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Genetic technologies helping breed disease-resistance traits in tilapia

Tilapia farming is catching up to the salmon industry in its application of selective breeding to improve resistance against key pathogens, according to a leading geneticist.

Big productivity gains have been made in terrestrial livestock species through genetic selection, explained Morten Rye, PhD, Head of Genetics at Benchmark Genetics — but aquaculture could see even greater benefits.

“When we are looking at the aquaculture species, we see that the genetic gains that are important are actually substantially higher than what is seen in the conventional livestock species. And this is giving us great opportunities,” he said.

Salmon leads, tilapia follows on genetic innovation

The Atlantic salmon industry has led the way in the use of genetics in production, but the tilapia sector has also made use of such innovations, with Rye pointing to one Chinese tilapia breeding program which saw growth improvements of 130%.

“In advanced breeding programs for tilapia, they are really closing the gap on the technology side, and we are not very far behind the most advanced programs in aquaculture,” he said.

“What we see is that we are following the same path that we saw in Atlantic salmon — that you have consolidation on the genetic resources and genetic developments.”

From growth to fighting disease

With significant steps forward in tilapia growth, the industry is now looking to advanced genetics to bring about disease resistance through selective breeding, he told the audience at a Food and Agriculture Organization of the United Nations event.

Resistance to pathogens is highly heritable in tilapia, he explained, and Benchmark Genetics routinely tests genetically grouped “families” of tilapia for disease resistance, with 30% to 50% differences in such resistance seen between groups.

Advances in technology increasingly means that the genome is being explored for traits not just at family level, but the best individuals.

“Our issue is that when we are selecting only based on family performance, we are ignoring the 50% of the genetic variance within the families, and this was what paved the way for uptake of genomic technologies,” he said.

“With the genomic technologies, we have the ability to identify not only the best families, but we can also find the best candidates within the family and then utilize the whole genetic variance.”

Genetic markers show striking links to resistance

Finding genetic markers linked to certain traits can have even more profound results. The “classic example” of this, he said, is the case of infectious pancreatic necrosis in salmon, where a marker discovered in 2007 could be linked to 90% of the variability in disease resistance.

In tilapia, a marker explaining 30% of tilapia resistance to the bacterium Streptococcus iniae has been found, as well as a marker of similar magnitude for tilapia lake virus. Explaining the difference in fish response to disease, he noted that those fish with the favorable area of DNA linked to resistance to S. iniae had zero cumulative mortality in challenge studies, while those without saw 73% mortality.

Advanced technology looks across whole genome

For most diseases, however, such a single, unambiguous connection between genetics and resistance traits will not be seen; more likely resistance occurs as a result of many minor markers.

“This paves the way for the state-of-the-art technology from genomics in the applied programs today — what we call genomic selection,” he continued.

“What we are doing is that we are screening the genome of the candidate elements that we are working with for thousands and thousands of markers. And then we are calibrating this information with a very carefully designed training dataset with phenotypic observations. Then we can estimate the effect of all these minor markers, and we can summarize it across the whole genome.”

This, he said, increases the accuracy in selecting breeding candidates and reduces the accumulation of inbreeding in populations.

Genomic selection is currently being applied to S. agalactiae and Francisella spp, where there is no obvious single part of the genome to target for breeding programs.

“[Advanced breeding programs] offer a major opportunity for improved animal welfare, because we now have tools available to speed up selection for disease resistance,” Rye added.