* Co-supervisors: Prof. Laurent GENTZBITTEL (gentz@ensat.fr) & Ass. Prof. Cécile BEN (ben@ensat.fr, http://www.ecolab.omp.eu/profils/BEN_Cecile)
* Host Laboratory: Laboratoire d'Ecologie Fonctionnelle et Environnement, ECOLAB, UMR 5245 CNRS/UPS/INPT (http://www.ecolab.omp.eu/)
* PhD program context and objectives.
Heavy metal toxicity has become a global concern due to the ever-increasing contamination of soil, water and crops. Among those pollutants, cadmium (Cd) is an extremely toxic non-essential element widely present in polluted soils. This element, which is highly dangerous even at very low concentrations due to its high mobility (EFSA), has been identified as a major threat for human health and biodiversity.
As sedentary organisms, plants cannot move actively from a contaminated environment. Therefore, their only chance to survive unfavorable conditions is the implementation of adaptation or habitutation strategies and the mobilization of defense mechanisms. Physiological, biochemical and molecular analyses have been carried out on various plant models to decipher biological disorders triggered by Cd in plants (Andresen et al., 2013) as well as plant responses to Cd stress (Chmielowska-Bąk et al., 2014).
In the frame of this PhD research program, we intend to identify the genetic factors necessary for cadmium tolerance during early growth stage (mainly autotrophic) following germination, this developmental stage being crucial for subsequent plant establishment and development. Due to their ability to establish symbiosis with various soilborne micro-organisms and to fix atmospheric nitrogen, wild legumes (Medicago truncatula, Lotus japonicus, acacia, black locust…) or legume crops (soybean, alfalfa, pea, peanut, clover…) naturally improve nitrogen status of soils. Thus, these species are of major importance for ecosystems and of interest for sustainable agriculture.
During the past decades, Medicago truncatula, a wild species from the Mediterranean Basin which is genetically close to legume crops and presents significant advantages for genetic studies (large biodiversity, short generation cycle, small diploid genome, genetically transformable), has been adopted as a model for legume plants. A multitude of genomic and molecular tools and data are now available and its small diploid genome has recently been sequenced. Moreover, a wide biodiversity exists among this plant species and several collections of lines originating from regions with contrasted edaphic and climatic characteristics have been developed. We will use these resources (genomics and biodiversity) to study the mechanisms of plant adaptation to cadmium stress.
Two complementary genetic approaches will be developed to detect genomic loci putatively involved in Cd tolerance. The first one, based on the analysis of natural biodiversity throughout the plant species (Genome-Wide Association Studies GWAS), may help to identify in an exhaustive way the common alleles that are involved in Cd tolerance. The second methodology, based on the evaluation of recombinant inbred lines (RILs) derived from a cross between two parental lines with already known contrasted response to Cd stress (transmission genetics) may help in validating the results obtained by GWAS as well as in the identification of rare alleles impacting Cd tolerance.
The role in Cd tolerance of one or two candidate genes detected through these genetic analyses will be functionally validated by mutant analysis and/or transgenesis approaches. Knowledge transfer to spontaneous legume plants or crops (e.g. alfalfa) which may help in bioremediation, will be initiated.
* Sought skills from the PhD applicant and acquired expertise during the PhD program.
The PhD project that we propose requires knowledge in plant biology and genetics and in data analysis and statistics. Basics in molecular biology and bioinformatics will also be appreciated.
During the thesis, the candidate will be trained to acquire expertise in molecular quantitative genetics (use of molecular markers, linkage mapping, QTL detection through transmission and genome-wide analysis studies and QTL positional cloning). She/he will improve her/his knowledge in biostatistics and bioinformatics. She/he might also improve her/his skills in molecular biology and gene expression analysis (RNA extraction and qRT-PCR) methods as well as in functional validation approaches (transgenesis). The applicant will also learn some concepts of population genetics, functional ecology and plant stress physiology.
A fluent level in English is mandatory. Knowledge of the French language is not required for working in the lab but will be useful for daily life. Free language courses in ‘French for Foreigners’ are offered at the University of Toulouse.
* Major publications of the host research team in the field of the PhD.
Our research group studies the mechanisms for plant adaptation to environmental stresses. Making use of the large natural biodiversity existing within M. truncatula species (Branca et al., 2011), we develop genomics and genetics approaches to unravel molecular regulations leading to tolerance to either biotic stresses (in particular root diseases, Formey et al., 2014 ; Ben et al., 2013 a, b ; Negahi et al., 2013, 2014) or abiotic stresses (such as salinity, Foroozanfar et al., 2014 ; or heavy metals (Cd), Rahoui et al., 2014 ; Rahoui et al., 2015, Saedi et al., 2011).
Ben C, Debellé F, Berges H, Bellec A, Jardinaud MF, Anson P, Huguet T, Gentzbittel L, Vailleau F. (2013a) MtQRRS1, a R-locus required for Medicago truncatula Quantitative Resistance to Ralstonia solanacearum. New Phytol. 199(3):758-72.
Ben C, Toueni M, Montanari S, Tardin MC, Fervel M, Negahi A, Saint-Pierre L, Mathieu G, Gras MC, Noël D, Prospéri JM, Pilet-Nayel ML, Baranger A, Huguet T, Julier B, Rickauer M, Gentzbittel L. (2013b) Natural diversity in the model legume Medicago truncatula allows identifying distinct genetic mechanisms conferring partial resistance to Verticillium wilt. J Exp Bot. 64(1):317-32.
Branca A, Paape T, Zhou P, Briskine R, Farmer A, Mudge J, Bharti A, Woodward J, May G, Gentzbittel L, Ben C, Denny R, Sadowsky M, Ronfort J, Bataillon T, Young N, Tiffin P (2011) Whole genome nucleotide diversity, recombination, and linkage-disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci USA 108(42):E864-70.
Formey D*, Sallet E*, Lelandais-Brière C*, Ben C*, Combier JP, Debelle F, Frugier F, Gronenborn B, Hartmann C, Niebel A, Wincker P, Reynes C, Roux C, Gentzbittel L, Gouzy J and Crespi M. (2014) The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome. Genome Biology, 15:457. (*These authors contributed equally to the work - Research highlight by Huan Wang & Nam-Hai Chua, Genome Biology 2014, 15:475)
Foroozanfar M, Exbrayat S, Gentzbittel L, Bertoni G, Maury P, Naghavie M, Peyghambari A, Badri M, Ben C, Debellé F, Sarrafi A. (2014) Genetic variability and identification of QTL affecting plant growth and chlorophyll fluorescence parameters in the model legume Medicago truncatula under control and salt conditions, Functional Plant Biology, 41(9):983-1001.
Negahi A, Sarrafi A, Ebrahimi A, Maury P, Prospéri JM, Ben C, Rickauer M. (2013). Genetic variability of tolerance to Verticillium albo-atrum and Verticilliumdahliae in Medicago truncatula, Eur. J Plant Pathol., 136:135–143.
Negahi A, Ben C, Gentzbittel L, Maury P, Nabipour AR, Ebrahimi A, Sarrafi A, Rickauer M. (2014) Quantitative trait loci associated with resistance to a potato isolate of Verticillium albo-atrumin Medicago truncatula. Plant Pathol. 63(2): 308–315.
Rahoui S, Ben C, Martinez Y, Chaoui A, Yamchi A, Rickauer M, Gentzbittel L, El Ferjani Ezzeddine. (2014) Oxidative injury and antioxidant genes regulation in six Medicago truncatula genotypes in response to cadmium treatment. Environmental Science and Pollution Research, 21 : 8070-8083.
Rahoui S, Chaoui A, Ben C, Rickauer M, Gentzbittel L, El Ferjani E. (2015). Effect of cadmium pollution on mobilization of embryo reserves in seedlings of six contrasted Medicago truncatula lines. Phytochemistry, pii: S0031-9422(14)00534-2. doi: 10.1016/j.phytochem.2014.12.002. [Epub ahead of print]
Saeidi G, Rickauer M, Gentzbittel L. (2012) Tolerance for cadmium pollution in a core-collection of the model legume, Medicago truncatula L. at seedling stage. AJCS, 6 : 641-648.
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