• Research

Preservation of wild tilapia genetic resources for aquaculture

Identifying and preserving threatened native tilapia genome resources for the benefit of the aquaculture industry globally and in Tanzania.

Project summary.

Led by: Di Palma Group

Start date: 01 April 2015

End date: 31 March 2017

Duration: 24 months

Most of the world's fisheries are overexploited and it seems inevitable that fish-farming will largely replace fishing, just as livestock farming has replaced hunting as the main source of food from land animals. Unfortunately, many farmed fish, such as salmon, are themselves predators and need to be fed on fish meal. Tilapia are tropical freshwater fish that can be grown largely on vegetable matter and agricultural waste and so promise much for future sustainable production. Global tilapia production grew 280 percent over the 10 years to 2012, with a harvest of ~4.5 million tonnes, more than 5 times greater than the entire UK fishery and aquaculture industry.

Tilapia is now a $7.6 billion dollar industry. Most tilapia production is based on a handful of strains, but there are more than 50 wild species throughout Africa which could harbour valuable genes for growth, disease resistance, temperature & salt tolerance etc. Many tilapia will hybridize readily, so that the natural genetic traits could easily be bred into farmed strains without the need for GM technology. However, this feature also renders them vulnerable to genetic swamping by stocking with alien farmed strains into natural water bodies, a practice now widespread in Africa. At present, little is known of the status of wild tilapia strains, and international agencies seem to be largely unaware that widespread stocking is in progress, and there is little appreciation of its possible consequences.

Millions of people rely on tilapia for food. Credit: Shutterstock / SZN Photography

Red tilapia fish farming, Thailand

In this project, we will survey the natural tilapia diversity of Tanzania, a particular hotspot for wild tilapia strains. We will assess the effects of stocking at the molecular genetic level through sequencing the genomes of native and stocked forms. We will locate pure stocks of native forms and make recommendations for their conservation in-situ and ex- situ (e.g. in pond culture or sperm banks). We will estimate the growth rates of pure and hybrid forms in their natural habitats using scale rings and relate these to particular genetic traits, making predictions of the likely genetic consequences of stocking. We will also investigate the ecological niches of pure and hybrid strains from stable isotope ratios. It is possible that genetic material from native strains is actually helping hybrid forms to establish themselves, or indeed that the stocked forms may be failing to get established, perhaps in some habitats, if not supplemented by regular stocking programmes.

We will develop quick molecular diagnostic tests of hybridization for the benefit of fishery managers in other locations, and use these to calibrate simple visual methods to identify hybrids in the field. The genome sequence information of all of these tilapia strains will be deposited in online public databases, where it will provide a major resource for future studies in tilapia strain development and conservation. We will also advise the government of Tanzania and international agencies such as WorldFish about remaining pure populations of native strains to prioritise their conservation. This will be backed up by depositing tissue/sperm samples for long-term deep-freeze storage, so that these unique and endangered genetic resources might be available to breeders seeking to improve tilapia strains in the future.

Details.

We will survey the wild genetic resources for one of the world's most significant aquaculture species (tilapias of the genus Oreochromis) in a particular hotspot of diversity (Tanzania), where native stocks are being heavily impacted by widespread introduction of exotic Nile Tilapia strains, and contaminants such as spotted tilapia (Oreochromis leucostictus). We will (i) assess the extent and predictability of hybridization following introduction from genomic data; (ii) estimate the nature of genomic introgression, including testing whether particular genomic regions or types of genes more likely to introgress into native and exotic phenotypes; (iii) estimate the relative growth and ecological niche of pure and alien genotypes in hybridizing systems from scales stable isotopes and relate this to phenotype; (iv) develop a quick economical diagnostic test of the extent of introgression; and (v) enhance the genomic resources for global strain improvement through bioinformatics (sequences of all species), tissue banking and identification of candidate stocks for in-situ conservation.

Technology used.

Sequencing

High coverage (~70x) genome sequencing (DISCOVAR, 250 bp Paired End, PCR-Free) on Illumina HiSeq2500 of three Oreochromis species (O. leucostictus, O. urolepsis, O. karongae). Low coverage (~5x) genome sequencing (125 bp Paired End) on Illumina HiSeq of 250 Oreochromis species (O. niloticus, O. leucostictus, O. urolepsis and hybrids) from Lower Wami, Ruvu, Kilombero, Ruaha, Rufiji, Ruhuhu (pond) and Lake Victoria catchments.

HPC

The High Performance Computing resource has been used extensively during this project. The high-coverage de novo genomes assembly tasks require up to 1Tb of RAM to run, whilst the large number of low-coverage resequencing genomes require a large number of processor cores in order to carry out the analysis in a timely manner. The Isilon storage facility has also been used to store the multiple terabytes of data locally.

SNP Chip Array

Develop a quick economical diagnostic test of the extent of introgression for both individuals and populations. From the collected sequencing data, we will characterise SNPs diagnostic of the native and alien species in a locations where hybridization is suspected, and use these to design a SNP chip which can readily allocate a ‘hybrid score’ to individuals within the population.

Collaborators.

Prof. George Turner

Morphometrics, fieldwork, experimental design and interpretation of results including genetic data.

Dr Martin Genner

Practical fieldwork, morphometrics, experimental design, and the use of molecular tools for phylogenetics / population genetics.

Project Partner: Tanzanian Fisheries Research Institute, Tanzania, United Republic of Tanzania

Tanzanian researchers from the Institute will be actively involved in the project via participating in the fieldwork and workshops of the project. We will work closely with the Tanzanian Fisheries Research Institute to prepare and distribute a field guide to the tilapiine cichlids of Tanzania to enable fish farmers and government staff to monitor local genetic diversity. Furthermore, we will develop quick and inexpensive methods to test for hybrids in the field, which will allow local staff to identify, preserve and culture unique local strains.

Project Partner: WorldFish Center, Malaysia

WorldFish provides a commitment to facilitate the sample collection and to provide long-term storage of the tilapia tissue samples collected during the project in the WorldFish biorepository. This will ensure that these samples and associated data are adequately stored, archived and made openly accessible for future use.

Impact statement.

Threatened native tilapia genome resources will be identified and preserved for the benefit of the aquaculture industry globally and in Tanzania in particular, disseminated through workshops organised with our partners in the Tanzanian Fisheries Research Institute (TAFIRI) and the University of Dar-es-Salaam. This will take the form of identifying native strains endangered by introduction of exotics and recommending their in-situ conservation, pond culture and restocking. This will be backed up by depositing tissue and sperm samples with WorldFish for cryopreservation and the depositing of genome sequence information in public databases, so that desirable traits can be identified for crossing into cultured strains. We will enhance capacity in research and identification of strains of tilapia within Tanzania, through

We will enhance capacity in research and identification of strains of tilapia within Tanzania, through participation of local staff and research students in our fieldwork and workshops and through preparation of a field guide to the tilapias of Tanzania. This will lead to improved research and monitoring and ultimately to enhancement of the aquaculture industry. We believe that this research will be of great interest to students and the general public in the UK and internationally and we will carry out a variety of dissemination activities through a range of media. Furthermore, the genome sequence information will be publicly available to future researchers, benefiting the wider academic community interested in research themes as diverse as fish health and evolutionary biology.

Tilapia is one of the most consumed fish across the world. Credit: Shutterstock / Bennyartist

Boy holding large tilapia fish

People working on the project.

Related reading.