Transcriptome and metabolic profiling of Solanum habrochaites LA1777 ILs to elucidate fruit carotenoid biosynthesis and regulation

Tomato fruit are a major dietary source of health promoting phytochemicals, and an excellent model system to investigate fleshy fruit development and ripening. A rich variation in health and sensory related compounds is found within germplasm of the tomato clade, and populations of introgression lines (ILs) originating from interspecific crosses provide powerful tools to harness this mostly untapped genetic potential for both fundamental biology studies and for crop improvement. In order to gain further insights into the regulatory systems controlling synthesis of flavour and nutrition chemicals in tomato, a systems approach was pursued that explores natural variation harbored in a new set of COSII-anchored S. habrochaites (LA1777) ILs in the genetic background of the processing cv. E6203. Transcriptome sequencing using Illumina RNA-seq was performed on red ripe fruit pericarps of 88 field grown LA1777 ILs, and of the recipient parent. Pericarp samples were also analyzed for carotenoids by HPLC. Variation in individual carotenoids within the population indicates both wide variation and presence of variation at numerous loci impacting carotenoid content within this population. RNA-Seq data were used for high-density IL mapping and gene expression profiling. High-density genotyping allowed precise definition of the boundaries of each IL facilitating use of this congenic resource also for breeding. Co-localization of S. habrochaites introgressions and known or putative genes provided candidate genes underlying carotenoid QTL for functional characterization.