Available from January 2017

Genetic and genomic determinants of response to water deficit in tomato (Solanum lycopersicum) and impact on fruit quality.

Under the supervision of Dr. Mathilde CAUSSE

Funded through the project ‘‘ANR ADAPTOM’’

Water scarcity will constitute a crucial constraint for agricultural productivity in a near future. High throughput approaches in model species have identified hundreds of genes potentially involved in survival under drought conditions, but very few having beneficial effects on quality and yield in crops plants. Nonetheless, controlled water deficits may improve fleshy fruit quality through weaker dilution and/or accumulation of nutritional compounds. (1) In this context, the first part of the PhD work was aimed at deciphering the genetic determinants of the phenotypic response to water deficit in tomato by exploring the genotype by watering regime (G x W) and QTL by watering regime (QTL x W) interactions in two populations. The first population consisted in recombinant inbreed lines (RIL) from a cross between two cultivated accessions and the second was composed of diverse ‘cherry type’ tomato accessions mostly native from South America. Plants were phenotyped for major plant and fruit quality traits and genotyped for thousands of SNP. Data were analyzed within the linkage and association mapping frameworks allowing the identification of QTLs and putative candidate genes for response to water deficit in tomato. (2) The second part of the PhD work had the objective to explore gene regulation in tomato plants stressed by water deficit. For this purpose, RNA-Seq data were collected on the two parental genotypes of the RIL population and their F1 hybrid. Data were analyzed to identify differentially expressed genes and allele specific expression (ASE). Then, the expression of 200 genes was measured in the full RIL population by high throughput microfluidigm qPCR. eQTLs and eQTL by watering regime interactions were identified for those genes using linkage mapping and colocalisation with the phenotypic QTLs were analyzed. The knowledge produced during this PhD will contribute to a better understanding of the tomato plant interaction with their environment and provide bases for improvement of fruit quality under limited water supply.

Educations

2013    ‘‘Ingénieur en Agriculture’’, equivalent to a MSc in Agronomic Sciences, University of Agriculture of Angers, France (ESA)

2013    ‘‘Spécialisation Ingénieur – Amelioration des plantes’’, equivalent to last year of MSc specialized in ‘Breeding and Plant Genetic’, University of Agriculture of Rennes, France (AGROCAMPUS Ouest)

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Link Research Gate

Publications 

Albert, E., Gricourt, J., Bertin, N., Bonnefoi, J., Pateyron, S., Tamby, J. P., ... & Causse, M. (2016). Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression. Theoretical and Applied Genetics, 129(2), 395-418.

Pascual, L., Albert, E., Sauvage, C., Duangjit, J., Bouchet, J. P., Bitton, F., ... & Bruguier, L. (2016). Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels. Plant Science, 242, 120-130.