It was the late 2000s. Atlantic salmon, rainbow trout and close relatives in the aquaculture industry were plagued by a viral disease. The infectious pancreatic necrosis virus (IPNV) caused high mortality and attacked the fish at early stages in life, but attempts at creating a vaccine hadn’t been successful.

Producers decided something had to be done, before more fish were lost and dollars disappeared. Scientists separated siblings from 200 commercial families of Atlantic salmon into three cage sites in Scotland, areas known to see high levels of the virus.

“What they were able to show is that between families, there was a great deal of variation in survival and a very high heritability of that trait — which is great news if you’re a breeder,” said Debbie Plouffe, co-founder and associate vice president of business development for the Center of Aquaculture Technologies, a full-service research and development company.

With the help of genomics, scientists found a single spot in the 130,000-SNP (single nucleotide polymorphism) marker panel of the salmon genome. That one spot on a single chromosome was responsible for more than 80% of the genetic variation that allowed certain individuals to survive the virus. Fish containing at least one copy of the trait were significantly less likely to contract IPNV than animals with two copies.

“Using that information, we were able to build a genomic test that could be used to accurately predict which fish, which breeders, were going to produce animals that were resistant for IPNV,” Plouffe concluded.

The test led to fewer IPNV outbreaks and a drop in overall mortality rates tied to the virus.

It’s a story of success for the aquaculture industry, but not the sort of tale expected from the main stage of Angus Convention. Yet, Plouffe was one of two speakers invited by Kelli Retallick-Riley, president of Angus Genetics, Inc. (AGI), to the “Innovations in Genomics,” second general session at this year’s Convention in Orlando, Fla.

While cattlemen often debate how emphasis should be paced on genomics vs. phenotype in breeding programs, Plouffe offered a new perspective. Her stories of the benefits of genotyping and gene editing from the aquaculture industry were coupled with Kristin Brogaard’s accounts of Inherent Biosciences’ research into human male fertility.

Their differing vantage points gave Angus producers a chance to take a look at what this technology can do for an industry.

“So where does the future lie?” Retallick-Riley asked. “I don’t know about you, but I always think day in and day out about this huge genomic database and how can we squeeze every little bit of information out of it that we can.”   

Keeping a head above water

At first glance, there likely isn’t much a fish farmer and a cattle producer have in common. Plouffe, however, was quick to inform Angus breeders otherwise.

“We are your colleagues in food production,” she said. “Aquaculture is agriculture, and it’s really important to providing food for the future.”

There are differences in these underwater critters compared to cattle herds — fish spawn externally, allowing for more progeny at a single time, and the aquaculture industry has hundreds of species to consider rather than one. But the goal remains the same: put a high-quality protein on the tables of consumers while allowing producers to bring home an income to support their families.

“For aquaculture, the application of genomics is going to be critical to continue domestication of new species and scalability of species we already have,” Plouffe explained. “We’re going to need all the tools in the box, including selective breeding, traditional selective breeding …and then the use of gene editing to help us stack traits that perhaps didn’t particularly play well together before, or to introduce new traits that are difficult to introduce using traditional techniques.”

Target traits for fish are similar to the beef industry, Plouffe said. Growth, performance, yield, overall survival and disease resistance are all production traits she and her colleagues look at.

While not every endeavor ends in the same success the salmon population saw with the IPNV virus, Plouffe said gene editing has a big potential to help increase productivity and profitability.

Already tilapia producers have seen the benefit. Gene editing allowed for the production of what Plouffe called a “double-muscled tilapia.” These fish had a reported 60% increase in yield, and since a gene edit doesn’t require new DNA to be added to the animal’s makeup, regulatory agencies deemed it safe for production and sale without restriction.

Plouffe said just an 8% increase in animal growth and 40% uptick in fillet yield with these tilapia equates to a total value increase of $30 million a year for farmers.

With results like this, Plouffe sees genomics as an application vital to the success of the aquaculture industry. Yet it’s not the “end all, be all.”

She added, “The key message I guess I want to bring is that we don’t see it replacing traditional selective breeding. This is just going to be another tool in the breeder’s toolbox that they can use to introduce traits of interest.”

There are still concerns with the genetic technology. Phenotypes of aquatic animals are hard to capture, inbreeding can quickly become a problem, offspring are hard to identify and edited genetics can be difficult to protect. The benefits of gene editing seem to far outweigh those challenges, however. There’s opportunity to not only increase yield, like the already-realized double-muscled tilapia, but also to create reproductively sterile generations.

As cattlemen see in the feedlot, Plouffe says sometimes male fish grow better than females. By producing a sterile animal, farmers can biologically contain genetics and reap the benefits as animals grow without diverting any resources to reproductive maturation. Retallick-Riley said sterility work is currently being conducted at University of California, Davis, similar to Plouffe’s examples. For the beef industry, sterility would eliminate the need to castrate bull calves.

Plouffe says the list goes on. There’s potential to use genetics to eliminate the need for antibiotics, reduce the amount of treatments livestock undergo, and improve overall productivity and sustainability.

“Those are all stories that consumers will want to hear,” Retallick-Riley explained. “And I think if you find the traits that are both interesting for the consumers and the producers, that’s where you’re going to be the most successful.”

A personal crossover

Kristin Brogaard calls it sixth-grade science.

“You look at the sperm and the semen under a microscope. You count the sperm, you see if it’s moving, and you see if its head is ‘funky,”’ she explains, noting the simple procedure is currently the primary method of determining the fertility of human males.

One in six couples suffers from infertility. Those couples likely invest an average of $80,000 annually for about two years of infertility work. Nearly 95% of the time, the burden of that infertility falls onto the female partner.

But 50% of the time, Brogaard says the infertility is actually tied to the male.

“Just until 10 years ago, people thought sperm was just a compacted DNA that goes into the egg,” she explained, “but it’s actually a super, super complex system.”

At Inherent Biosciences, Brogaard and her co-founder are devoted to bringing actual technology to the male infertility space, and they’re using epigenetics as their secret weapon.

“If every single cell in your body has the same DNA, from your neurons to your liver cells to your eggs to your sperm … it’s the epigenetics that turn the right genes off and the right genes on,” she said.

Simply put, epigenetics help cells function as they should. But Brogaard’s work found that environment plays a transgenerational role, too.

“The things you do influence the expression of your genes.”

Beyond that, the influence of sperm doesn’t stop at fertilization. Sperm actually affects embryo development, miscarriages and even offspring health.

With all that in mind, Brogaard analyzed thousands and thousands of semen samples, searching for what looked normal and what didn’t, and then correlated those findings to pregnancy outcomes. Brogaard was able to identify a total of 1,233 genetic promoters — specific regions in the DNA — in human males that were absolutely essential for sperm to function properly. A deviation from the proper genetic profile led to subfertility.

The Inherent team then created “Sperm QT,” a quality test for sperm specific to artificial insemination (AI). Brogaard and the company can now likely predict the success of AI, pregnancy and live birth based on the expression of genes, nearly tripling the success rates of pregnancy in couples struggling with infertility.

Brogaard also learned that even with normal semen concentration, good motility and morphology, males could still have fertility issues.

“What I’m seeing is not unique to humans,” she said. “It sounds like that’s sometimes the case in this industry, where you have semen parameters, but they’re not usually predictive of fertilization outcomes.”

Identifying epigenetics in the wide-reaching genomic database at AGI might just be the next big thing for the breed, Brogaard suggests, offering to lend a helping hand when the time comes.

By sharing the stage at Angus Convention, even for a short while, Brogaard, Plouffe and Retallick-Riley proved there’s room for crossover in the genetics world. By simply asking the right questions, new understanding can be unlocked.