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24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay


GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

PhD opportunity at INRA: Jouy-en-Josas / St Pée sur Nivelle

Appel à candidatures 2014 : offre de thèse Inra
© Inra
Genetics and genomics of adaptation of Rainbow trout (Oncorhynchus mykiss) to plant-based diets

Supervising labs: INRA UMR 1313 GABI, Animal Genetics & Integrative Biology and INRA UR 1037 NuMeA, Nutrition, Metabolism, Aquaculture

Be careful :the student will share his(her) time between the two labs, one in Jouy en Josas (near Paris), the other in St Pée sur Nivelle (South West of France).

Supervisors: Mathilde Dupont-Nivet / Sandrine Skiba / Françoise Médale

Funding (obtained) : ANR Agreenfish/ INRA division Phase / INRA Division Animal Genetics

Beginning of the phD: Fall 2014

Doctoral school: ABIES

Salary: around 1400 euros, net salary


Research will be conducted in the frame of an ANR funded project. This project gathers researchers from different fields and aquaculture stakeholders.


Global aquaculture has expanded continuously over the last 30 years (~9 % each year, FAO, 2014) and this expansion will continue because of increasing world population. Aquafeeds still contain fish meal and fish oil originated from fisheries. However, marine resources are limited and will not be able to meet the growing needs of aquaculture. Thus, for economical (high and fluctuating prices), environmental (marine resources preservation) and social (aquaculture image) reasons, substitution of marine ingredients is highly needed. Raw materials of plant origin are the main products used for substitution because of their diversity and their high availability. Many researches have optimized feed formulation so that, now, substitution of fish meal and fish oil by vegetable meal and oil is possible up to a substitution rate of 80 % (Médale et al., 2013). For higher fish meal substitution, growth and survival are reduced. For higher fish oil substitution, healthy value of the flesh is altered with a lower proportion of w-3 highly unsaturated fatty acids. Biological bottlenecks responsible of these decreased performances when diets are highly substituted are still poorly understood.

Thus, a better understanding of adaptation mechanisms to plant-based diets is a major issue to improve aquaculture sustainability

Recent results evidenced significant genetic variability for utilization of plant-based diet in Rainbow trout (Palti et al., 2006 ; Quinton et al., 2007a,b ; Pierce et al., 2008 ;  Dupont-Nivet et al., 2009 ; Le Boucher, et al., 2011). Selection experiments on simple criteria (growth, survival) have been carried out to obtain fish which better use plant-based diets (Overturf et al., 2012; Le Boucher et al., 2012). It can be a very efficient method (+35 % genetic gain for weight after one generation, Le Boucher et al., 2012).Thus genetic improvement seems to be a very helpful tool to face dietary shifts towards diets which preserve marine resources.However, underlying mechanisms are still not known: some genotypes can adapt to plant-based diets, being able to survive and grow, but how?

phD objectives and approaches

The aim of the phD is to study the genetic and genomic characteristics linked to better utilization of plant-based diets in Rainbow trout. The work will benefit from original genetic resources obtained during collaborative work between GABI and NuMeA: a selected line for better use of plant-based diet and isogenic lines chosen for their contrasted and reproducible performances when fed a plant-based diet.

Complementary studies will be developed to:

(i)             Identify differentially expressed genes according to the diet, at short and long term, through a transcriptome analysis of three isogenic lines with contrasted performances. This will result to the identification of putative molecular markers of adaptation

(ii)            Confirm the efficiency (survival, growth) of the selection by studying the response of the third generation of selection. Correlated nutritional responses (feed intake, nutrients retention, feed efficiency, digestibility, fatty acids profiles …) will be studied in order to better understand the indirect consequences of selection.

(iii)           Search for selection footprints with high density genotyping of control line and of the 4th generation of selection to identify parts of genome impacted by the selection.

(iv)          Analyze, in the selected line and the control line, expression by RT-qPCR of the main relevant genes found in the transcriptomic analysis of isogenic lines.

(v)           Gather all positional results (selection footprints, mining of identified genome parts), functional ones (expression) and literature data to precise interest of differentially expressed genes, establish a list of candidate genes and if possible, identify polymorphisms associated to performance variability.

Through the understanding of adaptation mechanisms and implementation of adaptation markers, the results of the phD will help dietary shift towards diets without any marine resources by allowing improvement of feed formulation and selection methods.


  • Geurden I., Borchert P., Balasubramanian M.N., Schrama J.W., Dupont-Nivet M., Quillet E., Kaushik S.J., Panserat S., Médale F., 2013. The positive impact of the early-feeding of a plant-based diet on its future acceptance and utilisation in rainbow trout. PLoS ONE 8(12): e83162. doi:10.1371
  • Le Boucher R., Dupont-Nivet M., Vandeputte M., Kerneis T., Goardon L., Labbé L., Chatain B., Bothaire M.J., Larroquet L., Médale F., Quillet E., 2012. Selection for adaptation to dietary shifts : towards sustainable breeding of carnivorous fish. PLoS ONE 7(9): e44898. doi:10.1371/journal.pone.0044898.
  • Le Boucher R., Quillet E., Vandeputte M., Lecalvez J.M., Goardon L., Chatain B., Médale F., Dupont-Nivet M., 2011. Plant-based diet in rainbow trout (Oncorhynchuss mykiss W.) : are there genotype-diet interactions for main production traits when fish are fed marine vs plant-based diets from the first meal. Aquaculture, 321:41-48.
  • Le Boucher R., Dupont-Nivet M., Laureau S., Labbé L., Geurden I., Médale F., Chatain B., Vandeputte M., Quillet E., 2013. Transitions alimentaires en pisciculture: l’amélioration génétique peut faciliter l’utilisation d’aliments à base de végétaux. INRA Prod. Anim., 26, 317-326.
  • Médale F., Le Boucher R., Dupont-Nivet M., Quillet E., Aubin J., Panserat S., 2013. Des aliments à base de végétaux pour les poissons d’élevage. INRA Prod. Anim., 26, 303-315

Scientific and technical skills required by the candidate

Initial training in biology. Solid knowledge in molecular biology and metabolism. Training in quantitative genetics or population genetics appreciated. Knowledge in bioinformatics and genomic data analysis. Good skills in statistical analysis. Interest for data analysis. Skills for writing and oral presentations. Ability to work in team. Geographical mobility (phD is under supervision of two distant labs). Motivation will also be an important selection criteria.


Send by e-mail a detailed CV, a cover letter, M1 notes, M2 notes and thesis, and two reference letters including one from your supervisor during M2.


Deadline: 15th of September, 2014.

Contact for sending applications (and ask for details if needed):

Mathilde Dupont-Nivet – GABI, INRA Jouy en Josas

Sandrine Skiba – NuMeA, INRA St Pée sur Nivelle

Françoise Médale – NuMeA, INRA St Pée sur Nivelle