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

Last update: May 2021

Menu Logo Principal Institut Agro Rennes-Angers Angers University   IRHS


Seed and seedling beneficial functional traits and associated loci

Seed and seedling beneficial functional traits and associated loci
Better understand mechanisms of seed quality and seedling resilience using multiscale approaches, from biometrics to metabolome and genetic diversity

■ Key molecular and cellular determinants and loci associated with seedling performance

We use Medicago truncatula as a model and study genetic and physiological bases of seedling pre-emergence growth (i.e. in darkness). This developmental phase is critical for successful crop establishment because (i) it is a prerequisite for seedling installation, and (ii) this phase is highly susceptible to environmental conditions (Brunel et al., 2009; Dias et al., 2011; Vandecasteele et al., 2011).

– We have shown the crucial role of cell elongation as a main mechanism controlling hypocotyl length in various genotypes under abiotic stresses (Pierre et al., 2014; Youssef et al., 2016). QTLs controlling epidermal cell number and cell length affecting hypocotyl elongation at low temperature were revealed (Dias et al., 2011; Youssef et al., 2016). Using proteomics, cell wall and soluble sugar composition of two genotypes of contrasted hypocotyl elongation capacity, we found that the protein PM34 was an excellent candidate. Furthermore, PM34 can be carbonylated during seed maturation, suggesting a role in seed quality acquisition, and has a cellulase activity, which is consistent with a role in cell elongation via cell wall reconfiguration required for growth. Also, our results suggest that PM34 (abundance and/or redox state) is important for crop seed quality (Satour et al., 2018), and this aspect is currently under investigation.

– Of particular interest is the response to nitrate since Legume seedlings depend on soil nitrogen before nodules are formed and functional. In addition, an interaction with temperature is anticipated since growth thermal conditions affect growth rate and nitrogen partitioning. Via the MeDi-SENS project (DBH’s PhD), we took advantage of a core collection of 192 accessions of M. truncatula in a factorial experiment of seedling growth assays with or without nitrate at two temperatures (17°C, 10°C). Accessions could be categorized into physiotypes differing in their relationship between seedling elongation and biomass partitioning, and we calculated a plasticity index relative to reference conditions (here, with nitrate at 17°C). We then used a GWAS approach and revealed (i) a total of 45 associations with single or combined plasticity index traits supported by principal component analysis (PCA), and (ii) two clusters of genes encoding sugar transporters and glutathione transferases surrounding loci associated with seedling elongation traits (Ben Hdech et al., 2020).


The same approach is currently being conducted for low temperature and comparison of the two temperatures is in progress.

- Also, we contributed with SEED and ImHorPhen IRHS teams and SNES-GEVES to phenotyping collections of 200-400 accessions for seedling vigour traits in Legume crops (European project H2020 EUCLEG). SMS is in charge of characterising seedling heterotrophic growth traits for red clover, alfalfa and pea under low temperature or water deficit conditions. To do so, we improved phenotyping tools to automatise image analysis (collaboration with ImHorPhen). We will use these data to identify marker associations with seedling traits vigour using GWAS.



■ Searching for biomarkers of seed vigour and seedling resilience

Our specific objectives are (i) to identify metabolic biomarkers (isotopic and metabolomics signatures) of seed and seedling quality/vigour, which can be implemented on a high-throughput basis; (ii) to identify metabolic seedling functional traits driving genotype-specific response to the environment (GxE). Objective (ii) will exploit outcomes of objective (i) and will use combined genetic, (eco)physiological, and metabolomics approaches.The examination of GxE aspects (nitrate supply, temperature) has already been initiated (DBH’s PhD) and some metabolite abundance have already been determined in seeds and seedling organs of the collection of 192 accessions of M. truncatula. This continues during JBD’s PhD. Metabolic QTLs will be searched through techniques of mGWAS with isotopic, metabolome or fluxome features, using M. truncatula as a model. In the longer term, we will thus contribute to identifying metabolic physiotypes to guide the design of ideotypes implementable in the field.

This research theme is strongly supported by the Région Pays de la Loire and Angers Loire Métropole via the research grant Isoseed (ConnectTalent, 2019-2024) awarded to G. Tcherkez. The rationale of this project is simply that in the past 40 years, metabolic determinants of seed quality have been often overlooked and it is only recently that functional genomics tools have been approached to seek for relationships between metabolic or protein signatures and seed quality. We are amongst the first to restart research work to fill this gap of knowledge, and we published a review on the link between primary metabolism and quality (Domergue et al., 2019). In addition, in the project Isoseed, we intend to examine metabolic markers associated with seed quality, not only using metabolomics but also stable isotopes. In fact, the natural abundance in stable isotope is not only determined by source material but also by fractionations in metabolism and therefore, it is likely that varieties with different performance harbour different natural isotopic signatures. The project will be coupled to the exploitation of genetic diversity (in Medicago) with the objective to discover metabolic quantitative traits that can be ultimately implemented in a GWAS approach. To do so, our team will take advantage of high-resolution GC-MS analysis that gives access to comprehensive and high-quality metabolomics datasets.