Transcriptome profiling of three fruit tissues from the fw11.3 NILs in cultivated background

Experiment description: Two sets of fw11.3 NILs from Solanum lycopersicum c.v. Rio Grande background were used for RNA-seq experiment. fw11.3-D (EE) and fw11.3-WT (PP) are NILs carrying cultivated and wild alleles for fw11.3 locus. The fw11.3-NILs were grown in 2-gallon pots in the greenhouse using standard fertilization (15-9-12 slow release supplemented by 20-20-20), completely randomized design was used. Flowers were tagged a day before anthesis and self-pollinated at anthesis. Developing fruits were sampled between 1:00 pm to 3:00 pm. The three tissues collected were pericarp, columella, and developing seeds with placenta at the following developmental stages: 4, 7, 10, 15, 25, 33 days post anthesis (DPA) and turning stage fruit. For 4DPA fruit, the columella, placenta and developing seeds were collected together. The first two replicates from the same family BC2F6 were collected in May 2013, and second two replicates from family BC2F7 were collected in November 2013. An additional collection was made to include 33DPA and turning stage fruit from family BC2F7 in January 2014. In all, most samples consisted of four replicates, except 7DPA and 25DPA (three replicates), 33DPA (one replicate) and turning stage (one replicate for columella tissue and two replicates for pericarp and developing seeds with placenta). The low number of replicates for the latter tissues was due to severe incidence of blossom-end rot in the greenhouse from November 2013 to January 2014. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.

Author: Qi Mu

Contact: Esther van der Knaap (, Department of Horticulture and Crop Science, Ohio State University