Benchmark Genetics uses DNA tools to produce resistant shrimp

White spot syndrome virus (WSSV) has devastated shrimp farming when severe outbreaks occur in the early growth period growers may lose entire ponds and, with later infestations, ponds are harvested before all the animals die. Breeding disease-resistant populations is an attractive potential addition to disease management as it could greatly reduce the need for complex sanitary measures that frequently involve the use of toxic products.

Breeding for resistance to WSSV with traditional approaches up to now has been painstakingly slow. In collaboration with colleagues from the Norwegian Institute of Food, Fisheries, and Aquaculture Research NOFIMA, a team of scientists from Benchmark Genetics announces a major breakthrough in the use of genomic selection to speed up the development of WSSV resistance in shrimp populations in a paper published in Nature Scientific Reports on the 25th November.

Here the joint team reports not only on the potential of genomic selection but critically and for the first time in crustaceans, also shows that the genomic selection of parents leads to a substantial increase in WSSV resistance of their progeny and that the measured, realized genetic gain with genomic selection is sufficiently large to be commercially interesting. Also, genomic selection holds great promise for improving resistance to other diseases as well, as is currently being implemented by Benchmark Genetics. Furthermore, the genetic variation in the selected population remained high, ensuring further improvement in WSSV resistance in the Benchmark stock through continued selection.

Benchmark Genetics now uses genomic selection for WSSV resistance in its commercial breeding programs for shrimps, with similar work in the pipeline for other major pathogens impacting shrimp farming globally. Based on these results, parallel work in Nile tilapia, and solidly building on the company’s extensive genomics work in salmon, Benchmark is consolidating its leading position in the transfer and uptake of state-of-the-art genetics technology to ensure the sustainability of aquaculture, which now accounts for more than half the world’s total marine and freshwater harvest of aquatic animals, mainly fish and crustaceans.

Global viral pandemic in shrimp

White spot syndrome virus disease still causes multibillion annual US$ losses for shrimp farmers all around the world. The disease spreads quickly and preventative measures for contagion have proven ineffective. As it has not been possible to use a vaccination strategy for boosting the immune response against the virus. Stimulation of the innate immune system shows some promise but is so far unproven in the field. We know that some animals are inherently better able to resist or tolerate the virus than others, but we still do not understand the specific mechanisms underlying these differences. It is possible to breed animals with higher resistance to WSSV through conventional family selection, but progress has been slow. The industry desperately needs better solutions to prevent mass mortality caused by this aggressive pathogen and to boost profits.

Based on these results, we are consolidating our leading position in the transfer and uptake of state-of-the-art genetics technology to ensure the sustainability of aquaculture, which now accounts for more than half the worlds total marine and freshwater harvest of aquatic animals, mainly fish and crustaceans.


Genomic selection

Genomic selection is a methodology originally developed for livestock improvement employing the latest in DNA sequencing technologies. Breeding and genetics scientists in Nofima have worked with Benchmark Genetics on these technologies in P vannamei. Instead of relying on pedigree relationships for estimating the breeding value of individuals we used DNA sequence data to estimate the genomic relationships between individuals at tens-of-thousands of positions throughout the genome of the organism. This technology gives us a more precise means of predicting the breeding value of potential broodstock in the population (known as a genomic breeding value in this instance).

A major advantage of genomic selection over traditional selective breeding for a trait like viral disease resistance is that it allows us to more accurately predict which breeders have the best overall resistance genotype without exposing the candidate breeders themselves to the disease.

First application to genetic improvement of crustaceans

As part of the GenomResist research project funded by the Research Council of Norway, Nofima together with Benchmark Genetics tested how effective genomic selection would be for improving WSSV resistance in P vannamei, by designing an experiment using two source populations developed by Benchmark Genetics Colombia, one already mass-selectively bred for several generations for resistance to white spot syndrome virus, and the other bred for fast growth rate and general pond survival. Animals from both groups and their crosses, were randomly separated into two groups, one a test population which was challenged with the virus and the other a candidate broodstock population that was kept under high biosecurity conditions.

The test population was infected with WSSV and dead and moribund animals were tissued sampled each hour for the duration of the trial and the time of dead was recorded for all. All samples were analysed for DNA markers with Benchmark Genetics’ SNP chip that has strong coverage of every position across the shrimp genome, to give us accuracy for the genomic selection. Information about the survival and time of dead of shrimp following the challenge test was combined with the genomic relationship data from the DNA testing and used to predict genomic breeding values for survival for individual broodstock (animals not exposed to the virus).

In the second phase of the experiment, breeding candidates from the non-infected group were mated to produce two different populations of offspring, one from parents with high and the other with parents with low genomic estimated breeding values for WSSV. The survival of these two populations, and offspring from “randomly” mated parent stock, was compared in a challenge test. The results of that challenging test showed that more than 80% of individuals in the best genomically selected families survived when challenged with WSSV, while in contrast, animals from some of the worst families survived less than 5%. Like vaccinating a population against disease, having animals with this level of resistance in the shrimp population would likely be sufficient to provide a herd effect, greatly reducing the impact of the disease by preventing an exponential spread of the disease in the affected population. Genomic selection holds great promise for improving resistance to other diseases as well, as currently being implemented in Benchmark Genetics’ breeding program for P vannamei.

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Healthy whiteleg shrimps. Photo: Marcela Salazar, Benchmark Genetics Shrimp in Colombia.

Survival booster

The results demonstrated that the average survival of shrimp families increased from 38 % in the random population to 51 % in the high breeding population after only one generation of genomic selection for White Spot Syndrome Virus (WSSV) resistance. This realized selection response is dramatically higher than before reported for WSSV resistance.

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Percent survival plotted over days in challenge test for animals in the high blue- (closed circles), random- (closed red squares) and low- (closed grey triangles) genomic breeding value populations.

Implications for shrimp production

This pioneering collaborative work has demonstrated that relatively high levels of genetic improvement can be achieved for survival to WSSV in P vannamei after just one generation of genomic selection, and that genomic selection can be used to improve WSSV survival to levels that have commercial relevance for the industry. Compared with conventional methods of selective breeding for disease resistance, genomic selection is significantly more accurate at predicting, and better able to utilise, information about the underlying genetics affecting resistance. Like the effect of vaccinating members of a population, we expect that high levels of immunity in the best populations will have a “herd effect” because highly resistant animals will no longer infect other animals at the rate as typically seen. Furthermore, the inoculum pressure in commercial ponds is likely lower than it was with our experimental challenge tests in tanks, and the best families in our high genomic breeding value population showed survival of over 80%. Levels of 70% survival have been shown by other researchers to be sufficient for keeping another viral disease (caused by Taura syndrome virus) under control in shrimp.

By using genomic selection, we have demonstrated that we can rapidly increase the level of disease resistance in P vannamei. Benchmark Genetics now uses this tool to offer growers shrimp populations that can survive and produce in the presence of WSSV. Genomic selection also holds great promise for the improvement of other economically important traits in shrimp and other aquaculture species. The research shows that genomic selection could go some way towards solving this multi-billion US$ problem for the shrimp industry in the future.

More information:

The full study, which was published in Scientific Reports, can now be accessed here.

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