RNA-seq transcriptome analysis of fruit pericarp in a set of Solanum habrochaites LA1777 ILs

The tomato fruit is an ideal and well-studied model system for investigation of fruit development, flavor and nutrition. Exceptional variation in these traits is found within germplasm of the tomato clade and numerous genetic, molecular and germplasm resources enable efficient research in the tomato system. Populations of marker-defined introgression lines (ILs) originating from interspecific crosses represent powerful tools to harness the genetic potential stored in unadapted germplasm for both fundamental biology studies and to improve the agricultural performance of modern crop varieties. Recent developments of 'omics' platforms have further enhanced the power of such congenic and permanent resources. In order to gain further insights into the networks regulating key fruit metabolic pathways underlying flavor and nutritional quality, we have undertaken a systems approach that leverages natural variation stored in a new set of COSII-anchored Solanum habrochaites (LA1777) ILs in the genetic background of the S. lycopersicum processing tomato cv. E6203. Towards this end, we have performed RNA-seq analysis from red ripe fruit pericarps of 30 S. habrochaites ILs. Single nucleotide polymorphisms (SNPs) and indel profiles were identified for each IL based on RNA-Seq data. This high-density genotyping allows precise definition of the boundaries of each IL facilitating use of this resource for breeding of nutrient, flavor in addition to any other trait of interest. In several cases, the high resolution of introgression definition achieved through RNA-seq SNP analysis allowed the identification of small additional S. habrochaites introgressions missed in lower resolution genotyping studies based on RFLP or PCR markers. Replication of RNA-seq analysis of these and additional lines is under way and the status of this developing expression resource will be presented.