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Harnessing genetics to improve tilapia health and performance

An interview with Alejandro Tola-Alvarez, CEO, GenoMar Genetics


Q: Genetics is all about improvement. So, how can tilapia be improved?

AT-A: Tilapia is frequently called the “aquatic chicken” for a reason: It has a very fast generation time, converts plant-based feed ingredients into a high-quality, nutritious and affordable animal protein and produces fillets perfect for everyday cooking, just like chicken.

However, to truly become the aquatic chicken, tilapia has still some way to go. We need to improve yields through consolidation, farm intensification and technification. We need to improve survival rates and overall predictability of crop performance, and we need to increase the percentage of edible meat on the carcass to lower the cost of fillets.

An important component is the need for more cooperation and collaboration between stakeholders. The development of an industrial knowledge cluster, where knowledge is accumulated and disseminated, could bring many benefits to this industry.


Q: Tell us more about the issues with survival rates.

AT-A: The notion that tilapia is an easy species to cultivate is not real. It does have humbler diet requirements and broader environmental tolerance than many other species, but successful and profitable tilapia farming in intensive and semi-intensive conditions at scale is difficult because biological performance has too much variation, and margins are narrow in most markets, which make it a risky business.

The biggest cost to tilapia farmers is mortality rates, and I don’t talk here only about primary pathogens but anything that causes the animal to lose its homeostasis and die.

If you look at the loss tree from egg to harvest in many tilapia production areas around the world, you realize how much fish is lost in production and how much potential there is for improvements. The challenge is that really everything contributes to good or bad tilapia health: siting decisions, genetics, seed quality, husbandry, diseases, environment, farm management. So, you need to have a holistic approach.

In GenoMar, we strongly believe that genetics underpins most of the biological process behind adaptation, stress-coping and immune response. That is why we are investing in developing more robust, more adaptable and more resistant varieties — animals that grow fast but are also capable of dealing with the stressors at the farm. We need farmers to think of genetics as another element in the toolbox to improve health status in their operations.


Q: How has progress in tilapia genetics differed from what has been seen in salmon?

AT-A: Both species are pioneers in the application of genetics to aquaculture, and they both share similar historic trajectories. Breeding programs started in the ‘70s for Atlantic salmon and in the ‘80s for Nile tilapia. Both started as single-trait, family-based breeding programs, and they have gradually moved to more complex index-based selection with many traits and the use of genomic information. I would say that today´s breeders’ toolbox for salmon and tilapia is at the same technology level.

In Atlantic salmon, our colleagues have been lucky to find what we call quantitative trait loci, or QTLs — regions of the genome where there is specific variation that explains a high proportion of the variation in the trait. This enables what is called marker-assisted selection, a classic example of this is the infectious pancreatic necrosis virus, where a single base-letter change in the genome explains up to 70% of the resistance.

We are not finding high-impact QTLs for disease traits in tilapia. All the resistance looks to be what we call polygenic, meaning there is not a single or few genes but hundreds. In this case, genomic selection is the right tool, where we genotype every single individual at 50,000 points in the genome and use algorithms to estimate the infinitesimal contribution of each of these points to the phenotype to the resistance.


Q: Describe the roadmap from when a disease of significant impact occurs until genetic measures can be implemented.

AT-A: The first step is to have a business case for investing in a particular pathogen. This kind of research is expensive, and with limited resources, we need to look at pathogens with well-established morbidity — pathogens that create the biggest pains for the industry and which have the most market potential.

The second step is to identify genetic variation in resistance or tolerance to the pathogen through replicated challenge tests in wet labs or field conditions. This is what we call the heritability of the trait: how much of the variation to the resistance of the disease we observed is due to genetics.

The third step is that if heritability looks promising, then comes genetic evaluation of our families for survival in different environments but also for disease resistance. Every generation, some brothers and sisters of the families will get this kind of test, and we will get the information that we need for selection.


Q: Your company is involved in a lot of research. What would you say are the highlights? 

AT-A: We are an R&D-based company and so we invest a substantial part of our revenues in innovation and product development. The truth is that we have been an innovator in tilapia breeding for more than 20 years and have played a major role in bringing innovations to market such as DNA-based pedigree assignment, implementing fillet-yield and disease-resistance traits in the selection program, developing the first single nucleotide polymorphism array for tilapia and implementing full genomic selection.

We are, of course, not stopping there. We are continuously challenging ourselves to do better, and right now our main focus areas of innovation are phenomics for carcass traits, survivability and adaptation to different production systems and climate change.



Q: The accuracy of selection using genomic technology has increased dramatically. How does this relate to tilapia health?

AT-A: Genomic data is used in conjunction with advanced statistical models which take care of the architecture of the traits in fish to maximize the prediction accuracy.

Genomic technologies are helping us to increase the prediction accuracy by enabling within-family selection. Before we could just select good and bad families based on their response to a challenge test, but within families there are good and bad individuals. Genomics enables us to identify those individuals, which means selection by individual merit, not just pedigree. It is a triumph of meritocracy over aristocracy.


Q: Tell us more about your breeding infrastructure and how this guarantees high health status.

AT-A: We have two types of infrastructure. One is nucleus infrastructure, which is land-based infrastructure where we keep our elite fish populations in conditions of very high biosecurity. Here we collect information on the candidates themselves, and we rank all selection candidates with a single value called EBV (estimated breeding value) that integrates all information available in the selection index. The animals with highest genetic merit are then mated, and a new generation is produced.

Then there’s supporting infrastructure, which is all infrastructure used to collect information on animals that are not candidates. Typically, these are siblings of the candidate animals which are sent to different test facilities and environments to collect different information. These include, for example, wet labs for disease-challenge tests, our own and third-party farms for gene-environment interactions and fillet-yield test groups for both ponds and cages. Supporting infrastructure also includes genotyping and disease-screening laboratories which we use to run our surveillance programs.


Q: In developing markets, how important is genetics for producers when this is likely to have additional cost? 

AT-A: Farmers in developing countries and at almost any scale have a common goal: to produce tilapia protein at the lowest possible cost, highest quality and with the highest possible margin.

With the exception of a few industrial players, tilapia producers have very little power over selling prices and unitary cost of inputs which are dictated by the market, so the key to good economic and environmental performance is then biological performance, and I would argue that the genetic makeup of the fish underpins the most fundamental mechanisms of biological performance. It is not something a producer can ignore.

I would also argue that the price tag that farmers need to pay for improved genetics is negligible compared with the value genetics brings and compared with other inputs to production such as feed or energy.

Furthermore, the beauty of genetics is that it has no barriers to adoption. Genetics is delivered through a product that the farmer needs: the seed. The technology is inside the fish.


Q: Do you expect these technologies to become even more accessible to producers around the world?

AT-A: Absolutely! The use of improved high-yielding varieties is an important tool for improving biological and economic performance in any kind of farming. At a societal level, they are critical for reducing hunger and food insecurity and to reduce environmental impact in food production.

A critical aspect to consider is the ability of breeding programs to be scalable and reach the farmer´s production systems. To do that requires investment in distribution.

This is particularly tricky with tilapia because of the high fragmentation in production and the hatchery sector. In Atlantic salmon, for example, you have two to three core production countries you need to focus your investments, resources and strategy on. In shrimp aquaculture, you have a higher level of consolidation of the hatchery sector. In tilapia this is not the case. This is both a challenge and an opportunity, and we expect to see more and more consolidation of the breeding and hatchery sectors. GenoMar is and will be a central part of it.


Q: How would you persuade a skeptical producer of the value of investing in the genetic quality of their fingerlings and juveniles?

AT-A: This is a very good question. Markets and customers tend to forget what the performance of Nile tilapia was 5, 10 or 20 years ago. The only way to demonstrate the value of improved genetic material is through empirical evidence and data, and the closer the data is to the reality of the farmer, the better. We need to work patiently with individual farmers and local industry associations to build capacity and document performance and value. The number one rule is that at the end of their crop, they have more money in their pocket with your product than if they had grown another strain.

In a more holistic perspective, I would, of course, invite the industry to reflect on what other plant and animal productions are doing and how powerful genetics and artificial selection are to change phenotypes and improve performance. Fish are no different.