Tag Archives: CIRAD

The tilapia has been sequenced:News from CIRAD website for further dissemination

The news entitled,”The tilapia has been sequenced” has been taken from CIRAD website for further dissemination.You may access the news at the following link:



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.

The beneficial effects of climate change on rice in Madagascar(Taken from website of CIRAD)

In the highlands of Madagascar, upland rice growing has developed in recent years thanks to the availability of varieties suited to the prevailing low temperatures in this mountainous region. However, what repercussions is climate change likely to have on this crop, on which a large proportion of the island’s inhabitants depend? By simulating rice production over a century, depending on the extent of climate change and the cropping practices adopted, a team from CIRAD and FOFIFA came up with a surprising result: it was the most pessimistic climate scenario that enabled the best yields.

Global warming could have serious consequences for rice production, and as a result for food security. Precise data on the effects of global warming are few and far between, and primarily concern irrigated rice. Upland rice, on the other hand, has never been studied before.

A team of researchers from CIRAD and the Malagasy National Institute of Agricultural Research (FOFIFA) looked into the impact of global warming on upland rice productivity in the highlands of Madagascar, where the crop has developed recently. Their study covered a ninety-year period, from 2010 to 2099, depending on the cropping system adopted.

Two climate change scenarios

Rice yields were simulated using the CERES-Rice model, which was calibrated and then validated using the FOFIFA 161 rice cultivar, for which a set of experimental data was compiled over a six-year period. The cropping systems comprised two soil tillage systems – hand ploughing and no-tillage – and two nitrogen fertilizer rates – high and low.

In relation to the control, without climate change, two scenarios were tested. In the first, carbon dioxide emissions increased gradually up to 750 ppm and the temperature rose by 0.15 °C per decade. This was the optimistic scenario, in which the increase in carbon dioxide levels and the relatively moderate increase in temperature were supposed to foster rice growth.

In the second scenario, carbon dioxide emissions also rose gradually, but the temperature rose by 0.5 °C per decade and rainfall fell by 0.2 mm a day between December and February. This was the pessimistic scenario, in which the combination of a marked rise in temperature and a reduction in rainfall could have led to severe water stress in rice.

Surprising results

The analysis did not reveal any differences in yields between the soil tillage systems, irrespective of the degree of climate change and fertilizer rate. No-tillage did not improve yields compared to tillage, or the efficacy of water use or nitrogen uptake by the plant. It is likely that in order to significantly improve soil properties, no-tillage requires substantial dry matter production, which is impossible to achieve at the prevailing low temperatures in the region.

However, fertilization did have a significant effect on yields, with a gain of 1500 kg/ha of grain for nitrogen applications of 45 kg/ha. Nitrogen is a major constraint in this type of soil, in which its availability is reduced due to the soil’s poor anion exchange capacity and to leaching.

Rice yields, which were 5478 kg/ha on average, were markedly higher in the pessimistic scenario, with a gain of 576 kg/ha compared to the control. In that scenario, the increase in temperature speeded up flowering and grain maturity, in such a way that the demand for water and nutrients from the plant tallied better with their availability in the soil. Yield variability was lower, and the gap between this scenario and the others continued to grow over the years.

A positive effect on rice productivity

Although the initial hypotheses – crops without biotic constraints or marked weather events – limit the import of the results, global warming could have a positive effect on rice productivity in this cold region, where rice is grown at the lower limit of its temperature tolerance.

Unlike what it likely to happen in southern Asia, where rice is grown at the upper limit of its temperature tolerance and yields are likely to fall overall, the most “pessimistic” forecasts in terms of temperature could lead to a marked increase in yields in the highlands of Madagascar.

I acknowledge that the source of the important article ,’The beneficial effects of climate change on rice in Madagascar’ is the website of CIRAD which may be accessed at the following link:


The article has been published in this website to share and disseminate the research findings.All readers are invited to read and share their feelings about this article.