Genomestudio data analysis v2011

Genotype data were scored and validated from the GrapeReSeq 18K Vitis genotyping chip raw data using GenomeStudio Data Analysis v2011.1 (Illumina Inc, San Diego, CA, USA). The sequenced reference accession PN40024 was included as genotype control for allele standardization. In this process, we discarded SNPs that were monomorphic, with low amplification, more than 3 clusters, or missing data, as well as chloroplast SNPs. We obtained a data matrix of 10207 SNPs and 783 unique individuals with no missing data among our initial sample of 945 cultivars.This dataset is available at https://search.datacite.org/works/10.15454/1.4861359557068474E12 after registration at https://urgi.versailles.inra.fr/Species/Vitis/Data-Sequences/Genotyping-data.
A genetic map was drawn using a homemade script in C to automate scaling and Gnuplot for graphical view (http://www.gnuplot.info/). Theoretical Illumina SNP positions were recalculated by re-mapping the flanking regions (2x60 bp) with NCBI/BLAST^® v2.2.31 (https://blast.ncbi.nlm.nih.gov/Blast.cgi) against the whole PN40024 reference genome sequence (assembly version 12X.V0 and 12X.V2, URGI: https://urgi.versailles.inra.fr/Species/Vitis/Data-Sequences/Genome-sequences. Update 27 October 2015).

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.