Integration of QTL, eQTL and allele specific expression to unravel genotype by watering regime interaction in cultivated tomato
2017
Albert, Elise | Sauvage, Christopher | Bouchet, Jean-Paul | Bitton, Frederique | Beukers, Matthieu | Carretero, Yolande | Causse, Mathilde
Tomato is both a model species and important crop. Tomato fruit quality is characterized by a large number of components influenced by the genotypes and the environment, notably water status. In order to unravel the genetic control of these components, quantitative trait loci for metabolic and phenotypic traits (pQTL) have been mapped under control and drought conditions. We used a RIL population derived from an intraspecific cross between a cherry tomato line and a large fruited line. The genomes of both parents were sequenced and differ by more than 2 million SNPs. RNAseq of parental lines revealed a number of functions affected by water stress, but also some major differences according to the parents. On the RIL population we harvested fruit and leaf samples and performed eQTL mapping for 100 differentially expressed genes using the fluidigm technology. Several eQTL were mapped, some with strong effects, a majority of which acting as cis eQTL, and clusters of eQTL and pQTL were demonstrated. Analysis of the transcriptome of the F1 hybrid allowed the quantification of allele specific expression and identification of other strong effect cis eQTL. Results will be discussed in regard to the gene functions and co-localisations with metabolite or phenotype pQTLs.
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