Over the past century, tilapia have taken on immense importance in global aquaculture in terms of production volume, value and geographic scope. A number of species and hybrid-based varieties are cultured around the world (including many distinct lines of red tilapia), but the dominance of Nile tilapia (Oreochromis niloticus) within the sector is indisputable. 

According to the FAO, some 5 million tonnes of Nile tilapia were produced in 2022. And almost 1 million more tonnes of other tilapia species and hybrids were reported. 

With the emergence of new diseases and growing concern over limited therapeutic options, breeding for pathogen resistance has taken on new urgency in many aquaculture sectors, including tilapia production. While traditional approaches to selective breeding have already resulted in some genetic progress in growth, body conformation and disease resistance, these selection programmes are generally long-term propositions requiring significant infrastructure and expertise. This is due to the fact that only a portion of the variation we typically observe is controlled by genetic influences that are directly inherited. Even when a fish is clearly superior, much of that superiority may come from combinations of genes and other factors that do not persist from one generation to the next. 

Disease resistance is a notoriously difficult trait to measure in aquatic species, but the tools available for these evaluations continue to evolve, allowing for more efficient selection in a number of fishes. Unfortunately, the impacts of these gains are often limited for tilapia producers throughout the world due to the fragmented nature of the industry. In contrast, most of the major diseases facing the industry have spread more rapidly across the globe. Let’s review the progress being made on selecting for genetic resistance to these pathogens.  

TiLV

Over the past 15 years or so, a previously undescribed RNA virus known as tilapia lake virus (TiLV) has caused considerable losses for tilapia producers throughout the world. Following several years of unexplained mortality events in pond-raised tilapia in Israel, in 2014 the disease was originally described in the Sea of Galilee. Over the following five years TiLV spread quickly to a number of countries throughout Asia, Africa and Latin America. Dong et al. (2017) provided evidence that TiLV was already present in Thailand in 2012, adding that from 2012 to 2017 three major tilapia hatcheries in that country shipped fry and/or fingerlings to 40 other countries. 

Researchers quickly began to evaluate the possibility of selecting Nile tilapia for resistance to TiLV. Barria et al. 2020 examined underlying genetic variation for TiLV resistance, evaluating the survival of fish from 124 families following a pond outbreak. Although overall mortality was roughly 40 percent, survival rates within families ranged from 0 percent to 100 percent. Various statistical models indicated the heritability of TiLV resistance in this population was quite high, explaining 40 percent to 60 percent of the observed variation in survival. However, there was no genetic correlation between growth rate and TiLV resistance.     

Fortunately, tools have been developed over the past few years specifically to allow for genome-wide studies of tilapia, identifying individual genes with significant influence over various production traits. This approach can accelerate selection by more accurately identifying superior breeding stock. In follow-up studies on their Malaysian population of Nile tilapia, Barria et al. 2021 found a region on chromosome 22 that was highly associated with TiLV resistance. When looking at only the most significant genetic marker (among several) they found that fish with two copies of the “resistant” form of the gene exhibited only 11 percent mortality, while those with two copies of the “susceptible” form of the gene had 43 percent mortality. Selection to further improve TiLV resistance is ongoing in a number of countries. 

Francisellosis

Francisella orientalis is an intracellular bacterium that also causes significant disease problems (collectively referred to as Francisellosis) for tilapia producers in various countries, with frequent co-infections and mortalities occasionally reaching 90 percent. Shoemaker et al. 2022 evaluated data from four generations of Nile tilapia and determined that heritability for resistance was 0.31. Subsequently, offspring from selected broodstock exhibited superior resistance and survival. However, resistance to Francisellosis did not appear to be significantly correlated with resistance to Streptococcus agalactiae (see below), and neither resistance trait was correlated with harvest weight.  Joshi et al. (2021) reported high heritability estimates for Francisellosis resistance when using both pedigree and genomic data (0.37 and 0.51, respectively), and, taken together, these results indicate significant opportunities to reduce Francisellosis-related losses in tilapia production through selective breeding.

Flavobacterium columnare

Columnaris disease, caused by Flavobacterium columnare, is responsible for major mortality events in hatchery facilities for many finfish species throughout the world. Wonmongkol et al. (2017) used data from 43 Nile tilapia families (Chitralada strain) to evaluate the potential for improved resistance to columnaris disease. When challenged by waterborne exposure, mean survival of fry was 32.4 percent. Nonetheless, the authors reported survival rates of 70 percent and 8 percent for the most and least resistant families, respectively. Depending on the statistical model being used, heritability estimates for resistance ranged from 0.14 to 0.30, suggesting the possibility for gradual genetic improvement.   

Streptococcus 

Two distinct bacteria in the genus Streptococcus are responsible for severe economic losses in tilapia culture. S. iniae typically attacks the brain, kidneys and spleen of susceptible tilapia, resulting in severe (and occasionally total) mortality. Shoemaker et al. (2017) challenged fish from 144 Nile tilapia families with S. iniae via intraperitoneal injection. At the end of the trial cumulative mortality was 46 percent. Significant and high (0.52) heritability was calculated for resistance to this pathogen, indicating the potential for substantial improvement through selection. 

LaFrentz et al. (2024) characterised the response to S. iniae challenge in a line of Nile tilapia that had undergone selection for disease resistance for almost a decade. At the beginning of the process, they challenged Nile tilapia from 143 families with S. iniae, with subsequent within-family survivals ranging from 0 percent to 100 percent. They used these results to establish resistant and susceptible lines for further studies, ultimately developing a resistant line exhibiting 100 percent survival when challenged – compared to 10 percent survival in a susceptible line. One notable prior finding by this group was the identification of four distinct genes impacting resistance. Separately, these genes explained anywhere from 12 percent to 26 percent of the observed variation in survival. This accomplishment was the result of a cooperative effort involving the US Department of Agriculture, Benchmark Genetics, Auburn University, Spring Genetics and Fishhead Labs, and this resistant line is now being developed for commercial distribution.               

S. agalactiae also causes high mortality in tilapia, with multiple symptoms such as septicaemia, neurological disorders, and internal and external haemorrhaging. Shoemaker et al. (2017) challenged fish from 130 Nile tilapia families with S. agalactiae via intramuscular injection. Cumulative mortality was 68 percent at the end of the trial. Substantial (0.38) heritability was calculated for resistance to S. agalactiae, indicating the potential for efficient survival improvement through selection. However, no genetic correlation between S. iniae and S. agalactiae resistance was apparent, indicating a need for separate selection programs to address these two pathogenic bacteria. Spring Genetics recently announced the availability of an S. agalactiae resistant line of Nile tilapia designated “SGG12,” also developed in cooperation with Benchmark Genetics and the USDA.  

Suebesong et al. (2019) reported lower, but statistically significant, heritability estimates for Nile tilapia resistance to S. agalactiae in the initial generation of a selection programme in Thailand, as did Oliveira-Neto et al. (2024) in Brazil. Sukhavachana et al. (2019) reported similar results for a synthetic strain of red tilapia in Thailand.   

Industry insights

I asked Hideyoshi Segovia Uno, Spring Genetics’ CEO and co-owner, for more information about the SGG12 line. He replied: “One of the biggest challenges facing the tilapia industry, particularly in Latin America, has been the outbreak of Streptococcus agalactiae serotype Ia 2021. This bacterial strain has significantly affected production, leading to reduced survival rates and economic losses for farmers. Understanding the urgent need for disease resistance, we focused on developing a genetic line that could better withstand this pathogen while maintaining excellent growth and productivity. 

“SGG12 was made possible through a collaborative effort between Spring Genetics, Corpavet (Colombia), USDA-ARS, and Benchmark Genetics Norway. This partnership allowed us to apply rigorous disease challenge models and genetic selection techniques to enhance the resistance of our tilapia strain to Streptococcus agalactiae Ia 2021.”   

With regard to current and future focus when selecting for disease resistance, Segovia Uno explained: “We are continuously advancing our selective breeding programme to improve disease resistance in tilapia. While our success in selecting for resistance to Streptococcus iniae, where we identified a QTL [quantitative trait locus], was a significant achievement, our focus extends beyond this single pathogen to other major diseases affecting tilapia production, including S. agalactiae Ib, Francisella orientalis, and tilapia lake virus (TiLV). Moving forward, we remain committed to developing genetic solutions that enhance the health, efficiency, and sustainability of tilapia farming.”

And as for the genetic correlations in Spring Genetics’ selection programme?

“We haven’t found strong genetic correlations between the traits we select for, so we approach each one separately,” Segovia Uno replied.

“While this makes selection more challenging, we overcome it using advanced genetics and genomic tools like QTL mapping and genomic selection, ensuring we improve disease resistance without compromising growth and performance,” he added.    

And, it seems some of the barriers to widespread utilisation of improved lines by small-scale, low-tech producers may be coming down. 

As Segovia Uno summed up Spring’s approach to address this problem: “We ensure our improved lines reach these producers through a well-structured distribution network. We work with franchises [multipliers] in different countries, who produce and sell high-quality fingerlings to small and medium-sized farmers. Additionally, we collaborate with integrated companies, typically large producers, who produce their own fingerlings for internal use. This dual approach allows us to effectively supply high-performance tilapia to farmers of all scales, ensuring broad access to improved genetics.”

Clearly, the potential for developing disease resistant lines of Nile tilapia has been demonstrated. Producers throughout the world should look forward to more resilient varieties in the coming years, and increases in both profitability and sustainability.