ARS researchers developed a new rainbow trout line, ARS-Fp-R, that is resistant to bacterial cold-water disease, caused by Flavobacterium psychrophilum. The team, led by Tim Leeds, began working at the National Center for Cool and Cold Water Aquaculture (NCCCWA) in 2008, and he couldn’t have imagined that ARS would someday be doing genomic selection in fish. 

Resistance to bacterial cold-water disease, a leading killer of farm-raised trout, could not have been addressed with traditional breeding methods. “How do you phenotype? That’s always the challenge,” Leeds explained, referring to the process of identifying the physical manifestations of genes in an organism.

“Getting into a trait like a disease resistance is hard to do,” Leeds said. With traditional breeding, the team found that this trait was heritable. But with genomic technologies, the team can more accurately identify individual fish, not just families, that are more resistant, leading to more rapid improvement of the trait in the population. The wealth of genomic information also allows researchers to better understand actual genes and biological mechanisms that affect disease resistance. 

Leeds believes genomic technologies and his research will have a large impact on the aquaculture industry. “Where this is going is, it’s not really the fish that we produce, it’s the technologies and knowledge that we produce [that matter to producers], and I say that because of the advent of genomic selection,” he said. “Our scientists developed a 57,000 [loci] snip chip for rainbow trout. It’s kind of like the 23andMe that we use in humans, just for rainbow trout. That’s a very modern and effective way to improve populations.”