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The tilapia has been sequenced

03/10/2014 – Press release

The genomes of five species of cichlids, which include tilapia, were recently sequenced and compared by the CGC (Cichlid Genome Consortium), of which CIRAD is a member.

The results were published in the 18 September issue of the journal Nature .

The five genomes were sequenced at the Broad Institute in Washington (a leading sequencing centre), with funding from the NIH (National Institutes of Health, USA). Of the 27 laboratories that co-signed the article in Nature , CIRAD, the University of Stirling (UK) and the Agricultural Research Organization (Israel) are particularly interested in the consequences of the project for aquaculture, and will be using the tilapia reference sequence in order to speed up the identification of sequences linked to worthwhile characters.

CIRAD has primarily looked at the sex-ratio, thermosensitivity and salt tolerance, and is going on to study food efficiency.

Tilapia, the “aquatic chicken”

Tilapia, an African cichlid, is one of the world’s most widely used model fish species for studies of genetics, physiology, endocrinology, toxicology and behaviour. With an output of 4.3 million tonnes from more than 100 countries worldwide (primarily, but not exclusively in the Tropics), tilapia is currently the second largest group for aquaculture worldwide, after carp, which are mainly produced and consumed in China.

All the forecasts suggest that tilapia (which is often presented as the aquatic version of chicken) is set to become the main farmed fish species of the future.

Sex determinism and differentiation

With tilapia, sex has to be controlled if farms are to be profitable, since the males grow faster than the females, which lay eggs roughly every month and keep them in their mouth to protect them for around ten days, during which they are unable to feed.

Most producers currently use hormones to ensure single-sex, male populations. However, this raises many questions as to the sustainability of such treatments: what impact will these steroids have on the health of the farmers using them and of consumers, and on water quality and biodiversity?

Since 1985, CIRAD has been working on new ways of controlling sex without using hormones, based on genetic and/or environmental approaches. It was the first organization to demonstrate the possibility of producing YY males with single-sex male progenies without using hormones.


CIRAD was also ahead of the field in detecting the masculinizing effects of the high temperatures used with tilapia in its early stages; similar results have since been obtained for many other species. In order to optimize and speed up breeding programmes, its scientists (the AquaTrop group belonging to CIRAD’s INTREPID research unit) are working to find markers linked to sex and thermosensitivity.

Molecular markers were recently identified for early phenotypic sexing, and have been tested by an ANR project-Emergence (SexTil) with a view to producing commercial kits. These kits should serve to accelerate the production of YY males for genetic sex control and/or to breed parents with heat-sensitive progenies in order to control sex through temperature rather than using hormones.

Salt tolerance

Adaptation to salinity is necessary for a number of countries keen to farm tilapia in brackish water or in the sea (shortage of fresh water, conflicts of use or concerns about preserving the resource). For instance, in the Philippines, most tilapia is produced in brackish water. CIRAD and the BFAR (Bureau of Fisheries and Aquatic Resources) have developed a salt-tolerant strain (Molobicus ) using conventional genetics.

The reference sequence will facilitate the identification of salt tolerance markers, with a view to identifying and breeding highly tolerant parents locally (thus avoiding the dissemination of interesting strains from one country to another, and the resulting genetic contamination).

An omnivorous diet

Unlike most farmed sea fish (particularly salmon, sea bass, bream, etc), for which fish meal and oil are an essential or at least an important part of the diet, tilapia, which is microphytophagous (it can eat and convert phytoplanktonic algae and cyanobacteria), is sufficiently opportunistic to be classed as omnivorous. It is therefore towards the bottom of the trophic chain. Under extensive farming conditions, tilapia can thus be produced without artificial feed, by stimulating primary production (plankton) by fertilizing the ponds.

Along with carp, it is therefore one of the species that can be produced without using fish meal and oil obtained through fishing, hence without impacting on fish resources.

In practical terms, the tilapia reference sequence will therefore make it easier to breed strains suitable for farming, by identifying genetic markers linked to characters of aquacultural interest and developing kits like the one developed for early molecular sexing of tilapia. In the short term, it will also foster the switch to rational fish farming that pays greater heed to producers, consumers, and also the environment.

From a more fundamental point of view, this work enables a clearer understanding, on a genome level, of the mechanisms that lead to the birth of new species (speciation). In the great lakes of East Africa, speciation studies of cichlids over the past 75 years have revealed “adaptive radiation” phenomena, characterized by the very rapid appearance of a large number of species (explosive speciation) from a single ancestral species (or a very small number of species).

These new species are extremely morphologically and ecologically diverse, and each one is adapted to a specific trophic niche (adaptive radiation). These phenomena do not have any equivalent in vertebrates.

The CGC’s work shows that the mechanisms that lead to this type of adaptive radiation are based on an explosion in the duplication of genes, many of which have been conserved despite evolution and which will go on to develop new functions (neo-functionalization) and play a role in adaptation to new environments.