Genotyping module 1

Genome wide genotyping was done as described by Víquez-Zamora et al.[12 (link)]. In short, DNA samples were sent to ServiceXS (
http://www.servicexs.com/), Leiden, The Netherlands. A custom made Infinium HD Ultra Assay protocol
[30 ] was used for hybridization onto a BeadChip. The Genotyping Module 1.9.4 of Illumina’s GenomeStudio® V2011.1 software package was used to analyse the genotyping results under default settings. All samples corresponding to the RIL population and the parents were selected for a separate analysis in which manual inspection and adjustment were performed in order to discard questionable SNPs for the population and to optimize call rates. All polymorphic SNPs for the RIL population were named after their position on the SL2.40 version (
http://solgenomics.net/) of the tomato genome sequence published online
[1 (link)].

Genomic DNA was extracted from 100 mg of young leaf tissue by the DNeasy™ Plant Mini Kit (Qiagen - Hilden, Germany), following the manufacture’s instructions. The quality (260/230 and 260/280 ratios) and quantity of DNA extracted were checked using the NanoDrop Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and the Quant-iT dsDNA HS assay kit for Qubit 3.0 Fluorometer (Thermo Fisher Scientific), respectively.
The Vitis18kSNP array (Illumina Inc., San Diego, California), containing 18,071 SNPs, were used to genotype the 195 samples. The amplifications were performed on 200 ng of genomic DNA by the laboratory of Fondazione Edmund Much (San Michele all’Adige, Trento, Italy). SNP calls were scored with Genotyping Module 1.9.4 of the GenomeStudio Data Analysis V2011.1 software (Illumina Inc.). SNP loci showing call quality values (p50GC) lower than 0.54 were removed from the final dataset, as well as loci having GenTrain (GT) score values lower than 0.6. [39 (link)] and those with a percentage of missing data higher than 20% and minor allele frequency (MAF) lower than 0.05.