ABSTRACT

The renewed interest in plant proteins has stimulated research aimed at developing markers to aid in the selection of legume varieties better adapted to nutritional needs. Among the traits to be improved and stabilized is the amino acid balance of seeds, the essential amino acids methionine and tryptophan being particularly under-represented in legume seeds. This thesis focuses on seed protein composition, which is a major determinant of the seed amino acid balance. The objective was to explore the genetic and environmental variability in this trait and to identify genes potentially involved in its plasticity when subjected to environmental stresses.  

In the first part of the thesis, the protein composition of seeds from 200 Medicago truncatula genotypes cultivated in four contrasted environments (sufficient water supply, water stress, and two time-shifted sowing) was analyzed by one-dimensional electrophoresis. The plasticity indices calculated for each protein band made it possible to identify, by genome-wide association studies (GWAS), sequence polymorphisms associated with variations in the plasticity of the major storage proteins, the 7S and 11 globulins. The list of candidate genes is enriched in genes related to transcription, DNA repair and signal transduction. Other over-represented genes are involved in sulfur and aspartate metabolism leading to the synthesis of methionine and lysine. By exploiting publicly available expression datasets in Medicago truncatula, and by localizing these genes in the corresponding metabolic pathways, we discovered that methionine recycling pathways are likely to contribute to the plasticity of seed protein composition. This recycling involves the homocysteine S-methyltransferase 3 enzyme that regenerates methionine from S- methylmethionine, a long-distance transport form of methionine in the phloem. This part of the thesis has led to the identification of new genes to be targeted to improve and stabilize the amount of sulfur amino acids in seeds, opening prospects for translational research aimed at improving the quality of seeds in protein crops such as pea.  

The second part of the thesis aimed at exploring the variability of response of a collection of pea ecotypes to sulfur deficiency, at the levels of yield components and of seed protein composition, and to identify by GWAS genes potentially involved in this variability of response. Two experiments were carried out in two successive years with respectively 304 and 198 genotypes developed under two conditions: sufficient or deficient in sulfur. Since both year effect and sulfur deficiency effect were significant on the variables, plasticity indices reflecting the amplitude of the sulfur deficiency response were calculated for each variable. The results obtained by GWAS have revealed candidate genes for controlling the protein composition of seeds in low sulfur environments. Several are associated with transport mechanisms (e.g. amino acids) and post-translational regulation, while others play a role in sulfur metabolism or in the cross-talk between nitrogen and sulfur metabolisms. This work has shed light on pea genes that might control the nitrogen and sulfur status of seeds, and thus modulate the balance between the 7S and 11S globulins. The same GWAS approach conducted on yield component traits has led to the proposal of relevant candidate genes in particular for seed weight control. Altogether, these results offer prospects for varietal improvement to stabilize yield and the protein composition of legume seeds in fluctuating environments, in particular for the availability of sulfur.   

Composition du jury :

M. Olivier Loudet, Directeur de Recherche INRAE, Rapporteur

M. Olivier Leprince, Professeur AgroCampus Ouest, Rapporteur

Mme Julia Buitink, Directrice de Recherche INRAE, Examinatrice

M. Jacques Le Gouis, Directeur de Recherche INRAE, Examinateur

Mme Christine Le Signor, Ingénieure de Recherche INRAE, Co-directrice de thèse

Mme Karine Gallardo, Directrice de Recherche INRAE, Co-directrice de thèse