Genetically altered tilapia genome touted as food security breakthrough
07 Feb 2023 --- The “first” high-quality reference genome for a genetically improved tilapia strain has been published following a collaboration between the Earlham Institute, the Roslin Institute and WorldFish, which leads CGIAR’s FISH research program. The scientific breakthrough offers the potential to improve food security for billions of food insecure people.
The resource allows fish breeders to develop strains that grow bigger fish faster and with improved resilience to global warming.
“A reference genome provides a full, annotated catalog of all the genes in an organism. This crucial resource is the basis for modern breeding programs,” says Dr. Wilfried Haerty, study author and group leader at the Earlham Institute.
The researchers found more than 11 million bases of Oreochromis mossambicus genomic material within the genome, including genes associated with immunity and growth rate. The discovery will help guide future breeding programs and improve the understanding of genes associated with beneficial traits in farmed fish species.
Genetic variation
The genome provides information about genetic variation in farmed strains of tilapia. The global appetite for fish has driven many species to the brink of extinction or threatened status. However, fish protein is an essential source of nutrients for billions of people.
It is estimated that by 2050 the food demand (including animal proteins) will increase by 36-51% as a result of reduced quality of land and water sources.
Consequently, aquaculture has increased in the last 25 years to meet the demand. Aquaculture production is nearly on par with wild capture output. Nile tilapia (Oreochromis niloticus), for example, is the third most farmed fish in the world. Its success is largely due to the continued breeding of strains that can grow and gain weight quickly.
The GIFT strain allows fish breeders to develop tilapia strains that grow bigger fish.
One of the “elite” strains was developed through the Genetically Improved Farmed Tilapia (GIFT) program, spearheaded by WorldFish. The strain, however, was created through selective breeding without a complete reference genome.
“WorldFish can use the reference genome as the baseline to work from when looking to breed beneficial traits,” says Haerty. The institutes partnered to accelerate the development of improved GIFT strains through genomic selection.
Annotated genome
The paper, “Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia” (GIFT, Oreochromis niloticus), which was published in BMC Genomics, highlights regions of introgression with O. mossambicus.
WorldFish provided tissues to Earlham Institute researchers, who combined short- and long-read sequencing techniques to create a chromosome-level genome assembly for GIFT.
This was supported by a linkage map developed at the Roslin Institute, built on work from WorldFish to develop an SNP chip, a type of DNA microarray used to detect polymorphisms within a population.
The genome was then annotated using an approach developed by the Swarbreck Group.
“This collaboration has laid a strong foundation for us to produce new strains of GIFT that are more resilient to a changing climate – reducing production risks for fish farmers and increasing yield to feed nutritious animal protein to a growing global population,” explains Dr. John Benzie, acting director, aquatic foods biosciences, WorldFish. The strain was originally developed from a mix of commercial and wild Nile tilapia strains and crossed with other species. By using the genomes of closely related species, including Oreochromis mossambicus and Oreochromis aureus, the scientists revealed the extent to which genetic material may have passed between species in the past, thereby identifying the extent to which genetic material may have passed specific regions in the genome.
“We’ve generated a chromosome-level assembly of the strain,” explains Dr. Haerty, “characterizing its mixed origins and the potential contributions of introgressed regions to selected traits. This gives breeders the information they need to develop new programs with confidence.”
“Because of the breeding history of elite strains, we now realize the reference genomes currently available might not be suitable to support further studies into elite strains.” 
Aquaculture production has increased significantly and is almost on the same level as wild capture output.
Significant strain
The GIFT strain is the first Nile tilapia population to have undergone genetic improvement through selective breeding for survival and increased growth rate. The strain has now been distributed across five continents in at least 14 countries.
By leveraging PacBio HiFi long reads, the researchers identified an increase of nearly 50 Mb in genome content between their assembly and the O.niloticus reference genome. Although a significant proportion of the difference could be due to technological differences, some of the differences can also reflect genomic variation between the sequenced strains.
To further develop the strain and enable future improvements, several studies have investigated the genetic bases underlying traits of economic interest.
Meanwhile, Aker BioMarine received the US Food and Drug Administration’s approval for its Qrill Aqua and Qrill High Protein (QHP) salmon feed in North America.
Edited by Inga de Jong
