Systems biology is headed in interesting directions, but scientists warn that research will lag without proper funding. The NIFA grants help, but there may not enough support for farm animal research.
Working with farm animals is naturally more expensive than working with smaller species. To study traits in mice, for example, researchers can breed “knock out” mice, where certain genes are inactive. Researchers could use the same strategy to pinpoint genes in cattle, but the cost of raising a cow is much higher than the cost of raising a mouse.
“It is very expensive to do that kind of work,” said Cole.
Cole said some researchers could be tempted to assume that certain genes affect certain traits without observing the connection in live animals.
“The problem is that you start stacking speculations on top of each other,” said Cole.
To really advance research, Cole said scientists must develop new tools to test genes and analyze data. Scientists will need to share ideas at conferences and make sure the science is built on facts, not speculations.
If the varied presentations at the 2012 JAM are any indication, genomics and systems biology could improve animal health. The field just needs funding and teamwork.
“This is going to happen because of lots of people working together,” Cole said.
Cole’s summary of the 2012 JAM Breeding and Genetics Symposium is titled “Breeding and Genetics Symposium: Systems biology in animal breeding: Identifying relationships among markers, genes and phenotypes.” His coauthors are R. M. Lewis, C. Maltecca, S. Newman, K. M. Olson and R. G. Tait Jr. Publication of the summary was sponsored by the American Society of Animal Science. Read the full summary at http://journalofanimalscience.org/content/91/2/521.full.