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Offspring of Wild-, Hatchery-Raised Trout Exhibit Differential Gene Expression

NEW YORK (GenomeWeb) – Offspring of fish raised in hatcheries express hundreds of genes at different levels than the offspring of wild-raised fish, according to a new study from researchers at Oregon State University and elsewhere.

The researchers crossed wild and first-generation hatchery steelhead trout Oncorhynchus mykiss, raised the offspring in a hatchery, and compared their transcriptomes. As OSU's Michael Blouin and his colleagues reported today in Nature Communications, they found that more than 700 genes are differentially expressed between the offspring of fish raised in hatcheries and the offspring of wild-raised fish.

"We expected hatcheries to have a genetic impact," Blouin said in a statement. "However, the large amount of change we observed at the DNA level was really amazing. This was a surprising result."

These genes, he and his colleagues further found, were enriched for involvement in wound healing response, immunity, and metabolism.

To find these differentially expressed genes, the researchers crossed fish raised in hatcheries with each other and fish raised in the wild with each other. They also crossed fish raised in hatcheries with wild-raised fish, with the mothers coming from both source populations —HxW and WxH. The wild fish were obtained from the Hood River in Oregon.

Through RNA sequencing, Blouin and his colleagues uncovered 723 genes that were differentially expressed between the offspring of wild fish and the offspring of hatchery fish. Of these, they noted, many more genes were upregulated in the offspring of hatchery fish as compared to the offspring of wild fish.

They noted only an average of 51 genes that were differentially expressed between HxW and WxH fish, as compared to the average 477 genes that differed between the offspring of hatchery fish and the offspring of wild fish.

These differences, Blouin and his colleagues added, cannot be attributed to either maternal effects or genetic drift.

If the differences in expression were due to maternal effects, the researchers noted that they would have found that the number of differentially expressed genes between the offspring of hatchery fish and the offspring of wild fish would equal that of those found between the HxW and WxH crosses— a finding they did not observe.

Likewise, they said that if maternal effects were the source of the differentially expressed genes, they should have seen normalized gene counts that were similar between the offspring of WxW fish and WxH fish, as they shared the same wild mother — again, something they did not see.

Similarly, when they aligned all the RNA-seq data to the O. mykiss genome and used those called SNPs to calculate a genome-wide Fstbetween the offspring of hatchery fish and the offspring of wild fish, they uncovered a low level of divergence.

This low divergence, they said, is what would be expected from a sampling error alone, suggesting that genetic drift is not the likely explanation for these differences in expression.

Blouin and his colleagues determined through a gene ontology analysis that these differentially expressed genes are enriched for functions in coagulation or wound healing, immune response, and metabolism. The expression of such genes, the researchers surmised, could help fish adapt to a crowded hatchery environment.

Captive fish, they noted, often have abrasions on their fins or other injuries that come from living in close quarters. Indeed, the aggressive nature of steelhead trout is exacerbated when they are raised at high densities, they added.

Immune genes may also help hatchery fish deal with diseases that may more easily spread in crowded conditions. This, the researchers said, suggests that one of the first steps toward domestication may be adapting to the high densities of captivity.

"A fish hatchery is a very artificial environment that causes strong natural selection pressures," Blouin added. "A concrete box with 50,000 other fish all crowded together and fed pellet food is clearly a lot different than an open stream."