Brazilian researchers develop South America’s first native fish lineage resistant to severe bacterium

In non-resistant pacu, infection by Aeromonas hydrophila causes hemorrhagic septicemia, whose symptoms include reddened fins, skin lesions and bleeding, often followed in a few hours by death.

By André Julião  |  Agência FAPESP – In Brazil, a group led by researchers at São Paulo State University (UNESP), supported by FAPESP, have developed for the first time in South America a native fish lineage that is resistant to a bacterium. They found genetically selected pacu (Piaractus mesopotamicus) to be increasingly resistant to Aeromonas hydrophila, a bacterium that causes losses to fish farms worldwide. On average, disease resistance in fish increases by 10%-20% with each new generation.

The improvement was made possible by four studies that determined, among other factors, the type of genetic heritage and the genes responsible for immunity to the bacterium. The group’s latest discoveries are published in the journal BMC Genomics.

“The only genetically improved fish currently produced in Brazil are exotic. Tilapia are a family of species originally from Africa, brought over under a breeding program developed abroad, and now being upgraded here. We chose pacu because it’s native and has been farmed for some 30 years, but without any genetic improvement,” said Diogo Teruo Hashimoto, a researcher at UNESP’s Aquaculture Center and principal investigator for the studies.

Hashimoto leads the project “Low-cost genome-wide association study and genomic predictions for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus)”, funded by FAPESP and Chile’s National Scientific and Technological Research Commission (CONICYT). The project lead abroad is José Yáñez, a professor at the University of Chile.

The first author of the studies is Vito Antonio Mastrochirico Filho. They were conducted during his master’s and PhD research at UNESP with a scholarship from FAPESP.

In the latest study, the researchers analyzed the genomes of the populations infected by the bacterium and discovered several chromosome regions associated with resistance to it. At least 38 genes were found to be linked to the immune system. “It’s very rare for only one or two genes to play a key role in resistance to a pathogen in fish. In this case, the species is probably protected by a combination of these genes,” Hashimoto said.

Infection by A. hydrophila causes hemorrhagic septicemia, whose symptoms include reddened fins, skin lesions and bleeding, frequently followed in a few hours by death.

Artificial selection

To develop the improved lineage, however, the researchers had first to know the genetic composition of the pacus available on the market. To this end they analyzed specimens collected from seven fish farmers in the state and from a wild population in the Paraná River. The results were published in 2019 in the journal Genes.

The researchers selected different specimens on the basis of their analysis, to obtain the greatest possible genetic variability, cross-breeding them to give rise to 36 families with a total of 1,094 individuals. Some 30 individuals in each family were divided into three tanks and submitted to a 14-day challenge test consisting of infection with the bacterium. Survival rates ranged from zero to 65%. In addition, further genomic analysis showed that the traits associated with resistance to the pathogen were heritable. The study was published in Aquaculture.

“For biosecurity reasons we couldn’t use the animals that survived infection as reproducers because they could transmit the bacterium to other individuals. We used siblings that hadn’t been submitted to the challenge test,” Hashimoto explained. “The analysis showed that the survivors had heritable genetic traits, and resistance to the pathogen was likely to be present in siblings, which we also analyzed genomically.”

The fish submitted to the challenge test were analyzed in another study, published in Frontiers in Genetics, to find out how infection by the bacterium affects the expression of certain genes in pacu. Analysis of their transcriptomes (all RNA transcripts in their cells) pointed to an immune system imbalance, with a surplus of anti-inflammatory cytokines and interleukins, dysregulation of phagocytosis (destruction of invading microbes), and impairment of the complement system, which activates the immune response.

Coagulation was also compromised, favoring the hemorrhaging characteristic of the septicemia caused by the bacterium.

Animals with superior genetics for resistance were also selected for higher growth rates, and reproducers from the new lineage were then distributed to partner fish farms in São Paulo state. These farms disseminate the genetic material to other breeders.

Other animals live at UNESP’s aquaculture genetic improvement center in Jaboticabal, where the studies were conducted. Pacu take three years to reach maturity, and so every three years a new selection will add favorable traits to the lineage. In the next generation, the researchers plan to select individuals with resistance to Flavobacterium columnare, which causes the columnaris disease that affects fish all over Brazil.

“There are no commercial vaccines for native fish, and handling antibiotics and other medications is problematical in aquatic environments, so the development of disease-resistant lineages is fundamental to guarantee quality fish,” Hashimoto said.

The article “Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus)” is at: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07090-z.  

The article “Transcriptome profiling of pacu (Piaractus mesopotamicus) challenged with pathogenic Aeromonas hydrophila: inference on immune gene response” is at: www.frontiersin.org/articles/10.3389/fgene.2020.00604/full. 

Subscribers to Aquaculture can read the full article “Genetic parameters for resistance to Aeromonas hydrophila in the Neotropical fish pacu (Piaractus mesopotamicus)” at: www.sciencedirect.com/science/article/abs/pii/S0044848619313754. 

The first article in the series is open access and can be found at: www.mdpi.com/2073-4425/10/9/668.