Genomic Technologies: Fabulous, Fit Fish

ARS genomics research has been instrumental in identifying economically significant genes not only in livestock, but also in fish.

Scientists Caird Rexroad and Yniv Palti, at the National Center for Cool and Cold Water Aquaculture in Leetown, West Virginia, have developed tools for rainbow trout genome research. This includes construction of a genetic map that is being integrated with a physical map to facilitate alignment of the trout genome with the sequenced genomes of model organisms.

The scientists and their collaborators have developed functional genomic technologies to identify genes that affect disease resistance and stress tolerance. In addition, the entire genome of the bacterial pathogen Flavobacterium psychrophilum—which causes bacterial cold water disease—has been sequenced and annotated by molecular biologist Greg Wiens, microbiologist Tim Welch, and collaborators. This work should help identify virulence genes and vaccine targets. Bacterial cold water disease is a chronic and potentially fatal condition, especially in young fish.

How fish use nutrients is another important aspect of aquaculture genomics. For fish geneticist Ken Overturf and colleagues at Hagerman, Idaho, the ideal rainbow trout’s genetic makeup would allow it to thrive well on feeds that provide nutritious proteins and oils from plants instead of from fish. That would give growers of plant crops a new market and reduce aquaculture’s reliance on ocean-going fish for trout-feed ingredients. A study that involved testing about 1 million rainbow trout identified a genetic characteristic that distinguishes those that may grow well on plant-based feed.

ARS research has also promoted the use of genomics to identify fish breeds. At Stoneville, Mississippi, scientists in the Catfish Genetics Research Unit—led by research leader Kenneth Davis, molecular biologist Geoff Waldbieser, and geneticist Brian Bosworth—have developed a genotyping system to identify blue catfish, channel catfish, and their hybrids as early as 1 day after fertilization.

The Stoneville team has also developed genotyping systems to identify the parents of catfish spawn collected from communally stocked ponds, as well as individual catfish strains. Now the scientists are developing molecular methods to determine the sex genotype of hormonally feminized channel catfish. It’s a big step toward developing a YY strain that will sire only faster growing males.